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/dev/null @@ -1,13 +0,0 @@ -:orphan: - -.. _bioamp-exg-pill-datasheet: - -BioAmp EXG Pill -############### - -.. toctree:: - :hidden: - :maxdepth: 1 - :caption: BioAmp - - hardware/bioamp/bioamp-exg-pill/index \ No newline at end of file diff --git a/_sources/courses/index.rst b/_sources/courses/index.rst new file mode 100644 index 00000000..05c9fb46 --- /dev/null +++ b/_sources/courses/index.rst @@ -0,0 +1,12 @@ +.. _upsidedownlabs_courses: + +Courses +######## + +.. toctree:: + :hidden: + :maxdepth: 1 + :caption: Courses + + open-ephys/index + \ No newline at end of file diff --git a/_sources/courses/open-ephys/exday1-nokit.rst b/_sources/courses/open-ephys/exday1-nokit.rst new file mode 100644 index 00000000..a5bcbf51 --- /dev/null +++ b/_sources/courses/open-ephys/exday1-nokit.rst @@ -0,0 +1,265 @@ +.. _exday1-nokit: + +Exercises Day 1: No Hardware +############################### + +.. |Na+| replace:: Na\ :sup:`+`\ +.. |Cl-| replace:: Cl\ :sup:`-`\ +.. |Ca2+| replace:: Ca\ :sup:`2+`\ +.. |K+| replace:: K\ :sup:`+`\ +.. |Rs| replace:: R\ :sub:`s`\ +.. |Rm| replace:: R\ :sub:`m`\ +.. |Re| replace:: R\ :sub:`e`\ +.. |Rsh| replace:: R\ :sub:`sh`\ +.. |Ce| replace:: C\ :sub:`e`\ +.. |Csh| replace:: C\ :sub:`sh`\ +.. |Vin| replace:: V\ :sub:`in`\ +.. |Vec| replace:: V\ :sub:`ec`\ +.. |Vout| replace:: V\ :sub:`out`\ +.. |Ve| replace:: V\ :sub:`e`\ +.. |Za| replace:: Z\ :sub:`a`\ +.. |Ze| replace:: Z\ :sub:`e`\ + +.. contents:: Table of Contents + :depth: 2 + :local: + + +1. Using a multimeter +*********************** + +We will be using a circuit simulator to model the different settings on a multimeter. A multimeter can be used to measure voltage, resistance, and current. + +.. admonition:: Exercises + + First we will measure resistance of a resistor. + + .. figure:: media/ohmmeter_sim.* + :align: center + :target: https://tinyurl.com/y65o842d + + Setup: + + - Add an Ohmmeter to the circuit (Draw/Outputs and Labels/Add Ohmmeter). + - Connect it to the resistor and Run the simulator. + - Right-click on the Ohmmeter, select 'View in New Scope'. + - Set the scope to display resistance values instead of voltage. Right-click on the scope and select 'Properties'. Select 'Show Resistance' instead of 'Show Voltage'. + + 1A. Read the value of the resistor in Ohms from the scope. + + Now we will measure the voltage across two batteries. + + .. figure:: media/voltmeter_sim.* + :align: center + :target: https://tinyurl.com/y35xq4tr + + Setup: + + - Add a Voltmeter to the circuit, connect it across the batteries, and run the simulator. + - What voltage do you measure? + - How can you get the Voltmeter to give a negative voltage measurement? + +2. Measuring voltages +********************** + +.. admonition:: Exercises + + Take a look at this simulation. A voltage output signal is being generated on the left, which turns an LED on and off at a specific frequency. Our goal is to measure the properties of this voltage output. + + .. figure:: media/squarewave_sim.* + :align: center + :target: https://tinyurl.com/y3fugler + + 2A. Connect a voltmeter across the LED. This is similar to using a multimeter in the lab. What is the amplitude of the signal in Volts? With what frequency does the signal change amplitude? + + 2B. Visualise the voltage across the LED in a new Scope. This is similar to using an oscilloscope in the lab. Is the voltage measured different now? With what frequency does the signal change amplitude, how would you describe the shape of this signal? + + 2C. What are the advantages of an oscilloscope over a multimeter? + + 2D. Change the voltage signal so that it outputs a 50Hz sinewave. + + +3. Ohm’s Law +*************** + +Ohm’s law describes how potential (V), current (I) and resistance (R) are related: + +.. math:: + + V = IR + +When looking at a whole circuit, we can use this to calculate how much current will flow. Here is a simple circuit with a battery and two resistors. Current flows from the positive terminal of the battery to the negative terminal of the battery. The resistors are 'in series' as there is only 1 path for current flow. + +.. figure:: media/resistors_series_sim.* + :align: center + :target: https://tinyurl.com/y4r8nsnj + +.. admonition:: Exercises + + 3A. Click on the image to go to the simulator. + Right-click on the top wire in the circuit, and then select Edit to display the current through that wire. Double-click on either of the resistors to decrease their value. What happens to the current in the circuit? + +4. Resistors +************** + +Here’s another simulation demonstrating Ohm’s law. This time, the current moves from a 5 Volt voltage source (bright green) into ground (grey, earth), across one of two resistors. The resistors are 'in parallel' as current can flow cross over one *or* the other resistor. + +.. figure:: media/resistors_parallel_sim.* + :align: center + :target: https://www.falstad.com/circuit/e-ohms.html + +.. admonition:: Exercises + + Setup: + + - Click the image open the simulator. + - Right click on a resistor and select 'View in new scope'. + - Do the same for the other resistor. You can click 'Reset' to restart the simulation and synchronise the scopes. + + 4A. What do you predict will happen to the voltage over the left resistor if you double its resistance? What will happen to the current? + + 4B. What will happen to the voltage and current over the right-hand resistor when the other doubles in resistance? + + Now double the value of the left-hand resistor in the simulator and see if your predictions were correct. + +5. Voltage Divider +******************** + +Voltage is always measured relative to a point that we consider 0V. For a battery, the negative terminal is 0V. + +Voltage (potential energy) ‘drops’ over each resistor, as potential energy is converted to another form of energy such as heat or light. In a circuit powered by a 9V battery, all 9V of potential energy from our battery source *must* drop over circuit components, to return to 0V at the negative terminal of the battery. + +In each circuit below, the current through R1 must equal the current through R2, as they are resistors in series. Following Ohm's law, given the same current, a higher resistor will have a higher voltage drop (V=IR). The total voltage drop over the circuit must equal the provided voltage. + +.. figure:: media/voltage_divider.* + :align: center + +Therefore, in a circuit with multiple resistors in series, the ratio of their resistances determines how much voltage will drop over each. We can therefore split up (divide) the voltage from a source across resistors to produce an output voltage |Vout|: + +.. math:: + + |Vout| = |Vin| \frac{R2}{R1+R2} + +.. admonition:: Exercises + + 5A. Using the simulator (here’s an empty full-screen https://tinyurl.com/y477e9qd) build a voltage divider circuit in which you use: + + - a 3V battery ('Draw' a 1-terminal voltage source set to 3V) + - 2 resistors + - a readout wire (right click and 'Edit' to show the voltage |Vout|) + + To provide an 2.1V output voltage |Vout| at the readout wire. + + 5B. Change the ratios of the resistors until the readout voltage is the size of an action potential measured in the extracellular fluid. + +6. Capacitors +*************** + +There are two types of capacitor. Polarised capacitors must be used in a specific orientation. Usually, ceramic capacitors are not polarised and you can use them in either direction, whereas tube-shaped electrolytic capacitors **are** polarised. The negative pin is indicated by a ‘-’ marking, and the positive leg is often longer. + +:ref:`As discussed in the Theory handout `, capacitors occur wherever charge can be separated along two conducting surfaces, separated by an insulating material that prevents the plates from touching. Cell membranes are capacitors, as are electrodes. + +.. math:: + + Q = C * V + +The amount of charge (Q) a capacitor can separate depends on is its capacitance (C, measured in farads) and the voltage (V) across the capacitor. + +.. figure:: media/capacitor_membrane.* + :align: center + :target: https://tinyurl.com/y5nglnv7 + +.. admonition:: Exercises + + Setup: + + The simulator shows a simplified 'cell membrane' represented as a capacitor and a resistor. Changing the intracellular voltage supply changes the voltage across the cell membrane. The extracellular fluid is always 0 V. + + 6A. The initial voltage over the capacitor should be -72mV. If not, set the Voltage slider to around -70mV. Click 'Reset' to see current move through the circuit until the capacitor is charged to 72mV. Which direction is the current flow? Why does current stop moving? + + 6B. Using the 'Voltage' slider, set the voltage supply to 0 mVolts, and then to 20mV. What happens to the current flow in the circuit? + + 6C. Can you mimic an action potential by changing the intracellular voltage? + +.. admonition:: Exercises + + In this simulation, you can charge and discharge a capacitor and see the current flow through the circuit. + + .. figure:: media/charging_cap_sim.* + :align: center + :target: https://tinyurl.com/y6ov8bnn + + 6D. Modify the simulation to power an LED (Draw/Outputs and Labels/Add LED) by the capacitor as it discharges. The simulator will turn the LED red when it is on. + + 6E. Visualise the charging and discharging of voltage over the capacitor. How can you make the charging and discharging slower? + + 6F. Increase the capacitance value of the capacitor. How long does it take the capacitor to discharge? + +7. Alternating signal (AC) +**************************** + +Batteries provide 'direct current' in a single direction. In contrast, the action potentials and LFPs we measure from neurons can go in both directions; they are **alternating currents**. You produced an alternating current yourself in exercise 6C. + +Alternating currents have a frequency, which is the rate at which they alternate direction. Action potentials have a very high frequency, whereas synaptic inputs and their sums are much slower. + +Here is a demo where an alternating signal increases and decreases in frequency. At the bottom of the page, you can see the wave visualised. + +.. note:: + + When you have capacitors in the simulator, it is a good idea to click 'reset' whenever you make changes, as they will otherwise store charge and can create weird effects. + +.. admonition:: Exercises + + 7A. Press ‘Play Audio’ to hear how the sound is modulated as the frequency increases. + + .. figure:: media/audio_sweep.* + :align: center + :target: https://tinyurl.com/yyrvugha + + +8. Impedance +**************** + +Alternating currents have a frequency, so we need to use the term 'Impedance' (Z) instead of 'Resistance' to describe how circuit components oppose current flow. See the theory handout for more information. + +The impedance magnitude of a capacitor, also called reactance (X\ :sub:`c`), depends on: + +.. math:: + + Xc = \frac{1}{2 \pi fC} + +Where f is the frequency with which the current alternates, and C is the capacitance. + +The impedance provided by capacitors varies with frequency. Because we are interested in signals at specific frequencies (e.g. 1000Hz for action potentials), we have to make sure to build our recording circuit so that the frequencies we are interested in experience little opposition. + +When you see a capacitor in a circuit, you know you need to think about the frequency of the signal. Steady direct current has no frequency, so X\ :sub:`c` is infinite: capacitors only pass alternating signals. + +.. admonition:: Exercises + + .. figure:: media/cap_freq_circuits.* + :align: center + :target: https://tinyurl.com/y3sbgfl6 + + Setup: + + Here are two circuits with an alternating voltage source of 15 and 40 Hz, respectively. In the oscilloscope at the bottom of the simulator, the voltage trace of the source and the capacitor are plotted. + + 8A. Visualise the current in the circuit (for instance the current flowing through the stretch of wire). You could add a new scope to do this or double-click the wire and 'show current'. Which circuit has higher amplitude current? + + 8B. Add a third circuit, powered by an alternating voltage source of 120 Hz. What happens to the current as the frequency increases? + + (Bonus question: what happens to the voltage drop across the capacitor as frequency increases?) + + +9. Capacitive voltage divider +********************************** + +Because capacitors impede current flow, we can use them to build voltage dividers, just like the resistor divider shown above. + +.. admonition:: Exercises + + .. figure:: media/cap_voltage_div.* + :align: center + :target: https://tinyurl.com/yxdwvulv + + 9A. Change the capacitance values C for the first capacitor to test whether the formula for the resistor voltage divider applies for capacitors. \ No newline at end of file diff --git a/_sources/courses/open-ephys/exday2-nokit.rst b/_sources/courses/open-ephys/exday2-nokit.rst new file mode 100644 index 00000000..a4e13efd --- /dev/null +++ b/_sources/courses/open-ephys/exday2-nokit.rst @@ -0,0 +1,137 @@ +.. _exday2-nokit: + +Exercises Day 2: No Hardware +################################ + +.. |Ve| replace:: V\ :sub:`e`\ +.. |Ce| replace:: C\ :sub:`e`\ +.. |Rm| replace:: R\ :sub:`m`\ +.. |Re| replace:: R\ :sub:`e`\ +.. |Cs| replace:: C\ :sub:`s`\ +.. |Vin| replace:: V\ :sub:`in`\ +.. |Vec| replace:: V\ :sub:`ec`\ +.. |Vout| replace:: V\ :sub:`out`\ + +.. contents:: + :depth: 2 + :local: + +1. Capacitor and Resistor in parallel +**************************************** + +In the circuit below, you will see a capacitor and a resistor in parallel. The voltage source alternates at 20Hz, going from -10 to +10 volts. The current travels over the resistor or via the capacitor to ground. + +.. figure:: media/cap_res_parallel_sim.* + :align: center + :target: https://tinyurl.com/y27sbtmr + +.. admonition:: Exercises + + 1A. Increase the value of the resistor to 200kOhm. What happens to the current through the resistor? + + 1B. Put the resistor back to 10kOhm. Now, increase the capacitance of the capacitor to around 10mF. What happens to the current? + + 1C. Return the values to 10kOhm and 100nF. + + Change the frequency of the alternating signal to + + - 1000 Hz (action potentials!) + - then to 1 Hz + + You may have to change the simulation speed using the red slider at the top right, and adjust the x-scaling of the scope below (right-click / properties / and slide the 'horizontal scale'). + + How does the frequency of the signal relate to how much current crosses either the capacitor or the resistor? + +2. The equivalent circuit of the electrode +*********************************************** + +In the theory handout, we discussed how we can represent an electrode as a circuit containing a resistance and a capacitance. We’ll now build this equivalent circuit in the simulator. + +.. admonition:: Exercises + + 2A. In the simulator, edit the circuit used above to build the equivalent circuit of a polarised, tungsten electrode. See the theory handout for more details. + + Here are some values to use: + + * |Rm|: the DC resistance of the metal electrode wire, 10-100 Ohms. + * |Ce|: the electrode tip capacitance, generated by the double layer generated around the electrode. |Ce| ~ 0.2 pF / µm2, so 10 - 20 pF (if the electrode is unplated) + * |Re|: electrode tip resistance, in parallel with |Ce|. ~ 100 MOhm. + * Edit the alternating voltage supply to provide 1V at 1Khz, mimicking the signal coming from your cell. 1V is larger than ephys signals, but makes the current flow easier to see. Change the sliders for simulation speed and current speed until you can see where the current is flowing. + + 2B. What happens if you delete the resistor |Re|? + + 2C. Bonus exercise: Can you change this circuit from a polarising, tungsten electrode, to a circuit representing a nonpolarizable electrode? + +3. Shunt Impedance +********************* + +Here is the circuit of the electrode with a shunt impedance added of 100 pF: + +.. figure:: media/day2circuit.* + :align: center + :target: https://tinyurl.com/y2jshzqc + +.. admonition:: Exercises + + 3A. What is shunt impedance here? + + 3B. What % of our signal are we losing between Vec and Vin? Why? + + 3C. What could we change to increase the signal at Vin? + + 3D. The tips of certain electrodes, e.g. nichrome tetrodes, can be electroplated in a thin layer of gold. This 'goldplating' increases the surface area of the tip, creating more space to separate charge. This increases tip capacitance by around 100x. Make this change in the circuit simulator. How similar are Vec and Vin now? + +Recording Circuit +==================== + +To actually perform a recording, we will have to attach the electrode to the rest of an acquisition system. The recording system has an analog to digital converter (ADC), and a recording computer. The leakage resistance here is where the recording system is connected to ground. + +.. figure:: media/day2withac.* + :align: center + :target: https://tinyurl.com/y6864vle + +.. admonition:: Exercises + + 3E. How much of the voltage at the electrode, Vec, are we recording at Vout? + + 3F. Add a headstage to this circuit, by placing an ideal operational amplifier between the electrode and the long wire. What happens to Vout? Why? + + 3G. Change the circuit to stop the amplifier from saturating. What is the amplifier gain now? + +4. Operational Amplifiers +**************************** + +Voltage rails +================= + +In the simulator, 'ideal' operational amplifiers are shown without their power supplies. However in real life, we need to provide our op-amp with power. We will use batteries to make voltage ‘rails’. We are going to make a -3V and +3V rail using simulated AA batteries that provide 1.5V each. + +To do this we use a common trick and turn two regular power supplies into a bipolar power supply. + +.. figure:: media/bipolar_power_supply.* + :align: center + +.. admonition:: Exercises + + 4D. Using 4x 1.5 DC voltage supplies simulated batteries, connect them together so that you have a +3, 0, and -3 power supply. + + .. figure:: media/aa_batteries_sim.* + :align: center + :target: https://tinyurl.com/yyo6n35w + + 4E. Replace the 'ideal' op-amp with a 'real' op amp in the simulator. Use a bipolar power supply to power it. What amplitude values do you get as output now? How is it different to the ideal op amp? + +Bypass capacitors +====================== + +Bypass capacitors are small capacitors that act like little secondary batteries. The batteries we use have a high ESR - ‘equivalent series resistance’, and some capacitance. This means that are not great at quickly providing current. Because of this, when our op-amp starts working, it can run out of current for a very short time until the battery can drive the rails back to their original voltage. This is bad for the signal quality. + +So, we allow these small capacitors to charge. If the battery briefly can’t provide current, the bypass capacitors will discharge, providing quick back-up current. We’re exploiting the fact that these caps have very low ESR and can provide current pretty much instantaneously. The fact that they’re too small to power anything for more than a millisecond does not matter here, at that point the batteries have caught up. + +.. admonition:: Exercises + + 4F. Add bypass capacitors to the simulation based on where they are in the bipolar power supply pictured here: + + .. figure:: media/fritz_bipolar_power_supply.* + :align: center + :target: https://tinyurl.com/y25z3vzh \ No newline at end of file diff --git a/_sources/courses/open-ephys/index.rst b/_sources/courses/open-ephys/index.rst new file mode 100644 index 00000000..d1c50527 --- /dev/null +++ b/_sources/courses/open-ephys/index.rst @@ -0,0 +1,76 @@ +.. _open-epyhs: + +Extracellular Electrophysiology Acquisition +##################################################### + +Introduction +*************** + +This course is designed to provide a thorough understanding of extracellular electrophysiology, a branch +for studying the electrical activity of neurons and other excitable cells. It includes recorded lectures with hands-on +electronics exercises to ensure that you gain both theoretical knowledge and practical skills. + +.. note:: We want to thank Open Ephys team for creating this course. Their hard work and expertise in developing and sharing this + material are greatly appreciated. You can find the original course at `OE Ephys Course `_. + +Materials for students +************************ + +The course consists of 2 segments - Theory and experiments. Read the theory segments carefully before performing the experiments to get a better understanding of all the concepts. + +To read before Day 1: + +- `How to use a breadboard `_ + +Day 1: Detecting Signals +===================================================== + +.. toctree:: + :maxdepth: 2 + + theory-day-1/index + +Day 2: Protecting and Amplifying Signals +===================================================== + +.. toctree:: + :maxdepth: 2 + + theory-day-2/index + +Day 3: Referencing and Grounding +===================================================== + +.. toctree:: + :maxdepth: 2 + + theory-day-3/index + +Day 4: Synchronization and Digitization +===================================================== + +.. toctree:: + :maxdepth: 2 + + theory-day-4/index + +No Hardware kit? Use these links! +********************************************* + +.. toctree:: + :maxdepth: 1 + + exday1-nokit + +.. toctree:: + :maxdepth: 1 + + exday2-nokit + + +.. note:: On completion, you'll be able to understand: + + 1. The basic principles of extracellular electrophysiology. + 2. Design and build basic electronic circuits for signal acquisition and processing. + 3. Perform extracellular recordings and analyze electrophysiological data. + 4. Design and troubleshoot electrophysiology experiments effectively. diff --git a/_sources/courses/open-ephys/theory-day-1/index.rst b/_sources/courses/open-ephys/theory-day-1/index.rst new file mode 100644 index 00000000..18c2f3c1 --- /dev/null +++ b/_sources/courses/open-ephys/theory-day-1/index.rst @@ -0,0 +1,416 @@ +.. _theory-day-1: + +*********************************** +Theory Day 1 +*********************************** + +.. |Na+| replace:: Na\ :sup:`+`\ +.. |Cl-| replace:: Cl\ :sup:`-`\ +.. |Ca2+| replace:: Ca\ :sup:`2+`\ +.. |K+| replace:: K\ :sup:`+`\ +.. |Rs| replace:: R\ :sub:`s`\ +.. |Rm| replace:: R\ :sub:`m`\ +.. |Re| replace:: R\ :sub:`e`\ +.. |Rsh| replace:: R\ :sub:`sh`\ +.. |Ce| replace:: C\ :sub:`e`\ +.. |Csh| replace:: C\ :sub:`sh`\ +.. |Vin| replace:: V\ :sub:`in`\ +.. |Vec| replace:: V\ :sub:`ec`\ +.. |Vout| replace:: V\ :sub:`out`\ +.. |Ve| replace:: V\ :sub:`e`\ +.. |Za| replace:: Z\ :sub:`a`\ +.. |Ze| replace:: Z\ :sub:`e`\ + +.. contents:: Table of Contents + :depth: 2 + :local: + +.. _refwot: + +Introduction +################################### + +Welcome to the Open Ephys Cajal course on extracellular electrophysiology acquisition! + +The goal of electrophysiology ('ephys') is to record signals generated by electrically active cells. There are many different +types of acquisition systems and setups, but they are built upon the same principles. +By understanding these fundamental ideas, we hope you will be able to see past branding and tradition, and decide for yourself what +you need your setup to be able to do. + +Talk: Introduction +################################### + +.. youtube:: eaAKn61R6MY + :align: center + :width: 100% + +Types of extracellular electrophysiology +############################################ + +Several biological processes in the body generate time-varying electrical signals that we can measure outside of cells, such as skeletal muscle contraction (electromyography, EMG), or the heartbeat (electrocardiogram, ECG). In systems neuroscience, we often use intracranial electrodes to measure action potential firing (spikes) or local field potentials (LFP). Electrodes outside the skull allow us to detect the electroencephalogram (EEG) non-invasively. + +Most of the theory in this course will focus on intracranial extracellular recordings of neuronal activity, as these are the most common in systems neuroscience. For the practical exercises, we will be building an EMG recording circuit, as it is straightforward to test on yourself. + +.. list-table:: Table 1: Overview of Extracellular Electrophysiology Methods + :widths: 20 25 35 20 + :header-rows: 1 + + * - Technique + - Signal + - Electrodes + - Typical amplitude + * - ECG/EKG + - Heart: Depolarisation/repolarisation of cardiac tissue + - Surface electrodes + - mV range + * - EMG + - Skeletal muscle: A train of motor unit action potentials. + - Surface electrodes placed on skin above muscle, reference electrode on skin above bone. + - mV range + * - EEG + - Brain: Summations of slow neural activity + - Surface electrodes on scalp + - 50 µV + * - LFP + - Brain: Summations of slow neural activity + - Intracranial electrode + - 100-1000 µV + * - 'Spike' recording + - Brain: Action potentials (fast ‘spikes’) from individual neurons + - Intracranial electrodes, e.g. tetrodes (4 insulated wires twisted together), Single-wire electrodes, Silicon probes. + - 20-200 µV + +Electronics Refresher +################################### + +Charged particles exert electric force +********************************************* +Electric signals in organic tissues are generated by positively charged (Na\ :sup:`+`\, |K+|, |Ca2+|) and negatively charged (|Cl-|) ions. Electrons are negatively charged particles in our electrodes and wires (i.e., metal). + +All charged particles exert an electric force on other charged particles. Coulomb's law (Eq 1) describes that this force will have both magnitude (it will be bigger if the charges are larger or closer together) and direction (it will either attract or repel, depending on whether the charges have different or the same polarity). + +.. math:: + + F= k\frac{q1q2}{r^2} + +Equation 1: F = electric force, k = Coulomb constant, q1 + q2 = charges, r = distance of separation + +.. figure:: ../media/coulombs_law_visual.* + :align: center + :alt: Representation of a positive and negative charge being attracted towards each other, and two positive charges being repelled from each other. + + `Figure 1: The magnitude of electric force between charges depends on their charge and the distance between them.` + +We often represent electric force using electric field lines surrounding the particle. These lines show that charges in the vicinity of the particle will be influenced by its force, and that this influence has a particular direction. + +.. figure:: ../media/electric_force_field.* + :align: center + :alt: A single positive charge represented as a circle, surrounded by a gradient (which is darkest close to the charge) representing the strength of the electric force, and electric field lines radiating out from the charge. + + Figure 2: Electric field lines show the direction of the force on a positive charge. Colour intensity represents electric potential + +If a charged particle is free to move and placed within an electric field, then the electric forces acting on it will cause it to move in a certain direction. An example is an ion in the cytoplasm; if not bound to a membrane, this ion will be moved by electric forces it experiences. + +Currents are moving charges +********************************************* + +Moving charges create a current (I) measured in amperes. The current tells us how much charge is moving per second. + +.. math:: I = \frac{Q}{t} + +Equation 2: Current (I) is equal to charge (Q) over time (t). + +By convention, the direction of this current is always the direction of positive charge movement. When currents are generated by a negatively charged ion, such as chloride, we describe them as a positive current moving in the opposite direction to the chloride ion. + +.. _refepot: + +Electric Potential Difference +********************************************* + +Figure 3 shows a negative and positive charge that are held in a certain position in space. These large charges are not allowed to move, but still exert an attracting force on each other. If we let them, they would move towards each other. We can see that their electric forces will interact. + +.. figure:: ../media/electric_potential.* + :align: center + + `Figure 3: Electric potential mapped around a positive and negative charge` + + `© 2010 Geek3 /CC BY-SA 4.0 `_ + +Each point in this image has a value that describes the **electric potential** at that point, represented by colour. If free to do so, positive charges will move from areas of higher potential to areas of lower potential. Just as a difference in gravitational potential energy can cause a river to flow down a mountain, a difference in electric potential can cause charged particles to flow from a region of higher potential towards a region of lower potential until the charges no longer experience a net electrical driving force. In an electric circuit, the driving force is therefore a difference in electric potential between two points. + +| + +The bigger the difference in electric potential between A and B, the higher the driving force on the charges. If there is no difference in electric potential, no net charges will move (no current). Our driving force is therefore the Electric Potential Difference between two points, measured in volts and often referred to as 'voltage'. + +| + + +If we placed a +1 'test' charge at any point in this space, it would experience a net electric force; some influence from the + charge, some influence from the negative charge. The vector description of the magnitude and direction of that force is the electric field, and is shown as field lines on Figure 3. + +| + +The electric potential is different to the electric field. While the electric field has both magnitude and direction, the electric potential only has magnitude, and is represented as colour in Figure 3. High, (orange) positive electric potential surrounds our positive charge, and low (blue) negative potential surrounds our negative charge. + +| + +If we placed our positive +1 test charge at an area of high potential, like point 'A', it would follow the gradient of the electric potential until it reached the negative particle at point 'B'. The difference in electric potential between point A and B therefore generated a current (a moving charge). We could use that converted potential energy to power something else. + +| + +In contrast, to move the same particle from point B to point A, we would need to provide additional energy to counteract the repelling force generated by the positive point charge. The difference in electric potential between two points tells us how much energy we need to move a charge from one place to another. If we were to add more point charges (that are not allowed to move) to this image, their generated forces will sum, giving a more complex map of electric potentials at every point in space. + +| + +Because it is defined as a difference between two points, voltage always has to be measured between two points. When we do extracellular recordings, we measure the electric potential difference between the tip of our electrode and our ground or reference point. + +Where is 0 volts? +----------------------------------------------- + +To describe the height of a mountain, there is no such thing as absolute altitude; instead, we use ‘sea level’ as our point 0 and measure from there. A similar thing goes for voltage. We pick a point to call ‘0 V’ and compare the rest of the circuit to that. This point can be the negative terminal of a battery, the extracellular fluid, or a point at infinity, far from all sources of electric potential (Einevoll et al., 2013). + +| + +The terms ``ground``, ``reference``, and ``earth`` are often used interchangeably, but are not quite the same thing. + +Reference: A point in the circuit that you labelled 0V, so that you can measure the other values from there. + +Ground: Often used as a reference point and considered 0V, but has the additional capacity to provide (source) or get rid of (sink) a lot of current, without its own potential changing. + +Earth: The actual planet earth is the best ground we have. Metal poles in the earth are used to sink current from lightning bolts because the sheer size of the earth means that such a tiny bit of extra current is not a problem, and won't change the potential of the earth. + +Resistance +********************************************* + +Resistance opposes current flow. The electric potential difference (V) drives a current (I) from point A to B across a resistance (R). A resistance can be measured between any two points A and B; it may be so high as to be infinite in which case we consider the points isolated from each other. The resistance may be very low, such as in a wire, in which case we consider the two points short circuited. + +This is described by Ohm's law: + +.. math:: + + I = V/R + +Equation 3: Current (I) is equal to voltage (V) over resistance (R). + +.. _refcapacitancetheory: + +Capacitance +********************************************* + +Capacitors for use in electronics are made of two conducting plates, separated by a thin layer of insulating material that prevents the plates from touching. When a capacitor is connected to a voltage source, such as a battery, charges collect on one of the plates. The charges cannot move through the insulating layer, but they can exert a force through it. This electric force pushes away similar charges on the opposite plate. This movement of charge is what gives us current flow in the circuit, even though charges cannot flow directly through the capacitor. + +.. math:: + + Q = C * V + +Equation 4: The amount of charge (Q) a capacitor can separate depends on is its capacitance (C, measured in farads) and the voltage (V) across the capacitor. + +.. figure:: ../media/capacitor_charge.* + :align: center + :alt: two capacitors are represented as vertical lines. The left capacitor is uncharged, and has balanced positive and negative charges on each side represented as circles with +1 or -1 charge. The capacitor on the right has been charged; a voltage has been applied and now the positive charges are aligned on one side of the plate, and the negative charges on the other. + + `Figure 4: An uncharged capacitor has no net charge on either plate (left). A charged capacitor separates charges with positive charges on one plate, and negative charges on the other (right).` + +In a direct current circuit, current will flow while the capacitor charges, as charge is pushed or pulled on either plate. Current flow will stop once the capacitor is fully charged. This electric charge can be discharged (and, for instance, used to power something) by providing a path that connects the positive and negative charges of the capacitor. + +.. _refimpedanceintro: + +Impedance +********************************************* + +A battery provides a positive current flow in a single direction. In contrast, neuronal currents can move both towards and away from our measuring electrode. After all, |Na+| ions can both enter and exit the cell. Neuronal signals are therefore **alternating signals**. The **frequency** of an alternating signal tells us how often the direction of flow changes. The power supply in buildings is also alternating: the current direction switches at a fixed frequency, producing a sinewave (the notorious 50/60Hz frequency noise in ephys recordings). + +For alternating signals, we need to use impedance (Z) to describe opposition to current flow, instead of using resistance. The impedance represents opposition to current flow measured in both magnitude and phase, which allows us to describe the relationship between voltage and current for time-varying signals. We can measure the impedance of a component at different frequencies, so that we understand both the magnitude and phase relationship between V and I over a broad frequency range (from 1 Hz to 10 kHz). Let’s examine the response of resistors and capacitors to an applied sinusoidal voltage (an alternating signal). + +Impedance: Resistors +----------------------------------------------- + +For resistors, the impedance magnitude (Z) is constant and does not vary with the frequency of signal applied. The impedance follows Ohm's Law (V = IR), which doesn't take the frequency of the signal into account. + +Impedance: Capacitors +----------------------------------------------- + +In contrast, for a capacitor, the magnitude of impedance decreases as the frequency increases (see Eq 5). We can therefore only describe the impedance of a capacitor at a specific frequency. A second component of impedance is phase offset; in capacitors, the current is 90° out of phase with the voltage. This second aspect of impedance is not within the scope of this course. + +.. math:: + + Zc = \frac{1}{2 \pi fC} + +Equation 5: The magnitude of impedance of a capacitor (Zc) will decrease with increasing frequency (f). The larger the capacitance (C), the lower the impedance at a specific frequency. + +Equivalent circuits in the brain +############################################ + +Let's apply the electronics concepts above to our neuronal tissue. Neuronal activity relies mainly on ions such as |Na+|, |K+| and |Ca2+|. Whenever these charges flow, we have a **current**. In neurons, our **resistance** to current flow is largely formed by the permeability of the cell membrane to our ion, and changed by opening or closing ion channels in the membrane. When more channels open, the resistance to a certain ion is lowered, and the charge is able to flow in or out of the cell. + +The driving force in this scenario is the membrane potential, i.e. the **difference in electric potential** between the inside of the cell membrane and the extracellular fluid. A neuron typically has a resting membrane potential of around -70 mV compared to the extracellular fluid, if we decide that the extracellular fluid has 0 V. + +In addition to electric forces, ions in neurons are affected by a second driving force; concentration gradients. Ions will tend to diffuse away from areas where there is a high concentration of the ion, to areas with a lower concentration. The interaction of the concentration and electrical driving forces is the electrochemical gradient and this balance is described by the Nernst equation. This will not be covered in this course, but `Wright 2004 `_ provides a clear refresher on this, and to understand how the -70mV is maintained by the cell. + +Neuronal output: Action Potentials +********************************************* + +Input signals to the neuron can trigger the opening of voltage-dependent |Na+| ion channels, greatly reducing membrane resistance to |Na+|. This allows |Na+| to follow its concentration and electrical gradient, an travel from outside the cell, where the |Na+| concentration is high, to the inside of the cell, where |Na+| concentration is low and the intracellular medium has a lower potential (Kandel, Schwartz, & Jessel, 2000). In neurons, voltage-sensitive |Na+| channels are usually concentrated at the initial segment of the axon, and it is therefore more likely that an action potential will be generated there, rather than in other regions of the cell. The subsequent opening of |K+| channels begins the process of returning the membrane potential to resting conditions (Hodgkin and Huxley, 1939). + +Neuronal input: Postsynaptic potentials +********************************************* + +Slower frequencies in extracellular recordings are the focus of the LFP or EEG. These are thought to be largely generated by postsynaptic potentials, as these occur over slower timescales (10s of ms) than the action potential (1-2 ms), so there is more opportunity for signals from multiple cells to summate and result in larger signals. When activated, AMPA and NMDA synapses mediate excitatory currents as |Na+| and |Ca2+| enter the cell. + +Capacitors in the brain +********************************************* + +The definition of a capacitor was described above. This configuration of two conducting materials separated by a thin, insulating layer, does not only happen in specifically designed electronics components, but can occur anywhere. One example is the neuron, where both the intracellular and extracellular medium are conductive, but the cell membrane is not. The cell membrane is therefore also a capacitor, and charge can be separated along the membrane depending on the potential difference between the inside and the outside of the cell. + +Remember that: + +.. math:: + + Q = C * V + +The amount of charge (Q) a capacitor can separate depends on is its capacitance (C, measured in farads) and the voltage (V) across the capacitor. That means that when the voltage across the cell membrane is reduced (i.e. the cell depolarises), the ability for the membrane to store charge is also reduced. These charges are released from the membrane and generate capacitive currents (see Fig 5 below). + +Importantly for acquisition systems, cables are capacitors too; imagine a cable containing two wires. These wires are conductive, and are separated by a thin layer of insulation. These wires will separate and release charge depending on the electric potential difference between them. + +Extracellular measurements +********************************************* + +When we perform extracellular recordings, we are measuring the electric potential induced at the electrode (V\ :sub:`electrode`\ or |Vec| ) by these currents. The effect on the induced electric potential depends on the magnitude, sign and location of the current sources, and on the conductivity of the extracellular medium (Buzsaki et al., 2012; Nunez and Srinivasan, 2006). The effect of these currents diminishes with distance, depending on how well the extracellular fluid conducts electricity. The extracellular potential Vec at position re and time t, with respect to a point at infinity, can be computed with the following equation (Einevoll et al., 2013; Nunez and Srinivasan, 2006): + +.. figure:: ../media/point_source_equation.* + :align: center + + `Equation 6: The point source equation` + +Conceptually, this point-source equation (Equation 6) is key for computing the extracellular potential in response to any transmembrane current (Buzsaki et al., 2012). In(t) represents the nth point current source and re – rn represents the distance between the point source and the position of measurement, with n = 1...N, where N is the number of individual point sources and ρ is the extracellular conductivity. If the extracellular medium is considered homogeneous and isotropic, we can use a constant conductivity value for the extracellular fluid (Einevoll et al., 2013). + +| + +Extracellular action potential waveforms usually last on the order of 1-2 ms, and are in the range of tens to hundreds of microvolts in amplitude, with the largest potential deflections being detected close to the soma of a neuron. These stereotypical temporal deflections of the electric potential in the extracellular space are called action potentials or spikes. The model in Fig 5 below illustrates how the electric potential varies depending on electrode location relative to a spiking neuron. + +| + +Fig 5 depicts the (modelled) time-varying extracellular potential measured at 3 different locations close to a neuron. Each extracellular waveform results from the superposition of ionic and capacitive transmembrane currents. The peaks in the potential waveforms correspond to the current (right column) that is dominant at that time-point: the first positive peak of the waveform is attributed to the positive capacitive current resulting from the strong |Na+| current entering the axon initial segment; the main negative peak is attributed to the influx of |Na+|; and finally, the second positive peak results from repolarising |K+| current flowing out of the cell (Gold et al., 2006). As the effect of a current decreases with distance, the relative position of the electrode determines the relative contribution of each current and therefore the net overall current shape (left column). For instance, if the electrode is close to the axon initial segment (where many voltage-dependent |Na+| channels are), the |Na+| current will be larger. + +.. figure:: ../media/electric_potential_spike.* + :align: center + + `Figure 5: Electric potential generated by current sources in a conductive volume.` + +.. note:: Electric potential generated by current sources in a conductive volume. The extracellular potentials and currents are adapted from Gold et al., 2006. The shape of the extracellular potential waveforms at various spatial positions 're' (marked with black dots) are simulated for a CA1 pyramidal neuron. + + Currents: simulated net membrane current (first column) across the soma and proximal dendrites that best estimates the extracellular potential waveform and membrane current components in terms of Na+, K+ and capacitive currents (second column). In the soma, the positive capacitive current coincides with the larger Na+ current. At locations along the apical trunk, the initial capacitive peak becomes visible. In dendritic compartments the membrane depolarisation is initially driven by Na+ current from the soma, until local Na+ currents are activated and the action potential regenerates. In the brief time before the local Na+ currents activate, the positive capacitive current is the dominant membrane current and a capacitive-dominant phase is visible in the net current (Gold et al., 2006, adapted by Joana Neto). + +What does an acquisition system do? +################################################## + +There are several things that any extracellular acquisition system has to be able to do. Here is a quick overview so that you can start to imagine what the acquisition system does, but don't worry if they don't make sense yet. We will go through each of these points carefully during the course. + +The extracellular electrophysiology techniques in Table 1 all share the same major goal: to measure activity occurring in biological tissue. They do that by detecting changes in electric potential due to cellular activity, compared to a reference or ground point, and by faithfully shuttling these signals to an output where the experimenter can view or record them. In most cases this output will be a computer where we can visualise and store our data. + +The signal at the electrode is measured in volts (V) and is very small, in the microvolt range. This is tiny compared to the voltages we encounter elsewhere in the lab: for instance, a battery is around 3V, and the building main power supply 120 or 230V. The world, and your lab, is also an electrically noisy place, which you will know if you have done any ephys before. Electrical equipment, communications devices, but also just walking around (static electricity) creates electric potential differences many orders of magnitude larger than the biological signal you are trying to measure. The acquisition system needs to be designed so that it can detect our tiny signals even in the face of surrounding noise signals generated by other sources. + +.. figure:: ../media/black_box_recording_system.* + :align: center + :alt: An extracellular voltage beside a neuron is detected by an electrode. The signal coming out of the electrode is Vin. This goes into a recording system, and the output of that system is called Vout. + + `Figure 6: The voltage at the electrode tip (Vec), the voltage after the electrode (Vin) and the voltage we read out (Vout). We can only read Vout, and must design our acquisition system so that it is as similar to Vec as possible.` + +To know what is going on in our cells, we need as much as possible of the signal at the electrode tip (|Vec|) to make it through the electrode (|Vin|) and acquisition system and arrive at our output (|Vout|). If we lose signal magnitude, or lose certain frequencies because of the way our acquisition system is designed, we may miss important data or come to wrong conclusions about our cells. We therefore have to design our acquisition system to pass on signals as faithfully as possible, losing little signal to the environment. + +An acquisition system must therefore: + +* **Detect changes in electric potential difference** +* Faithfully *transfer* this signal to our acquisition system output +* Distinguish interesting biological *signals* from other sources of electrical *noise* + +The electrode detects changes in electric potential +##################################################### + +Getting from neuronal activity (|Vec|) to the input to the recording system (|Vin|) relies first on the interface between the electrode and the extracellular space. Extracellular microelectrodes are usually made from metallic conductors. A thin insulated metal wire with an exposed tip is the most basic, and still widely used, device for in vivo extracellular recording from brains. Metals such as platinum, gold, tungsten, iridium, titanium nitride, stainless steel, iridium, iridium oxide, and alloys, nickel-chrome, platinum-iridium and platinum-tungsten have all been used in neural electrodes. + +The transition from ion flow in the extracellular space (due to neural activity) to electron flow in the electrode is made through the double layer interface. When a metal is placed in a saline solution two phenomena occur: water dipoles close to the metal surface become oriented, and assuming the metal surface is negatively charged, the solution close to the metal surface become depleted of negative ions (anions), leaving behind a cloud of positive ions (cations). This cloud of cations screens the electric field caused by the excess of charge on the metal. Electroneutrality across the interface requires that the charge on the metal is always equal and opposite to the total charge on the solution side of the interface (Musa et al., 2012). The resulting charge distribution - two narrow regions of equal and opposite charge - is known as the electrical double layer (EDL). The double layer region (represented in pink in the schematics) has the ability to separate charges on both sides, and therefore a capacitance '|Ce|'. The double layer also opposes the direct flow of current across it, and therefore has a resistance '|Re|'. + +.. figure:: ../media/double_layer_interface.* + :align: center + :alt: Depicts cartoon of metal and solution touching (electrode and extracellular fluid respectively). Negative ions within the metal are attracted to positive charges in the solution. + + `Figure 7: The double layer interface between an electrode and the extracellular fluid` + +We can describe the electrical behaviour of electrodes by making an ‘equivalent circuit’, getting rid of the specific shape or material and just representing the electrical properties of the double layer interface: + +.. figure:: ../media/circuit_double_layer_interface.* + :align: center + :alt: The components of the double layer interface abstracted as electrical components, where the metal electrode is a resistance called Rm, the double layer interface is a capacitor and resistor in parallel called Re and Ce, and the extracellular solution is a resistance named Rs. + + `Figure 8: The equivalent circuit describes the electrical properties of the double-layer interface between electrode and extracellular fluid` + +In the above figure, the double layer interface between the solution and the electrode is represented by a parallel resistance and capacitance, in combination with resistances |Rm| (metal) and |Rs| (solution) in series. + +* |Re| represents leakage resistance of the electrode; the charge transfer due to charge carriers crossing the electrical double layer. +* |Ce| is the capacitance of the electrical double layer at the interface of the exposed metal and the solution. +* |Rm| (metal) is the resistance within the electrode itself, which depends on what the electrode is made of. +* |Rs| (solution) is the resistance of the fluid surrounding the electrode. + +Because the resistance of the extracellular fluid |Rs| is small and independent of the electrode or acquisition system, we often simplify our equivalent circuits by leaving this value out. + +The ratio between |Ce| and |Re| determines how current can flow. If |Re| is relatively small, this low resistance allows individual charges to travel directly across the electrode-solution interface, transferring between the electrode and the extracellular fluid. This current over the small |Re| bypasses the capacitor |Ce|, which we can then ignore. Electrodes with this property are called 'non-polarised' electrodes. + +In contrast, if |Re| is very large, ions cannot cross the double layer directly. Instead, charge transfer relies on the capacitive properties |Ce| of the double layer. The double layer will separate charges, with negative charges inside the electrode and positive charges on the side of the extracellular fluid holding each other in place. When cellular activity causes a redistribution of ions in the extracellular fluid, the resulting increase or decrease in attractive force will recruit or release electrons in the electrode. Either direction, a current will flow inside the electrode. Electrodes with a large |Re| are called 'polarised' electrodes. + +Non-polarised electrodes +********************************************* + +The silver-silver chloride (Ag-AgCl) electrode approaches the ideal nonpolarisable type. In these ‘charge transfer’ electrodes, surface-confined species are oxidized and reduced (Bard & Faulkner, 2001, Merrill et al., 2005). Non-polarisable electrodes have a small |Re|. This low resistance allows individual charges to travel directly across the electrode-solution interface, transferring between the electrode and the extracellular fluid. This current over the small |Re| bypasses the capacitor |Ce|, thus providing a direct path for the measurement of steady potential levels. + +Polarised electrodes +********************************************* + +The tungsten microelectrode is considered a **polarised** electrode. Polarised electrodes have large |Re| values, in the order of several megaOhms, and so charges cannot cross the double layer. Instead, the transition from ion flow in the solution to electron flow in the electrode is capacitive. The double layer will separate charges, with negative charges inside the electrode and positive charges on the side of the extracellular fluid holding each other in place. When cellular activity causes a redistribution of ions in the extracellular fluid, the resulting increase or decrease in attractive force will recruit or release electrons in the electrode. Either direction, a current will flow inside the electrode. + +Therefore, processes in polarisable electrodes are purely electrostatic and caused by the charging and discharging of the double layer capacitance. Although charge does not cross the interface, currents inside the recording system can flow when the potential or solution composition changes (Cooper, 1971). + +To give an example of a polarised electrode, a tungsten microelectrode like the one used by Hubel and Wiesel in the 1950’s and 60’s has: + +* |Ce| ~ 0.2 pF / um2 ~ 10 - 20 pF (unplated) +* |Re| ~ 10 to 100 MOhm. +* |Rm| ~ 10 to 100 Ohm (Rm= (resistivity x length)/ cross sectional area) + + +References +################################### + +Bard, A. J., & Faulkner, L. R. (2001). Electrochemical methods Fundamentals and Applications. Molecular Biology (Second, Vol. 8). John Wiley & Sons, Inc. + +Buzsaki, G., Anastassiou, C.A., and Koch, C. (2012). The origin of extracellular fields and currents - EEG, ECoG, LFP and spikes. Nat Rev Neurosci 13, 407–420. + +Defelipe, J., Alonso-Nanclares, L., and Arellano, J. (2002). Microstructure of the neocortex: Comparative aspects. Journal of Neurocytology 31, 299–316. + +Einevoll, G.T., Kayser, C., Logothetis, N.K., and Panzeri, S. (2013). Modelling and analysis of local field potentials for studying the function of cortical circuits. Nature Reviews Neuroscience 14, 770–785. + +Gold, C., Henze, D.A., Koch, C., and Buzsáki, G. (2006). On the Origin of the Extracellular Action Potential Waveform: A Modeling Study. Journal of Neurophysiology 95, 3113–3128. + +Herculano-Houzel, S. (2009). The human brain in numbers: a linearly scaled-up primate brain. Front. Hum. Neurosci. 3. + +Hodgkin, A.L., and Huxley, A.F. (1939). Action Potentials Recorded from Inside a Nerve Fibre. Nature 144, 710–711. + +Kandel, E.R., Schwartz, J.H., and Jessel, T.M. (1991). Principles of neural science. + +Markram, H., Muller, E., Ramaswamy, S., Reimann, M.W., Abdellah, M., Sanchez, C.A., Ailamaki, A., Alonso-Nanclares, L., Antille, N., Arsever, S., et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163, 456–492. + +Merrill, D.R., Bikson, M., and Jefferys, J.G.R. (2005). Electrical stimulation of excitable tissue: design of efficacious and safe protocols. Journal of Neuroscience Methods 141, 171–198. + +Meyer, A.C., and Moser, T. (2010). Structure and function of cochlear afferent innervation. Curr Opin Otolaryngol Head Neck Surg 18, 441–446. + +Musa, R. (2011). Design, fabrication and characterization of a neural probe for deep brain stimulation and recording. + +Musa, S., Rand, D.R., Cott, D.J., Loo, J., Bartic, C., Eberle, W., Nuttin, B., and Borghs, G. (2012). Bottom-Up SiO2 Embedded Carbon Nanotube Electrodes with Superior Performance for Integration in Implantable Neural Microsystems. ACS Nano 6, 4615–4628. + +Nelson, M.J., Bosch, C., Venance, L., and Pouget, P. (2013). Microscale Inhomogeneity of Brain Tissue Distorts Electrical Signal Propagation. J. Neurosci. 33, 2821–2827. + +Nunez, P.L., and Srinivasan, R. (2006). Electric fields of the brain: the neurophysics of EEG (Oxford ; New York: Oxford University Press). + +Obien, M.E.J., Deligkaris, K., Bullmann, T., Bakkum, D.J., and Frey, U. (2015). Revealing neuronal function through microelectrode array recordings. Front. Neurosci. 8. + +Ray Cooper. (1971). Recording Changes in Electrical Properties in the Brain in Methods of Psychobiology. (R. D. Myers, Ed.) (Volume 1). London and New York: Academic Press. + +Wright, S. (2004). Generation of resting membrane potential. Adv Physiol Educ. 28: 139-142. \ No newline at end of file diff --git a/_sources/courses/open-ephys/theory-day-2/index.rst b/_sources/courses/open-ephys/theory-day-2/index.rst new file mode 100644 index 00000000..2bdcb564 --- /dev/null +++ b/_sources/courses/open-ephys/theory-day-2/index.rst @@ -0,0 +1,227 @@ +.. _theory-day-2: + +*********************************** +Theory Day 2 +*********************************** + +.. |Na+| replace:: Na\ :sup:`+`\ +.. |Cl-| replace:: Cl\ :sup:`-`\ +.. |Ca2+| replace:: Ca\ :sup:`2+`\ +.. |K+| replace:: K\ :sup:`+`\ +.. |Rs| replace:: R\ :sub:`s`\ +.. |Rm| replace:: R\ :sub:`m`\ +.. |Re| replace:: R\ :sub:`e`\ +.. |Rsh| replace:: R\ :sub:`sh`\ +.. |Ce| replace:: C\ :sub:`e`\ +.. |Cs| replace:: C\ :sub:`s`\ +.. |Vin| replace:: V\ :sub:`in`\ +.. |Vec| replace:: V\ :sub:`ec`\ +.. |Vout| replace:: V\ :sub:`out`\ +.. |Ve| replace:: V\ :sub:`e`\ +.. |Za| replace:: Z\ :sub:`a`\ +.. |Ze| replace:: Z\ :sub:`e`\ +.. |Zsh| replace:: Z\ :sub:`sh`\ +.. |Zcs| replace:: Z\ :sub:`cs`\ + + +.. contents:: Table of Contents + :depth: 2 + :local: + +| + +Yesterday, we said that an acquisition system must: + +* *Detect* changes in electric potential difference +* **Faithfully *transfer* this signal to our acquisition system output** +* Distinguish interesting biological *signals* from other sources of electrical *noise* + +Impedance ratios determine signal transmission +#################################################### + +.. figure:: ../media/black_box_recording_system.* + :align: center + +The signal |Vec| (V electrode) is measured at the electrode tip. |Vin| is the voltage that enters the acquisition system. |Vout| is the signal output of the acquisition system. Faithfully transferring the signal means not losing (much) signal between |Vec|, |Vin|, and |Vout|. This is all based on the idea of voltage dividers; that the voltage between two impedances in series will be determined by the ratio of their impedances. + +| + +.. raw:: html + +
+
+ +Why is impedance important? +*********************************** + +The figure below includes the equivalent circuit of the electrode, as discussed yesterday. The signal |Vec| must travel through the electrode, to |Vin|, the voltage before the acquisition system itself. From there, currents coming from our neurons travel to ground. They can do so either by passing through our acquisition system, or (in parallel) they can be lost to ground through shunt impedance. Shunt impedance is primarily capacitive (see section below) and represented as (|Cs|). Shunt capacitances are created by cables or the sides of electrodes; they are accidental but unavoidable capacitances in the system. + +.. figure:: ../media/circuit_electrode_shunt_capacitance.* + :align: center + :alt: equivalent circuit of the electrode, with a subsequent capacitance to ground representing shunt capacitance + +We can replace these components with a representation of the impedance (Z) they provide. + +.. figure:: ../media/circuit_impedance_shunt_capacitance.* + :align: center + :alt: equivalent circuit of electrode, shunt capacitance and acquisition system with each component represented as an impedance. + +The impedance of the shunt capacitance, |Zcs| and the impedance of the acquisition system |Za| are impedances in parallel. +We can simplify our circuit by combining their impedances and calling it |Za|'. + +.. figure:: ../media/shunt_amplifier_voltage_divider.* + :align: center + :alt: The electrode impedance and the shunt+amplifier impedance in series, showing how these two parts form a voltage divider. + +This gives us a voltage divider, similar to the one we built before, where: + +.. math:: + + Vin = \frac{Za'}{Za'+Ze} Vec + +The ratio of |Ze| and |Za|' therefore determines how much of our electrode tip voltage |Vec| reaches |Vin|. + +**To get more of our voltage Vec into our recording system, we want to keep electrode impedance Ze low, and system input impedance Za' very high.** + +If |Za|’ is not substantially greater than |Ze|, |Vin| will be much lower than |Vec|. To have high |Za|’, we need amplifiers with high input impedance and high shunt impedance. + +Electrode Impedance +*********************************** + +The impedance of an electrode is a measure of its ability to resist the flow of charge across the electrode-solution interface (i.e., across the electronic conductor (metal) and ionic conductor (extracellular fluid)). It is the impedance of the whole electrode equivalent circuit we built yesterday, consisting of the resistance of the electrode metal (|Rm|) and the resistance (|Re|) and capacitance (|Ce|) of the double layer at the electrode-solution interface. + +.. figure:: ../media/circuit_double_layer_interface.* + :align: center + +In polarized electrodes, the large |Re| prevents much current from taking this route. Therefore, in practice, the electrode is primarily the double-layer capacitor |Ce| in series with |Rm| and |Rs| (Robinson, 1968). + +So far, we know that the impedance magnitude of a capacitor decreases with increased capacitance, and that electrode impedance is dominated by double layer capacitor, |Ce|. Therefore, to decrease our electrode impedance, we need to increase the electrode capacitance |Ce|. +How can we increase the value of |Ce|? + +.. math:: + + C = \frac{\epsilon A}{d} + +`The capacitance of a capacitor (C, in Farads), is proportional to the area of the capacitor plates (A) divided by the distance (d) between them. ε is the electrostatic constant.` + +To make C bigger, we can increase the surface area (A) of the electrode, for instance by electroplating a thin layer of gold on to an electrode. We can also coat electrodes with materials complemented with pseudo-capacitance, such as conducting polymers or transition metal oxide films, such as IrOx (Green, Lovell, Wallace, & Poole-Warren, 2008; Musa, 2011). + +Electrode impedance magnitude is usually measured at 1 kHz, before and after electrode coating, allowing us to see an impedance decrease of up to 10-fold (Neto et al., 2018). + +By increasing the capacitance (|Ce|) of our electrode, the electrode impedance (|Ze|) will be smaller, preserving more of our signal amplitude at |Vin|. + +Shunt Impedance +*********************************** + +Shunt impedance is the total impedance of shunt capacitance |Cs| and shunt resistance |Rsh|. These are both routes to ground outside of the intended acquisition system. At the high frequencies (1kHz) we are interested in, the capacitive component will have relatively low impedance. It will therefore have more effect than the resistive component, so |Rsh| is often ignored. + +Remember that any two conducting surfaces, with a non-conducting layer in between, *is* a capacitor. Shunt capacitance arises mainly from the capacitance across the thin insulation layer isolating an electrode and the surrounding electrolyte, as well as the cumulative capacitance along cables and connectors (Robinson, 1968). + +The shunt capacitance for a tungsten wire (~50 to 100 pF) is usually higher than for a silicon probe (5-20 pF/cm). (Why? Think of what makes a capacitor, and the relative shape and conductances of these electrodes). + +.. admonition:: Try it yourself + + Here is a model of the electrode with shunt capacitance, resistance, and amplifier in parallel to ground. You should see that either decreasing electrode impedance or increasing shunt impedance gives you a larger output voltage. + + https://tinyurl.com/yepsdold + +We want a large shunt impedance, to prevent current from flowing down this route. Being capacitive, the impedance decreases with signal frequency (Nelson et al., 2008). Therefore, to create a large shunt impedance, the shunt capacitance should be small: + +.. math:: + Z = \frac{1}{2 \pi fC} + +However, some shunt capacitance is inevitable and often there is not much we can do about it. Because the shunt impedance is in parallel with the impedance of the acquisition system, we can focus on increasing the acquisition system impedance to give us a large |Za|'. + +.. _refamplifierintro: + +Amplifiers +##################################################################### + +Amplifiers in the headstage prevent current being drawn +******************************************************************** + +A perfect 5V voltage source would always provide exactly 5 Volts, no matter what the rest of the circuit looks like. If we put a lot of high impedance components in the rest of the circuit, less current will flow, and if we put low impedance components we will get a high current. + +A real voltage source has a bit of output impedance, which means it acts as a voltage source in series with an impedance. This is modelled here (click to view high-quality version in the simulator): + +.. figure:: ../media/output_impedance.* + :align: center + :target: https://tinyurl.com/yfvzdxbz + :alt: voltage sources passing a resistance to ground. Real and ideal voltage sources are compared, where real voltage sources act as a perfect voltage source in series with a small resistance. + +That invisible, small series resistance creates a voltage divider. Though the actual source voltage is the same 5V, the apparent voltage of the source varies depending on the ratio between the output impedance of the source, and the impedance of the rest of the circuit. The lower the impedance of the components used in the rest of the circuit, the higher the relative influence of the source output impedance, and the lower the apparent source voltage (the voltage droops). + +In our acquisition system, the voltage source is the potential changes in the extracellular fluid (|Vec|). The resistive and capacitive properties of the electrode create an output resistance. The relative impedance of the circuit before and after |Vin| influences the magnitude of the signal at |Vin|. If we allow a lot of current to flow from our electrode to ground, we have a low impedance circuit, which will distort our signal. We therefore need something with a very high impedance to stop current being drawn from our |Vec|. Amplifiers do exactly this: their high input impedance prevents current flow from the electrodes, and amplifiers provide the necessary current for the rest of the circuit from a separate source. + +The operational amplifier +****************************************************************** + +The `operational amplifier` or `op-amp` is a crucial building block of our acquisition system. The amplifier has two inputs (+ and -), one output, and two power rails (e.g. a 3 and -3V power rail). + +.. figure:: ../media/op-amp-basic.* + :align: center + :alt: an amplifier is represented as a triangle pointing towards the right. It has two inputs (+ and -) and one output. + +Amplifiers have high input impedance +****************************************************************** + +The amplifier input impedance, Z\ :sub:`a`\ is very high. The circuit acts as though the current has to cross a very high resistor to actually enter the amplifier. The current flow therefore becomes very low (Ferree et al., 2001), preventing us from drawing much current from the electrode to ground. + +Here is the amplifier added into our circuit diagram: + +.. figure:: ../media/circuit_electrode_shunt_amp.* + :align: center + +Amplifiers have low output impedance +****************************************************************** + +The output impedance of amplifiers is very low, which means that a lot of current can flow *from* the amplifier. This current enables the driving of the signal through all the subsequent circuits (e.g., interconnect lines, multiplexer, and ADC). By placing an amplifier in our circuit, we make sure that the rest of our recording circuit is driven by current provided by the amplifier, not by current provided by the electrode tip. + +Amplifiers output a voltage +***************************************************************** + +The amplifier outputs the voltage difference between the voltages at its two inputs. + +.. figure:: ../media/op-amp-basic.* + :align: center + +How does it do that? + +If the difference between its two inputs is **positive**, the amplifier connects its output to the positive ‘power rail’, giving a positive output voltage. If the positive power rail is 3V, the amplifier will output (pretty much) that. + +If the difference between the two inputs is **negative**, the amplifier will connect its output to the negative rail, outputting -3V. While doing that, the operational amplifier draws basically no current on its inputs. + +In this configuration, the amplifier does not distinguish between small or large differences in voltage across its inputs; it will only every output the most negative or most positive voltage it can. Another way to say that, is that it amplifies the difference between its inputs with a huge factor, also called ‘gain’. This gain is so large that the amplifier always saturates, providing either the maximum or minimum voltage it can. + +Negative feedback prevents saturation +*********************************************************** + +.. figure:: ../media/op_amp_feedback.* + :align: center + :target: https://tinyurl.com/ygby3xqh + :alt: an amplifier with the output and negative terminal connected + +If we connect the output of the operational amplifier to the ``-`` input, then the following happens: + +- Initially, if ``+`` is higher than ``-``, the operational amplifier will output a high voltage. + +- If we connect the output back to ``-``, the amplifier will continue to output a high voltage, but now this voltage starts to increase the value of ``-``, bringing the value of the inputs closer together. This behaviour will keep the voltages at its ``+`` and ``-`` inputs the same. + +- Now, the ``-`` input is always actively driven to follow the voltage on the ``+`` input. This means that whatever voltage we connect to the ``+`` input can be measured just by looking at the ``-`` input (which is connected to / the same as the output). Increasing ``+`` will induce a difference between ``+`` and ``-``, but the corresponding change in the amount of output voltage will bring ``-`` back up. + +We can measure the voltage that at ``+`` by just measuring the output of the operational amplifier, BUT because the ``+`` input draws almost no current at all (in other words, very high input impedance), we can now measure weak signals. The output of the operational amplifier on the other hand side has very low output impedance. In other words, we can draw a lot of current from it and it will keep its voltage. + +You can run this example in the simulator (click the image above), and see if what we said about the operational amplifier makes sense. + +An op-amp as a headstage +********************************************************** + +Our electrodes will be attached to a headstage, which contains an amplifier. This amplification step performs several functions: + +- Prevents us from drawing current and allows to drive current to ADC and computer +- Rejects common mode noise +- Increases the range of the signal to fit the dynamic range of our digitizer + +.. youtube:: NP6nE5P82e8 + :align: center + :width: 100% \ No newline at end of file diff --git a/_sources/courses/open-ephys/theory-day-3/index.rst b/_sources/courses/open-ephys/theory-day-3/index.rst new file mode 100644 index 00000000..9458512c --- /dev/null +++ b/_sources/courses/open-ephys/theory-day-3/index.rst @@ -0,0 +1,238 @@ +.. _theory-day-3: + +.. |Na+| replace:: Na\ :sup:`+`\ +.. |Cl-| replace:: Cl\ :sup:`-`\ +.. |Ca2+| replace:: Ca\ :sup:`2+`\ +.. |K+| replace:: K\ :sup:`+`\ +.. |Rs| replace:: R\ :sub:`s`\ +.. |Rm| replace:: R\ :sub:`m`\ +.. |Re| replace:: R\ :sub:`e`\ +.. |Rsh| replace:: R\ :sub:`sh`\ +.. |Ce| replace:: C\ :sub:`e`\ +.. |Csh| replace:: C\ :sub:`sh`\ +.. |Vin| replace:: V\ :sub:`in`\ +.. |Vec| replace:: V\ :sub:`ec`\ +.. |Vout| replace:: V\ :sub:`out`\ +.. |Ve| replace:: V\ :sub:`e`\ +.. |Za| replace:: Z\ :sub:`a`\ +.. |Ze| replace:: Z\ :sub:`e`\ + + +*********************************** +Theory Day 3 +*********************************** + +.. contents:: Table of Contents + :depth: 2 + :local: + +| + +An acquisition system must: + +* *Detect* changes in electric potential difference +* Faithfully *transfer* this signal to our acquisition system output +* **Distinguish interesting biological signals from other sources of electrical noise** + +Differential amplifiers remove common noise +######################################################### + +Referencing +************************************** + +We live in an (electrically) very noisy world. To get rid of some of this noise from our recording, we can use a reference point. This can be another electrode in the brain or a screw in the animal’s skull. The choice you make here is very important for your recording: the amplifier will output the difference between your recording electrode and your reference point. That means that the amplifier will do its best to get rid of any signal that the two share. If the recording electrode is picking up 50 Hz noise generated by the mains power supply in the walls, you want the amplifier to get rid of it, so it’s best to use a reference point that will also pick up this noise. However, if your reference is picking up signals that you are interested in, the amplifier will get rid of those too. To choose an appropriate reference, you have to decide what qualifies as noise in your experiment. + +Differential Amplifiers +************************************** + +Talk +*********************************** + +.. raw:: html + +
+ +The amplification of the potential difference between the measuring electrode and the reference electrode (in the order of microvolts) is a crucial step. This is accomplished with differential amplifiers that amplify the difference and rejecting the 'common-mode' noise (i.e., noise identical in the recording and reference electrodes typically caused by motion artifacts and capacitive coupling of the body and electrode lead with power line fields (Nunez & Srinivasan, 2009)). + +Instrumentation amplifiers +######################################################### + +Talk +*********************************** + +.. raw:: html + +
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+ +Why do we need instrumentation amps? +************************************* + +Why can't we just use 1 operational amplifier to get a nice signal? + +.. figure:: ../media/op_amp_spikes_ref.* + :align: center + :target: https://tinyurl.com/y4aps4r2 + + +To make this circuit differential, we need voltage dividers. But these are connecting our fragile signal to ground! Plus, any mismatch in the input impedances between ‘+’ and ‘-’ messes up the signal if there is a lot of common mode noise. In practical terms, there is always going to be a mismatch between these resistors, they simply cannot be produced in a way that makes them exactly equal. + +Why? Because this resistor is *also your electrode*. If you work with electrodes, have you measured their impedances? How similar are they? If you made these resistors as different as your electrodes are variable, this circuit will not work to eliminate common mode noise and amplify our spikes. + +The solution is to use *three* op-amps: + +.. figure:: ../media/three_op_amps.* + :align: center + :scale: 80 + +| + +Here it is in the simulator: +| + +.. figure:: ../media/instrumentation_amp_simulator.* + :align: center + :target: https://tinyurl.com/yjxekrv5 + :alt: two operational amplifiers with negative feedback receive the measurement and reference electrode, respectively. Their outputs are fed into a third operation amplifier with negative feedback to form an instrumentation amplifier. + +Gain resistor +----------------------------------- +The voltages on either side of the gain resistor are fixed, because the op-amps are keeping them in place. If we have the same V and lower RGain = more current must travel through the resistor, and therefore more current through the feedback resistors of the two buffer op-amps. Those are fixed resistors: now we have a higher I for same R and therefore a higher voltage drop across these resistors. Both buffer op-amps now have to work harder to overcome this voltage drop and will output more extreme voltages. By decreasing the value of RGain, we are basically making the inputs to the final op-amp more different to each other, and therefore increasing the gain of the instrumentation amp. + + +Common mode rejection ratio (CMRR) +*********************************** +When the input impedances of the differential amplifier weren’t matched, part of the input signal that was common to both inputs, and thus should be cancelled out, actually appeared in the output. A common way to model how well an amplifier subtracts one input to the other is the following: +We define each input (+ and -) to be a sum of an individual voltage (V1 or V2) plus a voltage common to both. In our arms, or the brain of an animal, this common voltage (Vc) could be electrical noise or muscle activity we are not interested in and want to discard. In this case, the inputs would be: + +.. math:: + V+ = V1 + Vc +.. math:: + V- = V2 + Vc + +(In some examples of a differential amplifier, V2 is ground 0V, which is a perfectly valid value). In an **ideal** differential amplifier, the output should be the difference of both amplified by a factor: + +.. math:: + Vout = Ad (V+ - V-) + +.. math:: + = Ad ((V1+Vc)-(V2+Vc)) + +.. math:: + = Ad (V1-V2) + +Where Ad is the differential gain, the factor by which the differential signal is amplified. +Here, the unwanted, common signals cancel out and only the signal we are interested in is amplified. + +A **real** amplifier, however, acts in a different way. As we’ve seen, small imperfections can lead to part of the common voltages being amplified as well. In this case, the output of a real amplifier ends up being: + +.. math:: + + Vout = Ad (V1 - V2 ) + Ac * Vc + +In addition to the differential gain, a new term 'Ac', or common gain, appears. This amplifies the signal common to both inputs. Of course, we want an amplifier to have a differential gain as high as possible and a common gain as low as possible (ideally, Ac would be 0). The relation between these two gains tells us how good an amplifier is at amplifying only the differential signals. This is called the Common Mode Rejection Ratio, or CMRR, simply defined as + +.. math:: + CMRR = \frac{Ad}{Ac} + +or + +.. math:: + CMRR = 20log\frac{Ad}{Ac} + +if measured in decibels. + +The higher the CMRR, the better the amplifier is at cancelling out the signals common to both inputs. +Instrumentation amplifiers are not completely immune to common input noise. They are real circuits and, as such, there are multiple ways for these common signals to bleed out into the output. They have, however, a very high CMRR. Comparing the two devices we’ve been using, the operational amplifier LM358 has a CMRR of 80dB while the instrumentation amplifier has a CMRR of 120dB, 100 times higher! (Sounds underwhelming? Remember decibels are logarithmic; the difference between 80 and 120 dB in terms of sound is the difference between a toilet flushing and a jet engine). + + +.. _refgroundref: + +Why do we need a ground electrode? +################################### + +When we build our EMG circuit, we will use three electrodes: measurement (+), reference (-), and ground. Why do we have a ground electrode (or ground pin or screw) when we already have ‘+’ and ‘-’ inputs? This is a bit tricky, and there's multiple ways to understand it. + +.. raw:: html + +
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+
+
+ +Imagine you just walked across a carpet and you're charged to 10kV. Now you want to do a differential measurement of EMG (or EEG). In theory, as far as we've really talked about until now, this should work via the magic of common-mode rejection. However, remember the circuit that is inside the instrumentation amp: + + +.. figure:: ../media/instrumentation_amp_simulator.* + :align: center + :target: https://tinyurl.com/yjxekrv5 + + +The ‘-’ inputs of the two input op-amps are connected to ground, via a bunch of resistors. If you are charged to 10kV compared to Ground, we’re asking these op-amps to deal with very high differences in voltage, and they will saturate. Even if here we did not include rails in the simulation, remember that each op-amp can only go as high or low as its voltage rails (3V in our case, so with a 100x gain, a 0.03V input saturates the amplifier). + +| + +Remember the common mode rejection ratio. If our amplifier is good at rejecting 99.99% of the common mode, but 0.01% makes it through, in the range of volts, this could still be enough to prevent us from resolving microvolt spikes. + +| + +Attaching a ground electrode to ourselves, and then connecting this to the ground of our acquisition system, brings our body to 0V from the perspective of the acquisition system. The remaining noise fluctuations are still there, but the voltage difference is not as big anymore. We will still have residual 50 or 60Hz noise from the mains supply, plus other muscles, electrostatic charge, bodies moving through the fields in the room and so on, but these can all be handled by the amplifier. + +| + +The last, related, issue is that the output of the whole thing is relative to ground. At some point you want to connect this to a PC, which sits at ground level. + +| + +Practically, all this means that we want to ground our subjects as well as possible. For tetrode recordings in mice, we use a large ‘ground screw’ with low impedance to ground, so that we can effectively discharge the mouse. + +| + +One more detail: Ground is not (always) earth, in many cases it is just a certain circuit we treat as 0 that can provide or sink a lot of current. That circuit can have noise on it, just like any other circuit. If the ground has a lot of 50/60Hz noise, we’ll be charging and discharging the animal (any animal is also a capacitor) constantly through the ground connection. If the ground screw/electrode is low enough impedance and close to our recording site, we’ll manage to keep the animal’s voltage equal to the changing GND level and we won't notice this noise. However, if we put the ground screw/electrode too far away from where we record, e.g. we put the ground connection on the tail (extreme example), then the head of the animal won’t be sufficiently charged/discharged and we’ll encounter what will look like 50/60Hz noise in our tetrode recordings. + +.. _reffilter: + +Low and High pass filtering +################################### + +Filters are used to remove certain frequencies from our data. We can do this in hardware or in software. Usually hardware filtering (implemented in the amplifier circuit) is used to increase (apparent) signal to noise ratio by rejecting unwanted frequencies and to prevent signal aliasing (e.g., bandpass between 0.5 and 2 kHz). +Remember the exercise where we measured the voltage across our fingers with the oscilloscope, and saw very high values. Even with a differential amplifier, we usually have a decent amount of slow (~<10Hz or so) voltages that are simply too big for the amplifier or ADC (analog to digital converter). Any voltages above or below the amplifier rails (or above/below the input range of the digitizer) will be ‘clipped’ and all we’ll see is a constant value. +The solution is to remove the large amplitude slow components, so we can fit the lower amplitude, faster, interesting components into our dynamic range. + +.. figure:: ../media/ADC_saturation.* + :align: center + :alt: The analog to digital converter cannot detect signals that cross over its +3 high rail. If the true signal is more than +3 V, this will still be represented as +3, resulting in a flat line for all values over +3, however high they may truly be. + +Therefore, high-pass filters first remove the large DC offsets present at the electrode-extracellular interface, along with any undesired low-frequency signals (e.g., movement artefacts). Additionally, low-pass filters must be configured to less than half of the ADC frequency sampling rate (Nyquist limit) to prevent aliasing, and may also be used to block undesired high-frequency signals and artefacts. For instance, if our sampling frequency is 30 kHz, the low pass filter should be ~15 kHz. Below is an example of the Intan headstage circuit. + +.. figure:: ../media/inside_intan.* + :align: center + :alt: The intan chip used in many headstages contains high pass analog filters and a differential amplifier for each ephys channel. + +Low-pass filters +*********************************** + +These filters block high frequencies. This is basically another voltage divider, with a frequency-dependent component. You’ve already seen one of these when you charged/discharged a capacitor! The exponential decay of the capacitor gets convolved with our signal. Remember that the impedance of our capacitor decreases as the signal frequency increases. At low frequencies, the high impedance of the capacitor means we get a large voltage drop over the capacitor, and more of our input signal can reach our Vout. + +.. figure:: ../media/low_pass.* + :align: center + :scale: 60 + :target: https://www.falstad.com/circuit/e-filt-lopass.html + :alt: a resistor with capacitor to ground forms a low-pass filter + + +High-pass filters +*********************************** + +This is the same `idea. `_ +With increasing signal frequency, the impedance of the capacitor decreases (day 1), reducing the voltage drop over the capacitor and sending more signal to the output. + +.. figure:: ../media/high_pass.* + :align: center + :scale: 70 + :target: https://www.falstad.com/circuit/e-filt-hipass.html + :alt: a capacitor with resistor to ground forms a low-pass filter + + +These are called `RC filters` because they’re built from a resistor (R) and a capacitor (C). Because there's only one of each, we call them ‘single pole’. In real life, filters are built from more than one pair in order to get specific characteristics. This goes beyond the scope of this course but there are entire classes on this topic. \ No newline at end of file diff --git a/_sources/courses/open-ephys/theory-day-4/index.rst b/_sources/courses/open-ephys/theory-day-4/index.rst new file mode 100644 index 00000000..089b02bd --- /dev/null +++ b/_sources/courses/open-ephys/theory-day-4/index.rst @@ -0,0 +1,64 @@ +.. _theory-day-4: + +*********************************** +Theory Day 4 +*********************************** + +.. |Na+| replace:: Na\ :sup:`+`\ +.. |Cl-| replace:: Cl\ :sup:`-`\ +.. |Ca2+| replace:: Ca\ :sup:`2+`\ +.. |K+| replace:: K\ :sup:`+`\ +.. |Rs| replace:: R\ :sub:`s`\ +.. |Rm| replace:: R\ :sub:`m`\ +.. |Re| replace:: R\ :sub:`e`\ +.. |Rsh| replace:: R\ :sub:`sh`\ +.. |Ce| replace:: C\ :sub:`e`\ +.. |Csh| replace:: C\ :sub:`sh`\ +.. |Vin| replace:: V\ :sub:`in`\ +.. |Vec| replace:: V\ :sub:`ec`\ +.. |Vout| replace:: V\ :sub:`out`\ +.. |Ve| replace:: V\ :sub:`e`\ +.. |Za| replace:: Z\ :sub:`a`\ +.. |Ze| replace:: Z\ :sub:`e`\ + +.. contents:: Table of Contents + :depth: 2 + :local: + +.. _refdigitization: + +Digitization +################################### +The purpose of digitization is to convert amplified signals into digital values. Why do we digitize neural signals? To protect them from noise, and so that we can process and store them. +First, the output of the amplifier (Vout) should match the digitizer dynamic range. Your analog signal should ‘occupy’ as much as possible, i.e. all discrete values in the digitization range. In other words, digitization range should match maximum analog signal. If the dynamic range is too small the signal will saturate, and if it is too large it will decrease effective signal resolution. + +.. figure:: ../media/3bitADC.* + :align: center + +If you have a voltage divider and an open-loop op-amp (comparator) you can already build a circuit that checks if your analog signal is above or below a certain value. Now instead of one voltage divider, you could have a whole ‘ladder’, creating intermediate values, and compare to these. This is an incredibly inefficient way to make an ADC. + +Here’s what this may look like: + +.. figure:: ../media/comparator_ladder.* + :align: center + :target: https://tinyurl.com/yadu834g + +In practice, many ADCs still use the same basic idea of using op-amps as comparators, but instead of comparing millions of values to obtain a precise measurement, they generate a reference voltage from an internal DAC and adjust that until it matches the input voltage, or use some other clever tricks. + +.. figure:: ../media/2vs3bitresolution.* + :align: center + +Typically AD converters have 12 to 16 bit resolution (4096 to 65536 discrete values) for neural signals, which is usually enough because of the size of the signals we want (spikes etc), and because the thermal noise floor of typical electrodes is similar to the achievable resolution anyway: better digitizers would just measure more of that noise. If you want to read more about that, have a look `here. `_ + +Talk: Acquisition and Synchronization +######################################## +One of the most common pitfalls in Neuroscience is correctly synchronizing multiple datastreams. How do you know whether your imaging and electrophysiology are aligned in time? How many different clocks do you have on your set up, and which of those can you trust? + +.. raw:: html + +
+
+
+ + +The code for the exercises Filipe shows is available `on google drive `_ if you want to try it out yourself. \ No newline at end of file diff --git a/_sources/guides/usage-guides/skin-preparation/index.rst b/_sources/guides/usage-guides/skin-preparation/index.rst index 5e3b91fb..c56152ef 100644 --- a/_sources/guides/usage-guides/skin-preparation/index.rst +++ b/_sources/guides/usage-guides/skin-preparation/index.rst @@ -8,12 +8,12 @@ Why skin preparation is important? Proper skin preparation is crucial before recording any biopotential signal be it Electrocardiography (ECG), Electromyography (EMG), Electroencephalography (EEG), or Electrooculography (EOG). -- ``Clean skin surface`` Removes dead skin cells, oils, & other substances that increases skin impedance. -- ``Improve impedance`` Improves the conduction of electrical signals from the body to the recording equipment and minimizes impedance. -- ``Electrode-skin contact`` Ensures optimal contact between the electrodes and the skin surface. -- ``Signal quality`` Enhances the overall quality of recorded signals, providing clear & reliable data for analysis & improves the ability to capture subtle variations in biopotential signals. -- ``Consistency in recordings`` Reduces variability in signal quality, making it easier to make any Human-Computer Interface (HCI), Brain-Computer Interface (BCI) project or a real-world application. -- ``Long term adhesion`` Facilitates long-term adhesion & stable placement of electrodes to the skin during extended signal monitoring. +- ``Clean skin surface:`` Removes dead skin cells, oils, & other substances that increases skin impedance. +- ``Improve impedance:`` Improves the conduction of electrical signals from the body to the recording equipment and minimizes impedance. +- ``Electrode-skin contact:`` Ensures optimal contact between the electrodes and the skin surface. +- ``Signal quality:`` Enhances the overall quality of recorded signals, providing clear & reliable data for analysis & improves the ability to capture subtle variations in biopotential signals. +- ``Consistency in recordings:`` Reduces variability in signal quality, making it easier to make any Human-Computer Interface (HCI), Brain-Computer Interface (BCI) project or a real-world application. +- ``Long term adhesion:`` Facilitates long-term adhesion & stable placement of electrodes to the skin during extended signal monitoring. Kit Contents ************** @@ -96,7 +96,9 @@ Wipe away excess gel with alcohol swabs or wet wipes. Wipe away access gel -.. warning:: Close your eyes while using the alcohol swabs for EOG recording else it may cause eye redness & irritation. +.. warning:: - Using alcohol swabs can dry out the skin, so don't use them if your skin is already dry. + + - Close your eyes while using the alcohol swabs for EOG recording else it may cause eye redness & irritation. Step 5: Measuring the signals ================================= diff --git a/_sources/guides/usage-guides/using-bioamp-bands/index.rst b/_sources/guides/usage-guides/using-bioamp-bands/index.rst index b41dd115..d52e3996 100644 --- a/_sources/guides/usage-guides/using-bioamp-bands/index.rst +++ b/_sources/guides/usage-guides/using-bioamp-bands/index.rst @@ -13,15 +13,15 @@ Why use BioAmp Bands? Usually, people use gel electrodes to record biopotential signals from the skin surface. But, it has its own disadvantages. So we came up with these BioAmp Bands using which users can enjoy a more comfortable, cost-effective, and hassle-free experience while recording biopotential signals. -- :bdg-primary:`Comfort` BioAmp Bands are generally more comfortable to wear than gel electrodes, especially for long-term recordings. They conform to the body's shape and avoid the sticky, sometimes irritating sensation of gel electrodes. +- :bdg-primary:`Comfort:` BioAmp Bands are generally more comfortable to wear than gel electrodes, especially for long-term recordings. They conform to the body's shape and avoid the sticky, sometimes irritating sensation of gel electrodes. -- :bdg-secondary:`Reusability` Unlike gel electrodes, which are often single-use and need to be replaced frequently, BioAmp Bands can be reused multiple times. This makes them more cost-effective and environmentally friendly. +- :bdg-secondary:`Reusability:` Unlike gel electrodes, which are often single-use and need to be replaced frequently, BioAmp Bands can be reused multiple times. This makes them more cost-effective and environmentally friendly. -- :bdg-success:`Ease of Use` These bands are easy to wear and adjust, reducing the hassle of setup and ensuring consistent placement. +- :bdg-success:`Ease of Use:` These bands are easy to wear and adjust, reducing the hassle of setup and ensuring consistent placement. -- :bdg-info:`Hygiene` They can be easily cleaned and sanitized between uses, reducing the risk of skin irritation and infections. Gel electrodes, on the other hand, can leave residue on the skin surface. +- :bdg-info:`Hygiene:` They can be easily cleaned and sanitized between uses, reducing the risk of skin irritation and infections. Gel electrodes, on the other hand, can leave residue on the skin surface. -- :bdg-danger:`Performance` The bands can provide stable and reliable signal recordings depending on your environment conditions. For hot/humid conditions, the bands usually perform better while recording the signals. But if the weather is cold causing dry skin, then it is recommended to prepare the skin properly and apply electrode gel between the metallic part of cable and skin surface. If you feel that the skin impedence is increasing, then reapply electrode gel frequently. The other option is to use gel electrodes after preparing the skin properly. +- :bdg-danger:`Performance:` The bands can provide stable and reliable signal recordings depending on your environment conditions. For hot/humid conditions, the bands usually perform better while recording the signals. But if the weather is cold causing dry skin, then it is recommended to prepare the skin properly and apply electrode gel between the metallic part of cable and skin surface. If you feel that the skin impedence is increasing, then reapply electrode gel frequently. The other option is to use gel electrodes after preparing the skin properly. Types of BioAmp Bands @@ -29,7 +29,7 @@ Types of BioAmp Bands There are 3 types of BioAmp Bands and all these bands offer targeted and efficient solutions for recording biopotential signals from the muscles, heart, and brain, making them versatile tools for a wide range of HCI/BCI applications. -1) Muscle BioAmp Band +1. Muscle BioAmp Band ========================== Muscle BioAmp Band (EMG Band) is a stretchable band that can be connected to any of our Muscle BioAmp Hardware or any EXG sensor using a BioAmp Cable. It allows you to record your muscle signals hassle-free. @@ -55,7 +55,7 @@ Muscle BioAmp Band (EMG Band) is a stretchable band that can be connected to any | Wearable | Yes | +---------------------+--------------------------------------------+ -2) Heart BioAmp Band +2. Heart BioAmp Band ========================== Heart BioAmp Band (ECG Band) is a stretchable band that can be connected to any of our Heart BioAmp Hardware or any EXG sensor using BioAmp Cable. It allows you to record your ECG signals hassle-free. @@ -81,7 +81,7 @@ Heart BioAmp Band (ECG Band) is a stretchable band that can be connected to any | Wearable | Yes | +---------------------+--------------------------------------------+ -3) Brain BioAmp Band +3. Brain BioAmp Band ========================== Brain BioAmp Band (EEG Band) is a stretchable band that can be connected to any of our Brain BioAmp Hardware or any EXG sensor using BioAmp Cable to record signals from the brain hassle-free. @@ -130,45 +130,90 @@ Assembly 1. Take your Muscle BioAmp Band, hold the side of the band that has buckle on it and align the top part of the buckle with the flat surface of the snap. -.. figure:: media/muscle-bioamp-band/emg-band-assembly-1.gif - :align: center +.. only:: html -2. Take the other end of the band and insert it in the buckle. + .. figure:: media/muscle-bioamp-band/emg-band-assembly-1.* + :align: center -.. figure:: media/muscle-bioamp-band/emg-band-assembly-2.gif - :align: center +.. only:: latex + + .. figure:: media/muscle-bioamp-band/images/emg-band-assembly-1.* + :align: center + +1. Take the other end of the band and insert it in the buckle. + +.. only:: html + + .. figure:: media/muscle-bioamp-band/emg-band-assembly-2.* + :align: center + +.. only:: latex + + .. figure:: media/muscle-bioamp-band/images/emg-band-assembly-2.* + :align: center + + .. figure:: media/muscle-bioamp-band/images/emg-band-assembly-3.* + :align: center 3. Your band is now ready to use. You can also adjust the size of the band according to your targeted muscle. -.. figure:: media/muscle-bioamp-band/adjust-band-size.gif - :align: center +.. only:: html + + .. figure:: media/muscle-bioamp-band/adjust-band-size.* + :align: center + +.. only:: latex + + .. figure:: media/muscle-bioamp-band/images/adjust-band-size.* + :align: center Skin Preparation =================== Apply Nuprep Skin Preparation Gel on the skin surface where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe. -For more information, please check out detailed step by step `skin preparation guide `_. +For more information, please check out detailed step by step :ref:`skin-preparation`. Measure EMG ============= 1. Flip the band and snap the dry electrodes of the BioAmp Cable on it as shown below. -.. figure:: media/muscle-bioamp-band/connecting-cable.gif - :align: center +.. only:: html -2. Flip the band again and wear it on your arm in such a way that IN+ and IN- are placed on the arm near the ulnar nerve and REF (reference) on the far side of the band. + .. figure:: media/muscle-bioamp-band/connecting-cable.* + :align: center -.. figure:: media/muscle-bioamp-band/wearing-band.gif - :align: center +.. only:: latex + + .. figure:: media/muscle-bioamp-band/images/connecting-cable.* + :align: center + +1. Flip the band again and wear it on your arm in such a way that IN+ and IN- are placed on the arm near the ulnar nerve and REF (reference) on the far side of the band. + +.. only:: html + + .. figure:: media/muscle-bioamp-band/wearing-band.* + :align: center + +.. only:: latex + + .. figure:: media/muscle-bioamp-band/images/wearing-band.* + :align: center .. note:: Make sure the dry electrodes (shiny parts of the BioAmp Cable) are in direct contact with the skin. 3. Now put a small amount of electrode gel or Ten20 paste between the skin and dry electrodes to get the best signal acquisition. + +.. only:: html -.. figure:: media/muscle-bioamp-band/applying-gel.gif - :align: center + .. figure:: media/muscle-bioamp-band/applying-gel.* + :align: center + +.. only:: latex + + .. figure:: media/muscle-bioamp-band/images/applying-gel.* + :align: center .. note:: - After using the band, don't leave the gel residue on the dry electrodes longer than an hour as it may corrode them over a period of time. - Wash the band with liquid soap and rinse it properly after every use. Use it again only when it is completely dry. @@ -181,20 +226,37 @@ Skin Preparation Apply Nuprep Skin Preparation Gel on your chest where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe. -For more information, please check out detailed step by step `skin preparation guide `_. +For more information, please check out detailed step by step :ref:`skin-preparation`. Assembly ============ 1. Take your Heart BioAmp Band and wrap the band around your chest in such a way that the pointy part of the snap touches your chest and the flat part is on the outer side. -.. figure:: media/heart-bioamp-band/wearing-band.gif - :align: center +.. only:: html + + .. figure:: media/heart-bioamp-band/wearing-band.* + :align: center + +.. only:: latex + + .. figure:: media/heart-bioamp-band/images/wearing-band.* + :align: center 2. Now insert the loose end of the band into the buckle and tighten it by pulling the strap. -.. figure:: media/heart-bioamp-band/band-assembly.gif - :align: center +.. only:: html + + .. figure:: media/heart-bioamp-band/band-assembly.* + :align: center + +.. only:: latex + + .. figure:: media/heart-bioamp-band/images/band-assembly.* + :align: center + + .. figure:: media/heart-bioamp-band/images/band-assembly-2.* + :align: center 3. Your band is now ready to use. You can also adjust the size of the band according to your chest size. @@ -203,15 +265,29 @@ Measure ECG 1. Snap the IN- cable on the left most side of the band, IN+ cable in the middle, and REF cable on the right side as shown below. -.. figure:: media/heart-bioamp-band/connecting-cable.gif - :align: center +.. only:: html + + .. figure:: media/heart-bioamp-band/connecting-cable.* + :align: center + +.. only:: latex + + .. figure:: media/heart-bioamp-band/images/connecting-cable.* + :align: center .. note:: Make sure the dry electrodes (shiny parts of the BioAmp Cable) are in direct contact with the skin. 2. Now put a small amount of electrode gel or Ten20 paste between the skin and dry electrodes to get the best signal acquisition. -.. figure:: media/heart-bioamp-band/electrode-gel.gif - :align: center +.. only:: html + + .. figure:: media/heart-bioamp-band/electrode-gel.* + :align: center + +.. only:: latex + + .. figure:: media/heart-bioamp-band/images/electrode-gel.* + :align: center .. note:: - After using the band, don't leave the gel residue on the dry electrodes longer than an hour as it may corrode them over a period of time. - Wash the band with liquid soap and rinse it properly after every use. Use it again only when it is completely dry. @@ -223,38 +299,38 @@ Assembly =========== You get the band in two parts - the longer part consists of buckles at both ends and the shorter one has loose ends on both sides. -1) Hold one end of the longer band and align the top part of the buckle with the flat surface of the snap. +1. Hold one end of the longer band and align the top part of the buckle with the flat surface of the snap. -2) Now take the shorter band and insert it into the buckle of longer band. +2. Now take the shorter band and insert it into the buckle of longer band. -3) Repeat step 1 and 2 for the other buckle on the longer band. +3. Repeat step 1 and 2 for the other buckle on the longer band. -4) Your band is now ready to use. You can also adjust the size of the band according to your head size. +4. Your band is now ready to use. You can also adjust the size of the band according to your head size. Skin Preparation =================== Apply Nuprep Skin Preparation Gel on your targeted area (visual cortex or prefrontal cortex) where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe. -For more information, please check out detailed step by step `skin preparation guide `_. +For more information, please check out detailed step by step :ref:`skin-preparation`. Measure 1-channel EEG ======================== -1) Flip the band, take your BioAmp Cable, and snap the REF cable on a gel electrode. Now snap the IN- and IN+ cable on: +1. Flip the band, take your BioAmp Cable, and snap the REF cable on a gel electrode. Now snap the IN- and IN+ cable on: - Fp1 and Fp2 positions for recording EEG from prefrontal cortex - O1 and O2 positions for recording EEG from visual cortex .. note:: The electrode positions mentioned above are according to `International 10-20 sytem for recording EEG `_. -2) Flip the band again and wear it in a way so that the dry electrodes (shiny parts of the cable) are in contact with: +2. Flip the band again and wear it in a way so that the dry electrodes (shiny parts of the cable) are in contact with: - skin surface on the forehead (if recording from prefrontal cortex) - scalp surface on the back side of your head (if recording from visual cortex) -3) Peel of the plastic backing of the gel electrode and place it on the bony part behind your earlobe. +3. Peel of the plastic backing of the gel electrode and place it on the bony part behind your earlobe. .. note:: While placing the gel electrodes on the skin, make sure to place the non-sticky tab of the electrode in the direction opposite to your hair growth. This allows you to remove the electrodes easily without pulling off much body hair. -4) Now put a small amount of electrode gel or Ten20 paste between the skin/scalp and dry electrodes to get the best signal acquisition. \ No newline at end of file +4. Now put a small amount of electrode gel or Ten20 paste between the skin/scalp and dry electrodes to get the best signal acquisition. \ No newline at end of file diff --git a/_sources/guides/usage-guides/using-gel-electrodes/index.rst b/_sources/guides/usage-guides/using-gel-electrodes/index.rst index cebee068..6a434f25 100644 --- a/_sources/guides/usage-guides/using-gel-electrodes/index.rst +++ b/_sources/guides/usage-guides/using-gel-electrodes/index.rst @@ -79,14 +79,14 @@ Using the electrodes Determine the target area from where you want to record the biopotential signals. -.. warning:: For people having sensitive skin, it is recommended to use either gel electrodes with hydrogel/standard adhesive or use `BioAmp Bands `_. +.. warning:: For people having sensitive skin, it is recommended to use either gel electrodes with hydrogel/standard adhesive or :ref:`use BioAmp Bands `. 1. Skin Preparation ====================== Remove any excessive hair on the targeted area. Apply Nuprep skin preparation gel on the skin surface where electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe. -For more information, please check out detailed step by step `skin preparation guide `_. +For more information, please check out detailed step by step :ref:`skin-preparation`. .. note:: Always ensure that the prepared skin area is dry prior to applying the gel electrodes. diff --git a/_sources/hardware/bioamp/bioamp-exg-pill/index.rst b/_sources/hardware/bioamp/bioamp-exg-pill/index.rst index 38e20754..45e967cd 100644 --- a/_sources/hardware/bioamp/bioamp-exg-pill/index.rst +++ b/_sources/hardware/bioamp/bioamp-exg-pill/index.rst @@ -15,7 +15,7 @@ just a few. It also works with any dedicated ADC, like the Texas Instruments ADS .. note:: It is recommended to use Arduino UNO R4 while recording biopotential signals since it has 14-bit ADC and can record the signals much accurately. -.. image:: ../../../media/bioamp-exg-pill.* +.. figure:: ../../../media/bioamp-exg-pill.* :align: center What makes it different? @@ -75,11 +75,11 @@ Software requirements - Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches in your development board and visualise the data on your laptop. -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* - Download Backyard Brains' `Spike Recorder `_ according to the operating system you are using (Windows, OSX, Linux). -.. image:: ../../../kits/diy-neuroscience/basic/media/byb.* +.. figure:: ../../../kits/diy-neuroscience/basic/media/byb.* Using the Hardware ********************* @@ -94,9 +94,13 @@ Insert the provided BioAmp cable's JST PH connector and header pins from top as .. figure:: media/assembly-step1.* :align: center + `Soldering the connector & header pins on BioAmp EXG Pill` + .. figure:: media/bioamp-exg-pill-soldered.* :align: center + `After soldering, BioAmp EXG Pill should look like this` + Step 2 (optional): Configure for ECG/EMG ========================================== @@ -129,6 +133,8 @@ For all the examples provided, we are using the A0 pin of Arduino UNO R3. Connec .. figure:: media/connections-with-arduino.* :align: center + `Connections with Arduino UNO R3` + .. warning:: Take precautions while connecting to power, if power pins are to be swapped, your BioAmp EXG Pill will be fried and it’ll become unusable (DIE). Step 4: Connecting electrode cable @@ -136,7 +142,10 @@ Step 4: Connecting electrode cable Connect the BioAmp cable to BioAmp EXG Pill by inserting the cable end in the JST PH connector as shown in the graphic below. -.. image:: media/connection-with-cable.* +.. figure:: media/connection-with-cable.* + :align: center + + `Connections with BioAmp Cable v3` Step 5: Skin Preparation =========================== @@ -171,18 +180,21 @@ We have 2 options to measure the EMG signals, either using the gel electrodes or 2. Peel the plastic backing from electrodes 3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram. -.. image:: media/emg.* +.. figure:: media/emg.* - **Using Muscle BioAmp Band:** 1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band. + 2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. + **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -191,11 +203,11 @@ Uploading the code Connect the Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste any one of the Arduino Sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: -EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ -EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ -Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu, +Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize @@ -203,14 +215,15 @@ the EMG signals. After opening the serial plotter make sure to select the baud rate to 115200. -.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. +.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. Visualizing the EMG signals ---------------------------- Now flex your arm to visualize the muscle signals in real time on your laptop. -.. image:: media/EMGEnvelop.* +.. figure:: media/EMGEnvelop.* + :align: center Step 6: Measuring ElectroCardioGraphy (ECG) ============================================= @@ -232,7 +245,8 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or 2. Peel the plastic backing from electrodes 3. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side as shown in the diagram. -.. image:: media/ecg.* +.. figure:: media/ecg.* + :align: center - **Using Heart BioAmp Band:** @@ -240,20 +254,22 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or 2. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side. 3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. -**Tutorial on how to use the band:** +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. -.. youtube:: fr5iORsVyUM - :align: center - :width: 100% + **Tutorial on how to use the band:** + + .. youtube:: fr5iORsVyUM + :align: center + :width: 100% Uploading the code --------------------- Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier: -ECG Filter: https://github.com/upsidedownlabs/Heart-BioAmp-Arduino-Firmware/blob/main/2_ECGFilter/2_ECGFilter.ino +:fab:`github;pst-color-primary` `ECG Filter `_ -Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu, +Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize @@ -261,12 +277,15 @@ the signals. After opening the serial plotter make sure to select the baud rate to 115200. -.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. +.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. Visualizing the ECG signals ----------------------------- -.. image:: media/bioamp-Exg-Pill-ECG.* +Sit back, relax and see your ECG signals in real time on your laptop. + +.. figure:: media/bioamp-Exg-Pill-ECG.* + :align: center Step 7: Measuring Electrooculography (EOG) ================================================ @@ -287,7 +306,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move - **Horizontal EOG recording:** -.. image:: media/eog-horizontal.* +.. figure:: media/eog-horizontal.* + :align: center 1. Connect the BioAmp cable to gel electrodes. 2. Peel the plastic backing from electrodes. @@ -295,7 +315,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move - **Vertical EOG recording:** -.. image:: media/eog-vertical.* +.. figure:: media/eog-vertical.* + :align: center 1. Connect the BioAmp cable to gel electrodes. 2. Peel the plastic backing from electrodes. @@ -306,9 +327,9 @@ Uploading the code Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier: -EOG Filter: https://github.com/upsidedownlabs/Eye-BioAmp-Arduino-Firmware/blob/main/2_EOGFilter/2_EOGFilter.ino +:fab:`github;pst-color-primary` `EOG Filter `_ -Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu, +Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize @@ -316,12 +337,15 @@ the signals. After opening the serial plotter make sure to select the baud rate to 115200. -.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. +.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. Visualizing the EOG signals ------------------------------ -.. image:: media/bioamp-exg-pill-eog.* +Move your eyes up-down or left-right to see your EOG signals in real time on your laptop. + +.. figure:: media/bioamp-exg-pill-eog.* + :align: center Step 8: Measuring Electroencephalography (EEG) =================================================== @@ -335,7 +359,7 @@ Step 8: Measuring Electroencephalography (EEG) For recording EEG from different parts of the brain, you have to place the electrodes according to the `International 10-20 system for recording EEG `_. -.. image:: ../../../kits/diy-neuroscience/basic/media/10-20-system.* +.. figure:: ../../../kits/diy-neuroscience/basic/media/10-20-system.* :align: center Electrodes placement @@ -345,7 +369,8 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or - **Using gel electrodes to record from prefrontal cortex part of brain:** -.. image:: media/eeg.* +.. figure:: media/eeg.* + :align: center 1. Connect the BioAmp cable to gel electrodes. 2. Peel the plastic backing from electrodes. @@ -357,27 +382,29 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or 2. In this case, the REF (reference) should be connected using gel electrode. So connect the reference of BioAmp cable to the gel electrode, peel the plastic backing and place it at the bony part, on the back side of your earlobe. 3. Now put a small drop of electrode gel on the dry electrodes (IN+ and IN-) between the skin and metallic part of BioAmp cable to get the best results. -.. note:: Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. + + **Tutorial on how to use the band:** -**Tutorial on how to use the band:** + .. youtube:: O6qp7teT-sM + :align: center + :width: 100% -.. youtube:: O6qp7teT-sM - :align: center - :width: 100% +.. note:: Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same. Uploading the code ----------------------- Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier: -`Spike recorder arduino code `_ +:fab:`github;pst-color-primary` `Spike recorder arduino code `_ -Go to tools from the menu bar, select "board" option then select Arduino UNO. In the same menu, +Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your development board is connected. To find out the right COM port, screen disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code. -.. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. +.. important:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. Visualizing the EEG signals ------------------------------- @@ -386,6 +413,9 @@ Open the Spike Recorder software. When the Spike Recorder starts, it will start the first icon on the top left corner of the screen, select the COM port on which your Arduino UNO is connected and click on connect. .. figure:: ../../../kits/diy-neuroscience/basic/media/spike-recorder-configurations.* + :align: center + + `Spike Recorder settings` Mute the speakers and apply the 50Hz notch filter by clicking on the checkbox as shown in the screenshot above. You should set the low band pass filter to 1Hz and high bandpass filter to 40Hz as we are only recording the EEG signals which range between @@ -393,7 +423,10 @@ these frequencies. Now everything is configured and connected. So close the settings window and start recording EEG signals. -.. image:: ../../../kits/diy-neuroscience/basic/media/bioamp-exg-pill-eeg.* +.. figure:: ../../../kits/diy-neuroscience/basic/media/bioamp-exg-pill-eeg.* + :align: center + + `EEG signals being visualised in Spike Recorder` The signals that you can see on the screen right now are originating from prefrontal cortex part of your brain and propagating through all the layers to the surface of your skin. @@ -458,25 +491,49 @@ Project ideas & tutorials :margin: 4 4 0 0 :gutter: 2 - .. grid-item-card:: Detecting heart beats + .. grid-item-card:: Controlling video game using brainwaves (EEG) :text-align: center - :link: https://youtu.be/uB5R-vGJjJo + :link: https://www.instructables.com/Controlling-Video-Game-Using-Brainwaves-EEG/ - .. grid-item-card:: Measuring heart rate + .. grid-item-card:: Visualising electrical impulses from eyes (EOG) + :text-align: center + :link: https://www.instructables.com/Visualizing-Electrical-Impulses-of-Eyes-EOG-Using-/ + + .. grid-item-card:: Recording EEG from visual cortex :text-align: center - :link: https://youtu.be/PvWtCFNK3_s + :link: https://www.instructables.com/Recording-EEG-From-Visual-Cortex-of-Brain-Using-Bi/ + + .. grid-item-card:: Recording EEG from prefrontal cortex + :text-align: center + :link: https://www.instructables.com/Recording-EEG-From-Pre-Frontal-Cortex-of-Brain-Usi/ + + .. grid-item-card:: Eye blink detection + :text-align: center + :link: https://www.instructables.com/Eye-Blink-Detection-by-Recording-EOG-Using-BioAmp-/ .. grid-item-card:: Creating a drowsiness detector :text-align: center - :link: https://youtu.be/h4F41mp4mWk + :link: https://www.instructables.com/Drowsiness-Detector-by-Detecting-EOG-Signals-Using/ + + .. grid-item-card:: Record publication-grade ECG + :text-align: center + :link: https://www.instructables.com/Record-Publication-Grade-ECG-at-Your-Home-Using-Bi/ + + .. grid-item-card:: Measuring heart rate + :text-align: center + :link: https://www.instructables.com/Measuring-Heart-Rate-Using-BioAmp-EXG-Pill/ + + .. grid-item-card:: Detecting heart beats + :text-align: center + :link: https://www.instructables.com/Detecting-Heart-Beats-Using-BioAmp-EXG-Pill/ - .. grid-item-card:: Detecting eye blinks + .. grid-item-card:: Record publication-grade EMG :text-align: center - :link: https://youtu.be/PfEJVa3gv6E + :link: https://www.instructables.com/Recording-Publication-Grade-Muscle-Signals-Using-B/ - .. grid-item-card:: Record EEG from visual cortex part of brain + .. grid-item-card:: Detecting up and down movement of eyes :text-align: center - :link: https://youtu.be/XENPUkfxLec + :link: https://www.instructables.com/Tracking-UP-and-DOWN-Movements-of-Eyes-Using-EOG/ These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech. @@ -487,11 +544,17 @@ Project ideas & tutorials Below are some project ideas that you can try making at your home. - 1. `Recording EEG from visual cortex `_ - 2. `Measuring heart rate `_ - 3. `Detecting heart beats `_ - 4. `Creating a drowsiness detector `_ - 5. `Detecting eye blinks `_ + 1. `Controlling video game using brainwaves (EEG) `_ + 2. `Visualising electrical impulses from eyes (EOG) `_ + 3. `Recording EEG from visual cortex part of brain `_ + 4. `Recording EEG from prefrontal cortex part of brain `_ + 5. `Eye blink detection `_ + 6. `Creating a drowsiness detector `_ + 7. `Record publication-grade ECG `_ + 8. `Measuring heart rate `_ + 9. `Detecting heart beats `_ + 10. `Record publication-grade EMG `_ + 11. `Detecting up and down movement of eyes `_ These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech diff --git a/_sources/hardware/bioamp/bioamp-v1.5/index.rst b/_sources/hardware/bioamp/bioamp-v1.5/index.rst index 9eebafec..926e1f52 100644 --- a/_sources/hardware/bioamp/bioamp-v1.5/index.rst +++ b/_sources/hardware/bioamp/bioamp-v1.5/index.rst @@ -73,20 +73,20 @@ Images below shows a quick overview of the hardware design. Contents of the kit ******************** -.. image:: media/kit-contents.* +.. figure:: media/kit-contents.* Software requirements ********************** Before you start using the kit, download Backyard Brains' `Spike Recorder `_ or `Audacity `_ according to the operating system you are using (Windows, OSX, Linux). -.. figure:: ../../../kits/diy-neuroscience/basic/media/byb.* +.. .. figure:: ../../../kits/diy-neuroscience/basic/media/byb.* - **Backyard Brains Spike Recorder** +.. **Backyard Brains Spike Recorder** -.. figure:: media/audacity.* +.. .. figure:: media/audacity.* - **Audacity (An easy-to-use, multi-track audio editor and recorder)** +.. **Audacity (An easy-to-use, multi-track audio editor and recorder)** Assembling the kit ******************** @@ -103,91 +103,91 @@ You can get your own BioAmp v1.5 bag of parts from our `online stores `. Step 4: Connecting 9V battery =============================== Connect any 9V battery to BioAmp v1.5 using the 9V snap cable. Now activate the board by flipping ON the power switch, and you'll notice an LED light up, showing that the board is ready to use. -.. image:: media/9v-battery.* +.. figure:: media/9v-battery.* + :align: center Step 5: Listen to your muscle signals ====================================== @@ -254,7 +269,8 @@ Using speakers 2. Switch on the speaker and turn the volume to maximum. 3. Flex and listen to your muscles. -.. image:: media/listening-emg-2.* +.. figure:: media/listening-emg-2.* + :align: center Using wired earphones/headphones ---------------------------------------------- @@ -263,7 +279,9 @@ Using wired earphones/headphones 2. Plug it in your ears. 3. Flex and listen to your muscles. -.. image:: media/listening-emg-3.* +.. figure:: media/listening-emg-3.* + :align: center + :width: 80% Step 6: Visualize EMG signals on mobile phone =================================================== @@ -277,7 +295,9 @@ Using Phone Recorder app 2. Flex your muscle to be able to record the muscle signals. 3. If you want to extract that data then it will be saved by default as a .wav file but you can convert it in any other format according to your project requirements. -.. image:: media/emg-in-mobile-2.* +.. figure:: media/emg-in-mobile-2.* + :align: center + :width: 80% Using Backyard Brains' Spike Recorder mobile app ------------------------------------------------ @@ -286,15 +306,17 @@ Using Backyard Brains' Spike Recorder mobile app 2. Open the app, click the setting icon on the top right corner and set the recording type to EMG. 3. Apply the 50Hz or 60Hz notch filter depending on the country you are living in. For example if you are in India then the AC current oscillates at a frequency of 50Hz but it oscillates at 60Hz frequency in USA. This AC current acts as a noise in the signals so we have to remove it by applying this notch filter. -.. image:: media/spike-recorder-mobile.* - :width: 80% +.. figure:: media/spike-recorder-mobile.* + :width: 60% :align: center 4. Again click on the setting icon to close it and you are ready. 5. Flex your muscles to be able to visualize the muscle signals (EMG). 6. You can record the EMG data as a .wav file by pressing the record button on the top right corner of the app and then convert it in any other format as per your project requirements. -.. image:: media/emg-in-mobile.* +.. figure:: media/emg-in-mobile.* + :width: 80% + :align: center Step 7: Visualize the EMG signals on laptop ============================================ @@ -308,13 +330,15 @@ Using Backyard Brains' Spike Recorder 2. Open the software, click the setting icon on the top right corner and set the low band pass filter to 72Hz and high band pass filter to 720Hz. 3. Apply the 50Hz or 60Hz notch filter depending on the country you are living in. For example if you are in India then the AC current oscillates at a frequency of 50Hz but it oscillates at 60Hz frequency in USA. This AC current acts as a noise in the signals so we have to remove it by applying this notch filter. -.. image:: media/spike-recorder-laptop.* +.. figure:: media/spike-recorder-laptop.* + :align: center 4. Again click on the setting icon to close it and you are ready. 5. Flex your muscles to be able to visualize the muscle signals (EMG) 6. You can record the EMG data as a .wav file by pressing the record button on the top right corner of the app and then convert it in any other format as per your project requirements. -.. image:: media/emg-in-laptop.* +.. figure:: media/emg-in-laptop.* + :align: center Using Audacity ---------------- @@ -324,6 +348,7 @@ Using Audacity 3. Flex your muscles to be able to visualize the muscle signals (EMG) 4. By default the EMG data would be recorded as a .wav file but you can convert it in any other format as per your project requirements. -.. image:: media/emg-in-audacity.* +.. figure:: media/emg-in-audacity.* + :align: center diff --git a/_sources/hardware/bioamp/muscle-bioamp-biscute/index.rst b/_sources/hardware/bioamp/muscle-bioamp-biscute/index.rst index ec737db2..f12c7e79 100644 --- a/_sources/hardware/bioamp/muscle-bioamp-biscute/index.rst +++ b/_sources/hardware/bioamp/muscle-bioamp-biscute/index.rst @@ -1,4 +1,4 @@ -.. _muscle_bioamp-biscute: +.. _muscle-bioamp-biscute: Muscle BioAmp Biscute ###################### @@ -44,52 +44,67 @@ Hardware ********** Images below shows a quick overview of the hardware design. -.. grid:: 1 1 2 2 - :margin: 4 4 0 0 - :gutter: 2 +.. only:: html - .. grid-item:: - - .. card:: + .. grid:: 1 1 2 2 + :margin: 4 4 0 0 + :gutter: 2 - **PCB Front** - ^^^^^ - .. figure:: media/front.* + .. grid-item:: + + .. card:: + + PCB Front + ^^^^^ + .. figure:: media/front.* + + .. grid-item:: + + .. card:: - .. grid-item:: - - .. card:: + PCB Back + ^^^^^ + .. figure:: media/back.* - **PCB Back** - ^^^^^ - .. figure:: media/back.* +.. only:: latex + + .. figure:: media/front.* + :width: 50% + + .. figure:: media/back.* + :width: 50% .. figure:: media/assembled.* :align: center + :width: 50% - **Assembled PCB** + Assembled PCB .. figure:: media/dimensions.* :align: center + :width: 100% - **PCB Layout** + PCB Layout .. figure:: media/schematic.* :align: center + :width: 90% - **Schematic Diagram** + Schematic Diagram Contents of the kit ******************** -.. image:: media/kit-contents.* +.. figure:: media/kit-contents.* + :align: center + :width: 60% Software requirements ********************** - Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* Assembling the kit ******************** @@ -98,100 +113,172 @@ You can get Muscle BioAmp BisCute from our `online stores ` or follow the youtube video given below. + **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -261,9 +353,9 @@ Uploading the code Connect your Arduino UNO to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: -EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ -EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, @@ -280,9 +372,9 @@ Visualizing the EMG signals Now flex your arm to visualize the muscle signals in real time on your laptop. -.. image:: media/using-biscute.* +.. figure:: media/using-biscute.* + :align: center - **Video tutorial:** .. youtube:: ujFsAE0E0nk diff --git a/_sources/hardware/bioamp/muscle-bioamp-blip/index.rst b/_sources/hardware/bioamp/muscle-bioamp-blip/index.rst index 90ac4c00..3bc804a5 100644 --- a/_sources/hardware/bioamp/muscle-bioamp-blip/index.rst +++ b/_sources/hardware/bioamp/muscle-bioamp-blip/index.rst @@ -46,43 +46,66 @@ Hardware Images below shows a quick overview of the hardware design. -.. grid:: 1 1 2 2 - :margin: 4 4 0 0 - :gutter: 2 +.. .. only:: html - .. grid-item:: +.. .. grid:: 1 1 2 2 +.. :margin: 4 4 0 0 +.. :gutter: 2 - .. card:: +.. .. grid-item:: - **PCB Front** - ^^^^^ - .. figure:: media/muscle-bioamp-blip-front.* +.. .. card:: - .. grid-item:: - - .. card:: +.. **PCB Front** +.. ^^^^^ +.. .. figure:: media/muscle-bioamp-blip-front.* - **PCB Back** - ^^^^^ - .. figure:: media/muscle-bioamp-blip-front.* +.. .. grid-item:: + +.. .. card:: + +.. **PCB Back** +.. ^^^^^ +.. .. figure:: media/muscle-bioamp-blip-front.* + +.. .. only:: latex + +.. .. figure:: media/muscle-bioamp-blip-front.* +.. :align: center .. figure:: media/muscle-bioamp-blip-assembled.* :align: center - :width: 400 + :width: 60% Assembled PCB Contents of the kit ******************** -.. image:: media/blip-kit-contents.* ++---------------------+-----+ +| Contents of the kit | Qty | ++=====================+=====+ +| Muscle BioAmp Blip | 1 | ++---------------------+-----+ +| BioAmp Cable v3 | 1 | ++---------------------+-----+ +| Muscle BioAmp Band | 1 | ++---------------------+-----+ +| Boxy gel electrodes | 6 | ++---------------------+-----+ + +.. figure:: media/blip-kit-contents.* + :align: center + :width: 80% Software requirements ********************** -- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. +Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* + :align: center + :width: 80% Using the kit **************** @@ -92,7 +115,9 @@ Step 1: Soldering connector & header pins Solder the header pins and JST Ph 2.0mm connector on the Muscle BioAmp Blip as shown below. If you ordered assembled kit then you can skip this step and directly move to step 2. -.. image:: media/soldering-blip.* +.. figure:: media/soldering-blip.* + :width: 80% + :align: center Step 2: Connections with the sensor ======================================== @@ -104,28 +129,35 @@ Directly connecting jumper cables You can directly connect the male to female jumper cables on the header pins of Muscle BioAmp Blip at ``5V``, ``GND``, ``AN``. -.. image:: media/blip-with-jumper-cables.* +.. figure:: media/blip-with-jumper-cables.* + :width: 80% + :align: center Connecting on breadboard --------------------------- If you are thinking to connect more components/sensors and want to integrate Muscle BioAmp Blip in the complete circuit then it will be better to use a breadboard. Snap the Muscle BioAmp Blip on the breadboard and connect the jumper cables (male to male) at ``5V``, ``GND``, ``AN``. -.. image:: media/blip-with-breadboard.* +.. figure:: media/blip-with-breadboard.* + :width: 80% + :align: center Connecting via mikroBUS port ----------------------------- You can also connect the Muscle BioAmp Blip to any hardware that has mikroBUS™ port like mikroBUS™ shuttle, mikroBUS™ Arduino UNO Click Shield to name a few. -.. image:: media/blip-with-shuttle.* +.. figure:: media/blip-with-shuttle.* + :width: 80% + :align: center Step 3: Connecting with Arduino UNO R3 ======================================= Connect ``5V`` of the sensor to ``5V`` of your Arduino UNO, ``GND`` to ``GND``, and ``AN`` to ``Analog pin A0`` via other end of the jumper cables. If you are connecting ``AN`` to any other analog pin, then you will have to change the `INPUT PIN` in the example arduino sketch accordingly. -.. image:: media/blip-arduino-connections.* +.. figure:: media/blip-arduino-connections.* + :align: center .. note:: For demonstration purposes we are showing connections of the sensor with Arduino UNO R3 but you can use any other development board or a standalone ADC of your choice. @@ -134,7 +166,8 @@ Step 4: Connecting electrode cable Connect the BioAmp cable to Muscle BioAmp Blip by inserting the cable end in the JST PH connector as shown. -.. image:: media/blip-bioamp-cable.* +.. figure:: media/blip-bioamp-cable.* + :align: center Step 5: Skin Preparation =============================================== @@ -155,13 +188,20 @@ Using gel electrodes 2. Peel the plastic backing from electrodes 3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram. -.. figure:: media/emg-connections-1.* +.. only:: latex + + .. figure:: media/emg-connections-1.* + :align: center + :width: 60% - Muscle BioAmp Blip with breadboard + Muscle BioAmp Blip with breadboard -.. figure:: media/emg-connections-2.* +.. only:: html - Muscle BioAmp Blip directly connected via jumper cables + .. figure:: media/emg-connections-1.* + :align: center + + Muscle BioAmp Blip with breadboard Using Muscle BioAmp Band --------------------------- @@ -169,11 +209,12 @@ Using Muscle BioAmp Band 1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band. 2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -182,9 +223,9 @@ Step 7: Uploading the code Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: -EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ -EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, @@ -201,7 +242,8 @@ Step 8: Visualizing the EMG signals Now flex your arm to visualize the muscle signals in real time on your laptop. -.. image:: media/emg-recording.* +.. figure:: media/emg-recording.* + :align: center .. rubric:: Footnotes diff --git a/_sources/hardware/bioamp/muscle-bioamp-candy/index.rst b/_sources/hardware/bioamp/muscle-bioamp-candy/index.rst index dc04086d..ef51dc69 100644 --- a/_sources/hardware/bioamp/muscle-bioamp-candy/index.rst +++ b/_sources/hardware/bioamp/muscle-bioamp-candy/index.rst @@ -7,7 +7,7 @@ Overview ********* A candy-size single-channel ElectroMyography (EMG) sensor for recording of muscle signals -at an affordable cost. It is an SMD version of :ref:`muscle_bioamp-biscute` that can be used to make +at an affordable cost. It is an SMD version of :ref:`muscle-bioamp-biscute` that can be used to make amazing Human-Computer Interface (HCI) projects. .. figure:: media/Muscle-BioAmp-Candy-front.* @@ -45,33 +45,49 @@ Hardware Images below shows a quick overview of the hardware design. -.. grid:: 1 1 2 2 - :margin: 4 4 0 0 - :gutter: 2 +.. only:: html - .. grid-item:: - - .. card:: + .. grid:: 1 1 2 2 + :margin: 4 4 0 0 + :gutter: 2 - **PCB Front** - ^^^^^ - .. figure:: media/PCBfront.* + .. grid-item:: + + .. card:: - .. grid-item:: - - .. card:: + **PCB Front** + ^^^^^ + .. figure:: media/PCBfront.* - **PCB Back** - ^^^^^ - .. figure:: media/PCBback.* + .. grid-item:: + + .. card:: + + **PCB Back** + ^^^^^ + .. figure:: media/PCBback.* + +.. only:: latex + + .. figure:: media/PCBfront.* + :width: 60% + + PCB Front + + .. figure:: media/PCBback.* + :width: 60% + + PCB Back .. figure:: media/muscle-bioamp-candy-front.* :align: center + :width: 60% Assembled PCB - Front .. figure:: media/muscle-bioamp-candy-back.* :align: center + :width: 60% Assembled PCB - Back @@ -88,14 +104,34 @@ Images below shows a quick overview of the hardware design. Contents of the kit ******************** -.. image:: media/kit-contents.* ++--------------------------+-----+ +| Contents of the kit | Qty | ++==========================+=====+ +| Muscle BioAmp Candy | 1 | ++--------------------------+-----+ +| BioAmp Cable v3 | 1 | ++--------------------------+-----+ +| Jumper cables (set of 3) | 1 | ++--------------------------+-----+ +| Muscle BioAmp Band | 1 | ++--------------------------+-----+ +| Boxy gel electrodes | 3 | ++--------------------------+-----+ + +.. figure:: media/kit-contents.* + :align: center + + Kit contents Software requirements ********************** -- Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. +Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* + :align: center + + Arduino IDE v1.8.19 Using the kit **************** @@ -103,10 +139,12 @@ Using the kit Step 1: Connect Arduino UNO R3 ================================= -.. image:: media/arduino-candy-connection.* - Connect ``VCC`` to either ``5V`` or ``3.3V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` of your Arduino UNO via jumper cables provided by us. If you are connecting ``OUT`` to any other analog pin, then you will have to change the `INPUT PIN` in the example arduino sketch accordingly. +.. figure:: media/arduino-candy-connection.* + :align: center + :width: 70% + .. note:: For demonstration purposes we are showing connections of the sensor with Arduino UNO R3 but you can use any other development board or a standalone ADC of your choice. .. warning:: Take precautions while connecting to power, if power pins (GND & VCC) are to be swapped, your sensor will be fried and it’ll become unusable (DIE). @@ -114,9 +152,11 @@ Connect ``VCC`` to either ``5V`` or ``3.3V``, ``GND`` to ``GND``, and ``OUT`` to Step 2: Connecting electrode cable ======================================== -.. image:: media/candy-cable-connection.* +Connect the BioAmp cable to Muscle BioAmp Candy by inserting the cable end in the JST PH connector as shown. -Connect the BioAmp cable to Muscle BioAmp Candy by inserting the cable end in the JST PH connector as shown above. +.. figure:: media/candy-cable-connection.* + :width: 70% + :align: center Step 3: Skin Preparation =============================================== @@ -139,18 +179,21 @@ We have 2 options to measure the EMG signals, either using the gel electrodes or 2. Peel the plastic backing from electrodes 3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram. -.. image:: media/candy-emg.* +.. figure:: media/candy-emg.* + :align: center - **Using Muscle BioAmp Band:** 1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band. 2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. + **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -159,9 +202,9 @@ Uploading the code Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: -EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ -EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, @@ -178,7 +221,8 @@ Visualizing the EMG signals Now flex your arm to visualize the muscle signals in real time on your laptop. -.. image:: media/using-candy.* +.. figure:: media/using-candy.* + :align: center **Video tutorial:** diff --git a/_sources/hardware/bioamp/muscle-bioamp-patchy/index.rst b/_sources/hardware/bioamp/muscle-bioamp-patchy/index.rst index 4d5247a7..c6513e67 100644 --- a/_sources/hardware/bioamp/muscle-bioamp-patchy/index.rst +++ b/_sources/hardware/bioamp/muscle-bioamp-patchy/index.rst @@ -14,6 +14,7 @@ powerful BioAmp sensing technology for precise muscle signal recording. This ena based Human-Computer Interface (HCI) easily. .. figure:: media/Patchy-All-Colors.* + :align: center Features & Specifications ************************** @@ -69,7 +70,8 @@ Images below shows a quick overview of the hardware design. Contents of the kit ******************** -.. image:: media/kit-contents.* +.. figure:: media/kit-contents.* + :align: center We have made a complete unboxing video of the kit. Please find the link below: @@ -82,7 +84,8 @@ Software requirements Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* + :align: center Using the kit **************** @@ -92,14 +95,15 @@ Step 1: Connect reference cable Connect the reference cable to the Muscle BioAmp Patchy as shown in the diagram. -.. image:: media/ref-cable-connection.* +.. figure:: media/ref-cable-connection.* + :align: center Step 2: Connecting sensor to gel electrodes ================================================ Snap the Muscle BioAmp Patchy on the gel electrodes (Don't peel the plastic backing from the electrodes at this moment). -.. image:: media/patchy-electrode-connection.* +.. figure:: media/patchy-electrode-connection.* :width: 80% :align: center @@ -115,7 +119,8 @@ Step 4: Electrode Placements Now peel off the plastic backing from the gel electrodes and place the Muscle BioAmp Patchy on the targeted muscle and the reference on the bony part of your elbow as shown in the diagram. -.. image:: media/patchy-on-hand.* +.. figure:: media/patchy-on-hand.* + :align: center .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -124,7 +129,10 @@ Step 5: Connect Arduino UNO R3 Connect ``VCC`` to ``5V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` of your Arduino UNO via jumper cables provided by us. If you are connecting ``OUT`` to any other analog pin, then you will have to change the INPUT PIN in the arduino sketch accordingly. -.. image:: media/pathcy-arduino-connections.* +.. figure:: media/pathcy-arduino-connections.* + :align: center + + Connections with Arduino UNO R3 .. note:: For demonstration purposes we are showing connections of the sensor with Arduino UNO R3 but you can use any other development board or a standalone ADC of your choice. @@ -133,11 +141,12 @@ Step 6: Upload the code Connect your Arduino UNO to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: -EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ -EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ -.. image:: media/setup.* +.. figure:: media/setup.* + :align: center Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, @@ -154,7 +163,8 @@ Step 7: Visualizing the EMG signals Now flex your arm to visualize the muscle signals in real-time on your laptop. -.. image:: media/patchy-emg.* +.. figure:: media/patchy-emg.* + :align: center **Video tutorial:** diff --git a/_sources/hardware/bioamp/muscle-bioamp-shield/index.rst b/_sources/hardware/bioamp/muscle-bioamp-shield/index.rst index f101e335..908ebcb5 100644 --- a/_sources/hardware/bioamp/muscle-bioamp-shield/index.rst +++ b/_sources/hardware/bioamp/muscle-bioamp-shield/index.rst @@ -13,7 +13,8 @@ BackYard Brains (BYB) `Muscle Spiker shield `_. Using this you'll be able to upload the arduino sketches on your development board and visualise the data on your laptop. -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.png - -Assembling the Kit -******************** +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* + :align: center -You can get your own Muscle BioAmp Shield bag of parts from our `online stores `_ (shipping worldwide) -and for assembling your shield you can take a look at `this interactive BOM `_ or the step by step guide below. + Download Arduino IDE v1.8.19 -.. note:: Follow the highlighted yellow shapes to assemble your shield! +.. only:: html -.. grid:: 1 1 2 2 - :margin: 2 2 0 0 - :gutter: 2 + Assembling the Kit + ******************** - .. grid-item:: - - .. figure:: media/Assembly/01_Bare_Board.* + You can get your own Muscle BioAmp Shield bag of parts from our `online stores `_ (shipping worldwide) + and for assembling your shield you can take a look at `this interactive BOM `_ or the step by step guide below. - **Step 1 - Bare Board** + .. note:: Follow the highlighted yellow shapes to assemble your shield! - .. grid-item:: + .. grid:: 1 1 2 2 + :margin: 2 2 0 0 + :gutter: 2 - .. figure:: media/Assembly/02_1M_Resistors.jpg + .. grid-item:: - **Step 2 - 1M Resistors** + .. figure:: media/Assembly/01_Bare_Board.* + + **Step 1 - Bare Board** + + .. grid-item:: + + .. figure:: media/Assembly/02_1M_Resistors.jpg + + **Step 2 - 1M Resistors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/03_330R_Resistors.jpg + .. figure:: media/Assembly/03_330R_Resistors.jpg - **Step 3 - 330R Resistors** + **Step 3 - 330R Resistors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/04_10K_Resistors.jpg + .. figure:: media/Assembly/04_10K_Resistors.jpg - **Step 4 - 10K Resistors** + **Step 4 - 10K Resistors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/05_22K_Resistors.jpg + .. figure:: media/Assembly/05_22K_Resistors.jpg - **Step 5 - 22K Resistors** + **Step 5 - 22K Resistors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/06_1K_Resistors.jpg + .. figure:: media/Assembly/06_1K_Resistors.jpg - **Step 6 - 1K Resistors** + **Step 6 - 1K Resistors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/07_220K_Resistors.jpg + .. figure:: media/Assembly/07_220K_Resistors.jpg - **Step 7 - 220K Resistors** + **Step 7 - 220K Resistors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/08_1nF_Capacitors.jpg + .. figure:: media/Assembly/08_1nF_Capacitors.jpg - **Step 8 - 1nF Capacitors** + **Step 8 - 1nF Capacitors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/09_100nF_Capacitors.jpg + .. figure:: media/Assembly/09_100nF_Capacitors.jpg - **Step 9 - 100nF Capacitors** + **Step 9 - 100nF Capacitors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/10_100pF_Capacitors.jpg + .. figure:: media/Assembly/10_100pF_Capacitors.jpg - **Step 10 - 100pF Capacitors** + **Step 10 - 100pF Capacitors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/11_Angled_Header_Pins.jpg + .. figure:: media/Assembly/11_Angled_Header_Pins.jpg - **Step 11 - Angled Header Pins** + **Step 11 - Angled Header Pins** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/12_5x5mm_Buttons.jpg + .. figure:: media/Assembly/12_5x5mm_Buttons.jpg - **Step 12 - 5x5mm Buttons** + **Step 12 - 5x5mm Buttons** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/13_OptoIsolator.jpg + .. figure:: media/Assembly/13_OptoIsolator.jpg - **Step 13 - OptoIsolator** + **Step 13 - OptoIsolator** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/14_JST_PH_Angled_Connectors.jpg + .. figure:: media/Assembly/14_JST_PH_Angled_Connectors.jpg - **Step 14 - JST PH Angled Connectors** + **Step 14 - JST PH Angled Connectors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/15_JST_PH_Straight_Connectors.jpg + .. figure:: media/Assembly/15_JST_PH_Straight_Connectors.jpg - **Step 15 - JST PH Straight Connectors** + **Step 15 - JST PH Straight Connectors** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/16_IC_Socket.jpg + .. figure:: media/Assembly/16_IC_Socket.jpg - **Step 16 - IC Socket** + **Step 16 - IC Socket** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/17_IC.jpg + .. figure:: media/Assembly/17_IC.jpg - **Step 17 - IC** + **Step 17 - IC** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/18_LEDs.jpg + .. figure:: media/Assembly/18_LEDs.jpg - **Step 18 - LEDs** + **Step 18 - LEDs** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/19_3.5mm_Headphone_Jack.jpg + .. figure:: media/Assembly/19_3.5mm_Headphone_Jack.jpg - **Step 19 - 3.5mm Headphone Jack** + **Step 19 - 3.5mm Headphone Jack** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/20_2.2uF_Capacitor.jpg + .. figure:: media/Assembly/20_2.2uF_Capacitor.jpg - **Step 20 - 2.2uF Capacitor** + **Step 20 - 2.2uF Capacitor** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/21_1uF_Capacitor.jpg + .. figure:: media/Assembly/21_1uF_Capacitor.jpg - **Step 21 - 1uF Capacitor** + **Step 21 - 1uF Capacitor** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/22_470uF_Capacitor.jpg + .. figure:: media/Assembly/22_470uF_Capacitor.jpg - **Step 22 - 470uF Capacitor** + **Step 22 - 470uF Capacitor** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/23_Header_Pins.jpg + .. figure:: media/Assembly/23_Header_Pins.jpg - **Step 23 - Header Pins** + **Step 23 - Header Pins** - .. grid-item:: + .. grid-item:: - .. figure:: media/Assembly/24_Assembled.jpg + .. figure:: media/Assembly/24_Assembled.jpg - **Step 24 - Assembled Shield** + **Step 24 - Assembled Shield** -Still can't figure out the assembly? You can follow the video provided below to assemble your Shield. + Still can't figure out the assembly? You can follow the video provided below to assemble your Shield. -.. youtube:: dcuCihh3yn4 - :width: 100% + .. youtube:: dcuCihh3yn4 + :width: 100% Using the Sensor ****************** @@ -288,7 +318,7 @@ Stack the Muscle BioAmp Shield on top of Arduino Uno properly. .. only:: html - .. figure:: media/gifs/shield-arduino-connection.gif + .. figure:: media/gifs/shield-arduino-connection.* :align: center .. only:: latex @@ -303,7 +333,7 @@ Connect the BioAmp Cable to Muscle BioAmp Shield as shown. .. only:: html - .. figure:: media/gifs/electrode-cable-connection.gif + .. figure:: media/gifs/electrode-cable-connection.* :align: center .. only:: latex @@ -340,20 +370,26 @@ Using gel electrodes .. figure:: media/images/electrode-placement-1.* :align: center + `Electrode placement for REF cable` + .. figure:: media/images/electrode-placement-2.* :align: center + `Electrode placement for IN+, IN- cables` + Using Muscle BioAmp Band --------------------------- 1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band. 2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. + **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -371,9 +407,11 @@ Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B .. figure:: media/images/arduino-laptop-connection-1.* :align: center + :width: 50% .. figure:: media/images/arduino-laptop-connection-2.* - :align: center + :align: center + :width: 50% .. warning:: Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition. @@ -382,9 +420,9 @@ Step 6: Visualise EMG signals on laptop Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: - EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ - EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, @@ -406,12 +444,14 @@ Now flex your arm to visualize the muscle signals in real time on your laptop. .. figure:: media/images/visualise-emg.* :align: center + `Visualise EMG signals on laptop` + Step 7: Visualise EMG signals on LEDs ========================================== Copy paste the Arduino Sketch given below in Arduino IDE: - LED Bar Graph: https://github.com/upsidedownlabs/BioAmp-EXG-Pill/blob/main/software/LEDBarGraph/LEDBarGraph.ino +:fab:`github;pst-color-primary` `LED Bar Graph `_ Make sure you have selected the right board and COM port. Now upload the code, and flex your arm. You'll see the LED bar going up. More strength you apply, more the LED bar goes up. @@ -425,6 +465,8 @@ Make sure you have selected the right board and COM port. Now upload the code, a .. figure:: media/images/led-graph.* :align: center + `Visualise EMG signals on LEDs` + Step 8: Listen to your EMG signals ==================================== @@ -447,6 +489,8 @@ Listening EMG on speakers .. figure:: media/images/listening-emg-speakers.* :align: center + Listening EMG on speakers + Listening EMG on a wired earphones/headphones ---------------------------------------------- @@ -464,6 +508,8 @@ Listening EMG on a wired earphones/headphones .. figure:: media/images/listening-emg-earphones.* :align: center + `Listening EMG on a wired earphones/headphones` + Step 9: Controlling a servo motor =================================== @@ -471,7 +517,7 @@ Connect the servo claw to Muscle BioAmp Shield. Copy paste the Arduino Sketch given below in Arduino IDE: - Servo Controller: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/5_ServoControl/5_ServoControl.ino +:fab:`github;pst-color-primary` `Servo Controller `_ Make sure you have selected the right board and COM port. Now upload the code, and flex your arm to control the servo claw in real time. @@ -487,7 +533,7 @@ Connect the servo claw to Muscle BioAmp Shield. Copy paste the Arduino Sketch given below in Arduino IDE: - Claw Controller: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/tree/main/4_ClawController +:fab:`github;pst-color-primary` `Claw Controller `_ Make sure you have selected the right board and COM port. Now upload the code, and flex your arm to control the servo claw in real time. diff --git a/_sources/index.rst b/_sources/index.rst index baa3f44c..db0c6c90 100644 --- a/_sources/index.rst +++ b/_sources/index.rst @@ -39,7 +39,7 @@ that you can use with our hardware. .. grid-item:: .. card:: - :link: muscle_bioamp-biscute + :link: muscle-bioamp-biscute :link-type: ref :img-top: media/muscle-bioamp-biscute.* :img-alt: @@ -143,4 +143,11 @@ that you can use with our hardware. :maxdepth: 1 :caption: Guides - guides/index \ No newline at end of file + guides/index + +.. toctree:: + :hidden: + :maxdepth: 1 + :caption: Courses + + courses/index \ No newline at end of file diff --git a/_sources/kits/diy-neuroscience/basic/index.rst b/_sources/kits/diy-neuroscience/basic/index.rst index 66fc290e..12288f4a 100644 --- a/_sources/kits/diy-neuroscience/basic/index.rst +++ b/_sources/kits/diy-neuroscience/basic/index.rst @@ -34,11 +34,17 @@ Software requirements - Before you start using the kit, please download `Arduino IDE v1.8.19 (legacy IDE) `_. Using this you'll be able to upload the arduino sketches in Maker UNO and visualise the data on your laptop. -.. image:: media/arduino-ide.* +.. figure:: media/arduino-ide.* + :align: center + + Arduino IDE v1.8.19 (legacy IDE) - Download Backyard Brains' `Spike Recorder `_ according to the operating system you are using (Windows, OSX, Linux). -.. image:: media/byb.* +.. figure:: media/byb.* + :align: center + + BYB spike recorder Using the kit ************** @@ -48,7 +54,8 @@ This kit is made in a way so that even beginners can use it and get started with Step 1 (optional): Configure for EMG/ECG ========================================= -.. image:: media/configuration-emg-ecg.* +.. figure:: media/configuration-emg-ecg.* + :align: center BioAmp EXG Pill is by default configured for recording EEG or EOG, so if you are recording any of the two signals you can skip this step. But if you want to record good quality ECG or EMG, then it is recommended to configure it @@ -59,7 +66,8 @@ by making a solder joint as shown in the image above. Step 2: Connect Maker UNO ========================== -.. image:: media/connection-with-maker-uno.* +.. figure:: media/connection-with-maker-uno.* + :align: center Connect ``VCC`` to ``5V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` of your Maker UNO via jumper cables provided by us. If you are connecting OUT to any other analog pin, then you will have to change the INPUT PIN in the arduino sketch accordingly. @@ -68,7 +76,8 @@ Connect ``VCC`` to ``5V``, ``GND`` to ``GND``, and ``OUT`` to ``Analog pin A0`` Step 3: Connecting electrode cable =============================================== -.. image:: media/bioamp-cable.* +.. figure:: media/bioamp-cable.* + :align: center Connect the BioAmp cable to BioAmp EXG Pill by inserting the cable end in the JST PH connector as shown above. @@ -80,7 +89,7 @@ Apply Nuprep Skin Preparation Gel on the skin surface where electrodes would be For more information, please check out detailed step by step :ref:`skin-preparation`. Step 5: Measuring EMG (ElectroMyoGraphy) -=============================================== +=========================================== Electrodes placement ---------------------- @@ -93,18 +102,21 @@ We have 2 options to measure the EMG signals, either using the gel electrodes or 2. Peel the plastic backing from electrodes 3. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram. -.. image:: media/emg.* +.. figure:: media/emg.* + :align: center - **Using Muscle BioAmp Band:** 1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band. 2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. + **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -113,9 +125,9 @@ Uploading the code Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste any one of the Arduino Sketches given below in Arduino IDE v1.8.19 that you downloaded earlier: -EMG Filter: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/2_EMGFilter/2_EMGFilter.ino +:fab:`github;pst-color-primary` `EMG Filter `_ -EMG Envelope: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/blob/main/3_EMGEnvelope/3_EMGEnvelope.ino +:fab:`github;pst-color-primary` `EMG Envelope `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Maker Uno is connected. To find out the right COM port, @@ -132,7 +144,8 @@ Visualizing the EMG signals Now flex your arm to visualize the muscle signals in real time on your laptop. -.. image:: media/EMGEnvelop.* +.. figure:: media/EMGEnvelop.* + :align: center Step 6: Measuring ECG (ElectroCardioGraphy) =============================================== @@ -148,7 +161,8 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or 2. Peel the plastic backing from electrodes 3. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side as shown in the diagram. -.. image:: media/ecg.* +.. figure:: media/ecg.* + :align: center - **Using Heart BioAmp Band:** @@ -156,18 +170,20 @@ We have 2 options to measure the ECG signals, either using the gel electrodes or 2. Place the IN- cable on the left side, IN+ in the middle and REF (reference) on the far right side. 3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results. -**Tutorial on how to use the band:** +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. -.. youtube:: fr5iORsVyUM - :align: center - :width: 100% + **Tutorial on how to use the band:** + + .. youtube:: fr5iORsVyUM + :align: center + :width: 100% Uploading the code --------------------- Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier: -ECG Filter: https://github.com/upsidedownlabs/Heart-BioAmp-Arduino-Firmware/blob/main/2_ECGFilter/2_ECGFilter.ino +:fab:`github;pst-color-primary` `ECG Filter `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Maker Uno is connected. To find out the right COM port, @@ -182,7 +198,8 @@ After opening the serial plotter make sure to select the baud rate to 115200. Visualizing the ECG signals ----------------------------- -.. image:: media/bioamp-Exg-Pill-ECG.* +.. figure:: media/bioamp-Exg-Pill-ECG.* + :align: center Step 7: Measuring EOG (ElectroOculoGraphy) ============================================= @@ -194,7 +211,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move - **Horizontal EOG recording:** -.. image:: media/eog-horizontal.* +.. figure:: media/eog-horizontal.* + :align: center 1. Connect the BioAmp cable to gel electrodes. 2. Peel the plastic backing from electrodes. @@ -202,7 +220,8 @@ We have 2 ways to measure the EOG signals, either record the horizontal eye move - **Vertical EOG recording:** -.. image:: media/eog-vertical.* +.. figure:: media/eog-vertical.* + :align: center 1. Connect the BioAmp cable to gel electrodes. 2. Peel the plastic backing from electrodes. @@ -213,7 +232,7 @@ Uploading the code Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier: -EOG Filter: https://github.com/upsidedownlabs/Eye-BioAmp-Arduino-Firmware/blob/main/2_EOGFilter/2_EOGFilter.ino +:fab:`github;pst-color-primary` `EOG Filter `_ Go to ``tools`` from the menu bar, select ``board`` option then select Arduino UNO. In the same menu, select the COM port on which your Maker Uno is connected. To find out the right COM port, @@ -228,7 +247,8 @@ After opening the serial plotter make sure to select the baud rate to 115200. Visualizing the EOG signals ------------------------------ -.. image:: media/bioamp-exg-pill-eog.* +.. figure:: media/bioamp-exg-pill-eog.* + :align: center Step 8: Measuring EEG (ElectroEncephaloGraphy) =============================================== @@ -236,7 +256,8 @@ Step 8: Measuring EEG (ElectroEncephaloGraphy) Let's understand the electrode placements before moving forward in this project. For recording EEG from different parts of the brain, you have to place the electrodes according to the `International 10-20 system for recording EEG `_. -.. image:: media/10-20-system.* +.. figure:: media/10-20-system.* + :align: center :width: 80% Electrodes placement @@ -246,7 +267,8 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or - **Using gel electrodes to record from prefrontal cortex part of brain:** -.. image:: media/eeg.* +.. figure:: media/eeg.* + :align: center 1. Connect the BioAmp cable to gel electrodes. 2. Peel the plastic backing from electrodes. @@ -260,11 +282,13 @@ We have 2 options to measure the EEG signals, either using the gel electrodes or .. note:: Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same. -**Tutorial on how to use the band:** +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. -.. youtube:: O6qp7teT-sM - :align: center - :width: 100% + **Tutorial on how to use the band:** + + .. youtube:: O6qp7teT-sM + :align: center + :width: 100% Uploading the code ----------------------- @@ -287,6 +311,7 @@ Open up your BackyardBrains Spike Recorder software. At first, it will monitor s the :fas:`gear` icon on the top left corner of the screen, select the COM port on which the Maker UNO is connected and click on connect. .. figure:: media/spike-recorder-configurations.* + :align: center Mute the speakers and apply the 50Hz notch filter by clicking on the checkbox as shown in the screenshot above. You should set the low band pass filter to 1Hz and high bandpass filter to 40Hz as we are only recording the EEG signals which range between @@ -295,6 +320,10 @@ these frequencies. Now everything is configured and connected. So close the settings window and start recording EEG signals. .. figure:: media/bioamp-exg-pill-eeg.* + :align: center + :alt: Recording EEG from pre-frontal cortex part of brain + + Recording EEG signals from pre-frontal cortex The signals that you can see on the screen right now are originating from prefrontal cortex part of your brain and propagating through all the layers to the surface of your skin. diff --git a/_sources/kits/diy-neuroscience/pro/index.rst b/_sources/kits/diy-neuroscience/pro/index.rst index 813f34a7..2c5399bc 100644 --- a/_sources/kits/diy-neuroscience/pro/index.rst +++ b/_sources/kits/diy-neuroscience/pro/index.rst @@ -12,6 +12,8 @@ applications, and gain valuable insights. .. figure:: media/diy-neuroscience-kit-pro.* :align: center + DIY Neuroscience Kit Pro + Contents of the kit ******************** @@ -45,6 +47,8 @@ Contents of the kit .. figure:: media/kit-content.* :align: center +Click on the link below to see the unboxing of the kit: + .. youtube:: Sn389Q7Izy4 :width: 100% :align: center @@ -62,7 +66,7 @@ Download the following according to the operating system you are using (Windows, - `Arduino IDE v1.8.19 (legacy IDE) `_ -.. image:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* +.. figure:: ../../../kits/diy-neuroscience/basic/media/arduino-ide.* Using the kit ************** @@ -84,7 +88,7 @@ just a few. It also works with any dedicated ADC, like the Texas Instruments ADS .. figure:: ../../../media/bioamp-exg-pill.* -.. note:: Checkout the complete documentation on `BioAmp EXG Pill `_ which includes how to use the sensor, record various biopotential signals from your body (ECG, EMG, EOG, EEG) and make different HCI/BCI projects using it. +.. note:: Checkout the complete documentation on :ref:`bioamp-exg-pill` which includes how to use the sensor, record various biopotential signals from your body (ECG, EMG, EOG, EEG) and make different HCI/BCI projects using it. Step 2: Using Muscle BioAmp Shield ======================================= @@ -96,7 +100,7 @@ signals to make amazing projects in the domain of Human-Computer Interface (HCI) .. figure:: ../../../media/muscle-bioamp-shield.* -.. note:: Checkout the complete documentation on `Muscle BioAmp Shield `_ which includes how to use the sensor, record/visualise/listen muscle signals and make different HCI projects using it. +.. note:: Checkout the complete documentation on :ref:`muscle-bioamp-shield` which includes how to use the sensor, record/visualise/listen muscle signals and make different HCI projects using it. Step 3: Using the sensors together ====================================== @@ -112,14 +116,16 @@ a. Connecting Muscle BioAmp Shield to MCU/ADC Stack the Muscle BioAmp Shield on top of your Arduino Uno properly. -.. only:: html +.. only:: latex - .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/gifs/shield-arduino-connection.gif + .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/images/shield-arduino-connection.* :align: center -.. only:: latex + Stacking Muscle BioAmp Shield on top of Arduino - .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/images/shield-arduino-connection.* +.. only:: html + + .. figure:: ../../../hardware/bioamp/muscle-bioamp-shield/media/gifs/shield-arduino-connection.gif :align: center b. Configure for ECG/EMG (optional) @@ -130,8 +136,9 @@ BioAmp EXG Pill is by default configured for recording EEG or EOG but if you wan .. figure:: ../../../hardware/bioamp/bioamp-exg-pill/media/assembly-step2.* :align: center -.. note:: Even without making the solder joint the BioAmp EXG Pill is capable of recording ECG or EMG but the signals would be more accurate if you configure it. + Configure BioAmp EXG Pill for EMG/ECG +.. note:: Even without making the solder joint the BioAmp EXG Pill is capable of recording ECG or EMG but the signals would be more accurate if you configure it. c. Connecting sensors together -------------------------------------- @@ -148,16 +155,39 @@ Connect the BioAmp EXG Pill to the A2 port of Muscle BioAmp Shield via 3-pin STE | A2 | OUT | +----------------------+-----------------+ -.. figure:: media/gifs/shield-pill-connection.* - :align: center +.. only:: latex + + .. figure:: media/images/shield-pill-connection.* + :align: center + + Inserting JST PH connector in A2 port of Muscle BioAmp Shield + + .. figure:: media/images/shield-pill-connection-2.* + :align: center + + Muscle BioAmp Shield to BioAmp EXG Pill connections + +.. only:: html + + .. figure:: media/gifs/shield-pill-connection.* + :align: center d. Connecting electrode cables -------------------------------- Connect one BioAmp cable to BioAmp EXG Pill and another BioAmp cable to Muscle BioAmp Shield by inserting the cable ends into the respective JST PH connectors as shown below: -.. figure:: media/gifs/bioamp-cables-connection.* - :align: center +.. only:: html + + .. figure:: media/gifs/bioamp-cables-connection.* + :align: center + +.. only:: latex + + .. figure:: media/images/bioamp-cables-connection.* + :align: center + + Connecting BioAmp Cables to the sensors e. Skin Preparation --------------------------- @@ -166,7 +196,7 @@ We'll create a 2-channel EMG acquisition system and to do so, we'll be using bot Apply Nuprep Skin Preparation Gel on the skin surface where electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe. -For more information, please check out detailed step by step `skin preparation guide `_. +For more information, please check out detailed step by step :ref:`skin-preparation`. f. Electrodes placement ------------------------- @@ -180,36 +210,60 @@ Using gel electrodes 2. Peel the plastic backing from electrodes. 3. Place the IN+ and IN- cables on the left arm near the ulnar nerve & REF (reference) at the back of your left hand as shown below. -.. figure:: media/gifs/gel-electrodes-connection.* - :align: center +.. only:: html + + .. figure:: media/gifs/gel-electrodes-connection.* + :align: center 4. Now snap the BioAmp Cable connected to Muscle BioAmp Shield to gel electrodes. 5. Peel the plastic backing from electrodes. 6. Place the IN+ and IN- cables on the right arm near the ulnar nerve & REF (reference) at the back of your right hand as shown below. -.. figure:: media/gifs/gel-electrodes-connection-2.* - :align: center +.. only:: html + + .. figure:: media/gifs/gel-electrodes-connection-2.* + :align: center + +.. only:: latex + + .. figure:: media/images/gel-electrodes-connection.* + :align: center + + Gel electrodes placement Using Muscle BioAmp Band +++++++++++++++++++++++++ 1. Snap the BioAmp Cable connected to BioAmp EXG Pill on Muscle BioAmp Band in a way such that IN+ and IN- are placed on the left arm near the ulnar nerve & REF (reference) on the far side of the band. -.. figure:: media/gifs/bioamp-band-connection-2.* - :align: center +.. only:: html + + .. figure:: media/gifs/bioamp-band-connection-2.* + :align: center 2. Snap the BioAmp Cable connected to Muscle BioAmp Shield on Muscle BioAmp Band in a way such that IN+ and IN- are placed on the right arm near the ulnar nerve & REF (reference) on the far side of the band. -.. figure:: media/gifs/bioamp-band-connection.* - :align: center +.. only:: html + + .. figure:: media/gifs/bioamp-band-connection.* + :align: center + +.. only:: latex + + .. figure:: media/images/bioamp-band-connection.* + :align: center + + Muscle BioAmp Band placement 3. Now put a small drop of electrode gel between the skin and metallic parts of BioAmp Cables to get the best results. +.. tip:: Visit the complete documentation on how to :ref:`assemble and use the BioAmp Bands ` or follow the youtube video given below. + **Tutorial on how to use the band:** -.. youtube:: xYZdw0aesa0 - :align: center - :width: 100% + .. youtube:: xYZdw0aesa0 + :align: center + :width: 100% .. note:: In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part. @@ -217,8 +271,8 @@ g. Uploading the code ---------------------- Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Download the github repository given below: - -Muscle BioAmp Arduino Firmware: https://github.com/upsidedownlabs/Muscle-BioAmp-Arduino-Firmware/ + +:fab:`github;pst-color-primary` `Muscle BioAmp Arduino Firmware `_ Go to the folder ``8_EMGScrolling``, open the arduino sketch ``8_EMGScrolling.ino`` in Arduino IDE. @@ -236,13 +290,42 @@ Go to ``tools`` from the menu bar, click on ``serial monitor`` to open it or cli Press the ``SW1 button`` on Muscle BioAmp Shield. Now you'll see green LED glowing on the LED bar. When you flex your right arm, you'll get output value 1 on the serial monitor and red LED will glow. Similarly, when you flex your left arm, you'll get output value 2 and yellow LED will glow. -.. figure:: media/gifs/testing.* - :align: center +.. only:: html + + .. figure:: media/gifs/testing.* + :align: center + +.. only:: latex + + .. figure:: media/images/testing-1.* + :align: center + + Press the SW1 button to start getting the output + + .. figure:: media/images/testing-2.* + :align: center + + Flex the right arm, red LED glows + + .. figure:: media/images/testing-3.* + :align: center + + Flex the left arm, yellow LED glows + + .. figure:: media/images/testing-4.* + :align: center + + Flex the right arm, serial monitor shows output value 1 + + .. figure:: media/images/testing-5.* + :align: center + + Flex the left arm, serial monitor shows output value 2 i. Running python script ------------------------- -Open Visual Studio Code, click on File < Open folder to open the folder ``8_EMGScrolling``. +Open Visual Studio Code, click on File > Open folder to open the folder ``8_EMGScrolling``. Open the terminal, and ensure that the path is configured to the location of the ``requirement.txt`` file. @@ -269,15 +352,26 @@ Run the Python script ``EMG_Scroll.py`` by writing the given command in the term j. Scrolling using EMG signals --------------------------------- +Press the ``SW1 button`` on Muscle BioAmp Shield again. + In the terminal, you will see Move Now prompt. When you flex your right arm, you'll see UP in the terminal. Similarly, when you move your left arm, you'll see DOWN in the terminal. -.. figure:: media/gifs/demo-1.* - :align: center +.. only:: html + + .. figure:: media/gifs/demo-1.* + :align: center + +.. only:: latex + + .. figure:: media/images/demo-1.* + :align: center Now, open youtube shorts on your laptop and start scrolling using your muscle signals. -.. figure:: media/gifs/demo-2.* - :align: center +.. only:: html + + .. figure:: media/gifs/demo-2.* + :align: center .. note:: What's happening in the background? Whenever an EMG signal is detected, it acts as a trigger to emulate UP or DOWN key on the keyboard. @@ -286,7 +380,7 @@ k. Calibrating the code **Changes in Arduino Sketch** -Modify the threshold values on lines 73 and 74. Threshold 1 is for the EMG signals recorded from the Muscle BioAmp Shield, and threshold 2 is for the EMG signals recorded from the BioAmp EXG Pill. +Modify the threshold values on **lines 73 and 74**. Threshold 1 is for the EMG signals recorded from the Muscle BioAmp Shield, and threshold 2 is for the EMG signals recorded from the BioAmp EXG Pill. Uncomment line 71 in the Arduino code and navigate to Tools > Serial Plotter. You’ll see two plots showing the EMG signals of both of your arms. Flex your right arm and observe the peak value on the y-axis. If the peak value is around 240, you can set threshold 1 anywhere between 150 to 200. The lower the threshold value, the easier it is to trigger the output as UP or DOWN, and vice versa. Repeat the process to determine the threshold 2 value for your left arm. @@ -294,7 +388,7 @@ After setting the thresholds, comment out line 71. **Changes in Python script** -Adjust the latency value on line 51. A higher latency value will make the output less responsive, requiring you to flex and hold longer to scroll through the screen. A lower latency value will make the output more responsive, allowing you to scroll through the screen more easily. +Adjust the latency value on **line 51**. A higher latency value will make the output less responsive, requiring you to flex and hold longer to scroll through the screen. A lower latency value will make the output more responsive, allowing you to scroll through the screen more easily. l. Conclusion ----------------- @@ -365,7 +459,7 @@ Some project ideas :text-align: center :link: https://www.instructables.com/Tracking-UP-and-DOWN-Movements-of-Eyes-Using-EOG/ - 2. Projects made using Muscle BioAmp Shield + 1. Projects made using Muscle BioAmp Shield ============================================= .. grid:: 2 2 2 2 @@ -392,7 +486,7 @@ Some project ideas :text-align: center :link: https://www.instructables.com/Making-a-Muscle-Strength-Game-Using-Muscle-BioAmp-/ - 3. Projects made using the sensors together + 1. Projects made using the sensors together ============================================== .. grid:: 2 2 2 2 @@ -410,3 +504,39 @@ Some project ideas These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech. +.. only:: latex + + You can find step-by-step tutorials for various HCI/BCI projects on our `Instructables `_. + + Projects made using BioAmp EXG Pill + ==================================== + + 1. `Controlling video game using brainwaves (EEG) `_ + 2. `Visualising electrical impulses from eyes (EOG) `_ + 3. `Recording EEG from visual cortex part of brain `_ + 4. `Recording EEG from prefrontal cortex part of brain `_ + 5. `Eye blink detection `_ + 6. `Creating a drowsiness detector `_ + 7. `Record publication-grade ECG `_ + 8. `Measuring heart rate `_ + 9. `Detecting heart beats `_ + 10. `Record publication-grade EMG `_ + 11. `Detecting up and down movement of eyes `_ + + Projects made using Muscle BioAmp Shield + =========================================== + + 1. `Record, visualise, and listen to EMG signals `_ + 2. `Controlling 3d-printed servo claw using EMG `_ + 3. `Controlling prosthetic hand using EMG `_ + 4. `Building the ultimate servo claw game `_ + 5. `Building muscle strength game `_ + + Projects made using the sensors together + ============================================ + + 1. `Control dino game using eye blinks `_ + 2. `Control servo claw using EOG `_ + + These are some of the project ideas but the possibilities are endless. So create your own Human Computer Interface (HCI) and + Brain Computer Interface (BCI) projects and share them with us at contact@upsidedownlabs.tech \ No newline at end of file diff --git a/_static/latex/bioamp-exg-pill.rst b/_static/latex/bioamp-exg-pill.rst new file mode 100644 index 00000000..4e3361f0 --- /dev/null +++ b/_static/latex/bioamp-exg-pill.rst @@ -0,0 +1,24 @@ +:orphan: + +BioAmp EXG Pill +############### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/bioamp-exg-pill/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst \ No newline at end of file diff --git a/_static/latex/bioamp-v1.5.rst b/_static/latex/bioamp-v1.5.rst new file mode 100644 index 00000000..3f3062b0 --- /dev/null +++ b/_static/latex/bioamp-v1.5.rst @@ -0,0 +1,24 @@ +:orphan: + +BioAmp v1.5 +############## + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/bioamp-v1.5/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst diff --git a/_static/latex/diy-neuroscience-kit-basic.rst b/_static/latex/diy-neuroscience-kit-basic.rst new file mode 100644 index 00000000..72ab3468 --- /dev/null +++ b/_static/latex/diy-neuroscience-kit-basic.rst @@ -0,0 +1,26 @@ +:orphan: + +DIY Neuroscience Kit Basic +########################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../kits/diy-neuroscience/basic/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst + + diff --git a/_static/latex/diy-neuroscience-kit-pro.rst b/_static/latex/diy-neuroscience-kit-pro.rst new file mode 100644 index 00000000..7397eb56 --- /dev/null +++ b/_static/latex/diy-neuroscience-kit-pro.rst @@ -0,0 +1,39 @@ +:orphan: + +DIY Neuroscience Kit Pro +######################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../kits/diy-neuroscience/pro/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/bioamp-exg-pill/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/muscle-bioamp-shield/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst + + diff --git a/_static/latex/muscle-bioamp-biscute.rst b/_static/latex/muscle-bioamp-biscute.rst new file mode 100644 index 00000000..0d7d7814 --- /dev/null +++ b/_static/latex/muscle-bioamp-biscute.rst @@ -0,0 +1,24 @@ +:orphan: + +Muscle BioAmp Biscute +####################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/muscle-bioamp-biscute/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst diff --git a/_static/latex/muscle-bioamp-blip.rst b/_static/latex/muscle-bioamp-blip.rst new file mode 100644 index 00000000..16c40938 --- /dev/null +++ b/_static/latex/muscle-bioamp-blip.rst @@ -0,0 +1,24 @@ +:orphan: + +Muscle BioAmp Blip +#################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/muscle-bioamp-blip/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst diff --git a/_static/latex/muscle-bioamp-candy.rst b/_static/latex/muscle-bioamp-candy.rst new file mode 100644 index 00000000..9766bb44 --- /dev/null +++ b/_static/latex/muscle-bioamp-candy.rst @@ -0,0 +1,24 @@ +:orphan: + +Muscle BioAmp Candy +#################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/muscle-bioamp-candy/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst diff --git a/_static/latex/muscle-bioamp-patchy.rst b/_static/latex/muscle-bioamp-patchy.rst new file mode 100644 index 00000000..a06bedb1 --- /dev/null +++ b/_static/latex/muscle-bioamp-patchy.rst @@ -0,0 +1,18 @@ +:orphan: + +Muscle BioAmp Patchy +#################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/muscle-bioamp-patchy/index + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + diff --git a/_static/latex/muscle-bioamp-shield.rst b/_static/latex/muscle-bioamp-shield.rst new file mode 100644 index 00000000..e4bf1dc6 --- /dev/null +++ b/_static/latex/muscle-bioamp-shield.rst @@ -0,0 +1,23 @@ +:orphan: + +Muscle BioAmp Shield +######################### + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../hardware/bioamp/muscle-bioamp-shield/index + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/skin-preparation/index.rst + + +.. toctree:: + :hidden: + :maxdepth: 3 + + ../../../guides/usage-guides/using-bioamp-bands/index.rst \ No newline at end of file diff --git a/_static/searchtools.js b/_static/searchtools.js index 92da3f8b..b08d58c9 100644 --- a/_static/searchtools.js +++ b/_static/searchtools.js @@ -178,7 +178,7 @@ const Search = { htmlToText: (htmlString, anchor) => { const htmlElement = new DOMParser().parseFromString(htmlString, 'text/html'); - for (const removalQuery of [".headerlinks", "script", "style"]) { + for (const removalQuery of [".headerlink", "script", "style"]) { htmlElement.querySelectorAll(removalQuery).forEach((el) => { el.remove() }); } if (anchor) { @@ -328,13 +328,14 @@ const Search = { for (const [title, foundTitles] of Object.entries(allTitles)) { if (title.toLowerCase().trim().includes(queryLower) && (queryLower.length >= title.length/2)) { for (const [file, id] of foundTitles) { - let score = Math.round(100 * queryLower.length / title.length) + const score = Math.round(Scorer.title * queryLower.length / title.length); + const boost = titles[file] === title ? 1 : 0; // add a boost for document titles normalResults.push([ docNames[file], titles[file] !== title ? `${titles[file]} > ${title}` : title, id !== null ? "#" + id : "", null, - score, + score + boost, filenames[file], ]); } diff --git a/bioamp-exg-pill.pdf b/bioamp-exg-pill.pdf index 7959e443..17bc22d0 100644 Binary files a/bioamp-exg-pill.pdf and b/bioamp-exg-pill.pdf differ diff --git a/bioamp-v1.5.pdf b/bioamp-v1.5.pdf index 1b84e835..5845e255 100644 Binary files a/bioamp-v1.5.pdf and b/bioamp-v1.5.pdf differ diff --git a/bioamp-exg-pill.html b/courses/index.html similarity index 70% rename from bioamp-exg-pill.html rename to courses/index.html index 59b0c45f..9f0bdaf8 100644 --- a/bioamp-exg-pill.html +++ b/courses/index.html @@ -2,13 +2,13 @@ - + - BioAmp EXG Pill — upsidedownlabs.github.io documentation + Courses — upsidedownlabs.github.io documentation @@ -18,40 +18,43 @@ - - - + + + - - - - + + + + - - - - + + + + - - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + - + @@ -85,7 +88,7 @@
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  • BioAmp EXG Pill
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BioAmp EXG Pill#

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Courses#

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- + @@ -663,7 +717,7 @@
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- Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

diff --git a/courses/open-ephys/exday1-nokit.html b/courses/open-ephys/exday1-nokit.html new file mode 100644 index 00000000..2a857c3c --- /dev/null +++ b/courses/open-ephys/exday1-nokit.html @@ -0,0 +1,990 @@ + + + + + + + + + + + Exercises Day 1: No Hardware — upsidedownlabs.github.io documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Exercises Day 1: No Hardware#

+ +
+

1. Using a multimeter#

+

We will be using a circuit simulator to model the different settings on a multimeter. A multimeter can be used to measure voltage, resistance, and current.

+
+

Exercises

+

First we will measure resistance of a resistor.

+
+../../_images/ohmmeter_sim.png +
+

Setup:

+
    +

  • Add an Ohmmeter to the circuit (Draw/Outputs and Labels/Add Ohmmeter).

    • +

  • Connect it to the resistor and Run the simulator.

    • +

  • Right-click on the Ohmmeter, select ‘View in New Scope’.

    • +

  • Set the scope to display resistance values instead of voltage. Right-click on the scope and select ‘Properties’. Select ‘Show Resistance’ instead of ‘Show Voltage’.

    • +
+

1A. Read the value of the resistor in Ohms from the scope.

+

Now we will measure the voltage across two batteries.

+
+../../_images/voltmeter_sim.png +
+

Setup:

+
    +

  • Add a Voltmeter to the circuit, connect it across the batteries, and run the simulator.

    • +

  • What voltage do you measure?

    • +

  • How can you get the Voltmeter to give a negative voltage measurement?

    • +
+
+
+
+

2. Measuring voltages#

+
+

Exercises

+

Take a look at this simulation. A voltage output signal is being generated on the left, which turns an LED on and off at a specific frequency. Our goal is to measure the properties of this voltage output.

+
+../../_images/squarewave_sim.png +
+

2A. Connect a voltmeter across the LED. This is similar to using a multimeter in the lab. What is the amplitude of the signal in Volts? With what frequency does the signal change amplitude?

+

2B. Visualise the voltage across the LED in a new Scope. This is similar to using an oscilloscope in the lab. Is the voltage measured different now? With what frequency does the signal change amplitude, how would you describe the shape of this signal?

+

2C. What are the advantages of an oscilloscope over a multimeter?

+

2D. Change the voltage signal so that it outputs a 50Hz sinewave.

+
+
+
+

3. Ohm’s Law#

+

Ohm’s law describes how potential (V), current (I) and resistance (R) are related:

+
+\[V = IR\]
+

When looking at a whole circuit, we can use this to calculate how much current will flow. Here is a simple circuit with a battery and two resistors. Current flows from the positive terminal of the battery to the negative terminal of the battery. The resistors are ‘in series’ as there is only 1 path for current flow.

+
+../../_images/resistors_series_sim.png +
+
+

Exercises

+

3A. Click on the image to go to the simulator. +Right-click on the top wire in the circuit, and then select Edit to display the current through that wire. Double-click on either of the resistors to decrease their value. What happens to the current in the circuit?

+
+
+
+

4. Resistors#

+

Here’s another simulation demonstrating Ohm’s law. This time, the current moves from a 5 Volt voltage source (bright green) into ground (grey, earth), across one of two resistors. The resistors are ‘in parallel’ as current can flow cross over one or the other resistor.

+
+../../_images/resistors_parallel_sim.png +
+
+

Exercises

+

Setup:

+
    +

  • Click the image open the simulator.

    • +

  • Right click on a resistor and select ‘View in new scope’.

    • +

  • Do the same for the other resistor. You can click ‘Reset’ to restart the simulation and synchronise the scopes.

    • +
+

4A. What do you predict will happen to the voltage over the left resistor if you double its resistance? What will happen to the current?

+

4B. What will happen to the voltage and current over the right-hand resistor when the other doubles in resistance?

+

Now double the value of the left-hand resistor in the simulator and see if your predictions were correct.

+
+
+
+

5. Voltage Divider#

+

Voltage is always measured relative to a point that we consider 0V. For a battery, the negative terminal is 0V.

+

Voltage (potential energy) ‘drops’ over each resistor, as potential energy is converted to another form of energy such as heat or light. In a circuit powered by a 9V battery, all 9V of potential energy from our battery source must drop over circuit components, to return to 0V at the negative terminal of the battery.

+

In each circuit below, the current through R1 must equal the current through R2, as they are resistors in series. Following Ohm’s law, given the same current, a higher resistor will have a higher voltage drop (V=IR). The total voltage drop over the circuit must equal the provided voltage.

+
+../../_images/voltage_divider.png +
+

Therefore, in a circuit with multiple resistors in series, the ratio of their resistances determines how much voltage will drop over each. We can therefore split up (divide) the voltage from a source across resistors to produce an output voltage Vout:

+
+\[|Vout| = |Vin| \frac{R2}{R1+R2}\]
+
+

Exercises

+

5A. Using the simulator (here’s an empty full-screen https://tinyurl.com/y477e9qd) build a voltage divider circuit in which you use:

+
    +

  • a 3V battery (‘Draw’ a 1-terminal voltage source set to 3V)

    • +

  • 2 resistors

    • +

  • a readout wire (right click and ‘Edit’ to show the voltage Vout)

    • +
+

To provide an 2.1V output voltage Vout at the readout wire.

+

5B. Change the ratios of the resistors until the readout voltage is the size of an action potential measured in the extracellular fluid.

+
+
+
+

6. Capacitors#

+

There are two types of capacitor. Polarised capacitors must be used in a specific orientation. Usually, ceramic capacitors are not polarised and you can use them in either direction, whereas tube-shaped electrolytic capacitors are polarised. The negative pin is indicated by a ‘-’ marking, and the positive leg is often longer.

+

As discussed in the Theory handout, capacitors occur wherever charge can be separated along two conducting surfaces, separated by an insulating material that prevents the plates from touching. Cell membranes are capacitors, as are electrodes.

+
+\[Q = C * V\]
+

The amount of charge (Q) a capacitor can separate depends on is its capacitance (C, measured in farads) and the voltage (V) across the capacitor.

+
+../../_images/capacitor_membrane.png +
+
+

Exercises

+

Setup:

+

The simulator shows a simplified ‘cell membrane’ represented as a capacitor and a resistor. Changing the intracellular voltage supply changes the voltage across the cell membrane. The extracellular fluid is always 0 V.

+

6A. The initial voltage over the capacitor should be -72mV. If not, set the Voltage slider to around -70mV. Click ‘Reset’ to see current move through the circuit until the capacitor is charged to 72mV. Which direction is the current flow? Why does current stop moving?

+

6B. Using the ‘Voltage’ slider, set the voltage supply to 0 mVolts, and then to 20mV. What happens to the current flow in the circuit?

+

6C. Can you mimic an action potential by changing the intracellular voltage?

+
+
+

Exercises

+

In this simulation, you can charge and discharge a capacitor and see the current flow through the circuit.

+
+../../_images/charging_cap_sim.png +
+

6D. Modify the simulation to power an LED (Draw/Outputs and Labels/Add LED) by the capacitor as it discharges. The simulator will turn the LED red when it is on.

+

6E. Visualise the charging and discharging of voltage over the capacitor. How can you make the charging and discharging slower?

+

6F. Increase the capacitance value of the capacitor. How long does it take the capacitor to discharge?

+
+
+
+

7. Alternating signal (AC)#

+

Batteries provide ‘direct current’ in a single direction. In contrast, the action potentials and LFPs we measure from neurons can go in both directions; they are alternating currents. You produced an alternating current yourself in exercise 6C.

+

Alternating currents have a frequency, which is the rate at which they alternate direction. Action potentials have a very high frequency, whereas synaptic inputs and their sums are much slower.

+

Here is a demo where an alternating signal increases and decreases in frequency. At the bottom of the page, you can see the wave visualised.

+
+

Note

+

When you have capacitors in the simulator, it is a good idea to click ‘reset’ whenever you make changes, as they will otherwise store charge and can create weird effects.

+
+
+

Exercises

+

7A. Press ‘Play Audio’ to hear how the sound is modulated as the frequency increases.

+
+../../_images/audio_sweep.png +
+
+
+
+

8. Impedance#

+

Alternating currents have a frequency, so we need to use the term ‘Impedance’ (Z) instead of ‘Resistance’ to describe how circuit components oppose current flow. See the theory handout for more information.

+

The impedance magnitude of a capacitor, also called reactance (Xc), depends on:

+
+\[Xc = \frac{1}{2 \pi fC}\]
+

Where f is the frequency with which the current alternates, and C is the capacitance.

+

The impedance provided by capacitors varies with frequency. Because we are interested in signals at specific frequencies (e.g. 1000Hz for action potentials), we have to make sure to build our recording circuit so that the frequencies we are interested in experience little opposition.

+

When you see a capacitor in a circuit, you know you need to think about the frequency of the signal. Steady direct current has no frequency, so Xc is infinite: capacitors only pass alternating signals.

+
+

Exercises

+
+../../_images/cap_freq_circuits.png +
+

Setup:

+

Here are two circuits with an alternating voltage source of 15 and 40 Hz, respectively. In the oscilloscope at the bottom of the simulator, the voltage trace of the source and the capacitor are plotted.

+

8A. Visualise the current in the circuit (for instance the current flowing through the stretch of wire). You could add a new scope to do this or double-click the wire and ‘show current’. Which circuit has higher amplitude current?

+

8B. Add a third circuit, powered by an alternating voltage source of 120 Hz. What happens to the current as the frequency increases?

+

(Bonus question: what happens to the voltage drop across the capacitor as frequency increases?)

+
+
+
+

9. Capacitive voltage divider#

+

Because capacitors impede current flow, we can use them to build voltage dividers, just like the resistor divider shown above.

+
+

Exercises

+
+../../_images/cap_voltage_div.png +
+

9A. Change the capacitance values C for the first capacitor to test whether the formula for the resistor voltage divider applies for capacitors.

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Exercises Day 2: No Hardware#

+ +
+

1. Capacitor and Resistor in parallel#

+

In the circuit below, you will see a capacitor and a resistor in parallel. The voltage source alternates at 20Hz, going from -10 to +10 volts. The current travels over the resistor or via the capacitor to ground.

+
+../../_images/cap_res_parallel_sim.png +
+
+

Exercises

+

1A. Increase the value of the resistor to 200kOhm. What happens to the current through the resistor?

+

1B. Put the resistor back to 10kOhm. Now, increase the capacitance of the capacitor to around 10mF. What happens to the current?

+

1C. Return the values to 10kOhm and 100nF.

+

Change the frequency of the alternating signal to

+
    +

  • 1000 Hz (action potentials!)

    • +

  • then to 1 Hz

    • +
+

You may have to change the simulation speed using the red slider at the top right, and adjust the x-scaling of the scope below (right-click / properties / and slide the ‘horizontal scale’).

+

How does the frequency of the signal relate to how much current crosses either the capacitor or the resistor?

+
+
+
+

2. The equivalent circuit of the electrode#

+

In the theory handout, we discussed how we can represent an electrode as a circuit containing a resistance and a capacitance. We’ll now build this equivalent circuit in the simulator.

+
+

Exercises

+

2A. In the simulator, edit the circuit used above to build the equivalent circuit of a polarised, tungsten electrode. See the theory handout for more details.

+

Here are some values to use:

+
    +

  • Rm: the DC resistance of the metal electrode wire, 10-100 Ohms.

    • +

  • Ce: the electrode tip capacitance, generated by the double layer generated around the electrode. Ce ~ 0.2 pF / µm2, so 10 - 20 pF (if the electrode is unplated)

    • +

  • Re: electrode tip resistance, in parallel with Ce. ~ 100 MOhm.

    • +

  • Edit the alternating voltage supply to provide 1V at 1Khz, mimicking the signal coming from your cell. 1V is larger than ephys signals, but makes the current flow easier to see. Change the sliders for simulation speed and current speed until you can see where the current is flowing.

    • +
+

2B. What happens if you delete the resistor Re?

+

2C. Bonus exercise: Can you change this circuit from a polarising, tungsten electrode, to a circuit representing a nonpolarizable electrode?

+
+
+
+

3. Shunt Impedance#

+

Here is the circuit of the electrode with a shunt impedance added of 100 pF:

+
+../../_images/day2circuit.png +
+
+

Exercises

+

3A. What is shunt impedance here?

+

3B. What % of our signal are we losing between Vec and Vin? Why?

+

3C. What could we change to increase the signal at Vin?

+

3D. The tips of certain electrodes, e.g. nichrome tetrodes, can be electroplated in a thin layer of gold. This ‘goldplating’ increases the surface area of the tip, creating more space to separate charge. This increases tip capacitance by around 100x. Make this change in the circuit simulator. How similar are Vec and Vin now?

+
+
+

Recording Circuit#

+

To actually perform a recording, we will have to attach the electrode to the rest of an acquisition system. The recording system has an analog to digital converter (ADC), and a recording computer. The leakage resistance here is where the recording system is connected to ground.

+
+../../_images/day2withac.png +
+
+

Exercises

+

3E. How much of the voltage at the electrode, Vec, are we recording at Vout?

+

3F. Add a headstage to this circuit, by placing an ideal operational amplifier between the electrode and the long wire. What happens to Vout? Why?

+

3G. Change the circuit to stop the amplifier from saturating. What is the amplifier gain now?

+
+
+
+
+

4. Operational Amplifiers#

+
+

Voltage rails#

+

In the simulator, ‘ideal’ operational amplifiers are shown without their power supplies. However in real life, we need to provide our op-amp with power. We will use batteries to make voltage ‘rails’. We are going to make a -3V and +3V rail using simulated AA batteries that provide 1.5V each.

+

To do this we use a common trick and turn two regular power supplies into a bipolar power supply.

+
+../../_images/bipolar_power_supply.png +
+
+

Exercises

+

4D. Using 4x 1.5 DC voltage supplies simulated batteries, connect them together so that you have a +3, 0, and -3 power supply.

+
+../../_images/aa_batteries_sim.png +
+

4E. Replace the ‘ideal’ op-amp with a ‘real’ op amp in the simulator. Use a bipolar power supply to power it. What amplitude values do you get as output now? How is it different to the ideal op amp?

+
+
+
+

Bypass capacitors#

+

Bypass capacitors are small capacitors that act like little secondary batteries. The batteries we use have a high ESR - ‘equivalent series resistance’, and some capacitance. This means that are not great at quickly providing current. Because of this, when our op-amp starts working, it can run out of current for a very short time until the battery can drive the rails back to their original voltage. This is bad for the signal quality.

+

So, we allow these small capacitors to charge. If the battery briefly can’t provide current, the bypass capacitors will discharge, providing quick back-up current. We’re exploiting the fact that these caps have very low ESR and can provide current pretty much instantaneously. The fact that they’re too small to power anything for more than a millisecond does not matter here, at that point the batteries have caught up.

+
+

Exercises

+

4F. Add bypass capacitors to the simulation based on where they are in the bipolar power supply pictured here:

+
+../../_images/fritz_bipolar_power_supply.png +
+
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Extracellular Electrophysiology Acquisition#

+
+

Introduction#

+

This course is designed to provide a thorough understanding of extracellular electrophysiology, a branch +for studying the electrical activity of neurons and other excitable cells. It includes recorded lectures with hands-on +electronics exercises to ensure that you gain both theoretical knowledge and practical skills.

+
+

Note

+

We want to thank Open Ephys team for creating this course. Their hard work and expertise in developing and sharing this +material are greatly appreciated. You can find the original course at OE Ephys Course.

+
+
+
+

Materials for students#

+

The course consists of 2 segments - Theory and experiments. Read the theory segments carefully before performing the experiments to get a better understanding of all the concepts.

+

To read before Day 1:

+ +
+

Day 1: Detecting Signals#

+
+ +
+
+
+

Day 2: Protecting and Amplifying Signals#

+
+ +
+
+
+

Day 3: Referencing and Grounding#

+
+ +
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+
+

Day 4: Synchronization and Digitization#

+
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Theory Day 1#

+ +
+

Introduction#

+

Welcome to the Open Ephys Cajal course on extracellular electrophysiology acquisition!

+

The goal of electrophysiology (‘ephys’) is to record signals generated by electrically active cells. There are many different +types of acquisition systems and setups, but they are built upon the same principles. +By understanding these fundamental ideas, we hope you will be able to see past branding and tradition, and decide for yourself what +you need your setup to be able to do.

+
+
+

Talk: Introduction#

+
+
+
+

Types of extracellular electrophysiology#

+

Several biological processes in the body generate time-varying electrical signals that we can measure outside of cells, such as skeletal muscle contraction (electromyography, EMG), or the heartbeat (electrocardiogram, ECG). In systems neuroscience, we often use intracranial electrodes to measure action potential firing (spikes) or local field potentials (LFP). Electrodes outside the skull allow us to detect the electroencephalogram (EEG) non-invasively.

+

Most of the theory in this course will focus on intracranial extracellular recordings of neuronal activity, as these are the most common in systems neuroscience. For the practical exercises, we will be building an EMG recording circuit, as it is straightforward to test on yourself.

+ + ++++++ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
Table 1: Overview of Extracellular Electrophysiology Methods#

Technique

Signal

Electrodes

Typical amplitude

ECG/EKG

Heart: Depolarisation/repolarisation of cardiac tissue

Surface electrodes

mV range

EMG

Skeletal muscle: A train of motor unit action potentials.

Surface electrodes placed on skin above muscle, reference electrode on skin above bone.

mV range

EEG

Brain: Summations of slow neural activity

Surface electrodes on scalp

50 µV

LFP

Brain: Summations of slow neural activity

Intracranial electrode

100-1000 µV

‘Spike’ recording

Brain: Action potentials (fast ‘spikes’) from individual neurons

Intracranial electrodes, e.g. tetrodes (4 insulated wires twisted together), Single-wire electrodes, Silicon probes.

20-200 µV

+
+
+

Electronics Refresher#

+
+

Charged particles exert electric force#

+

Electric signals in organic tissues are generated by positively charged (Na+, K+, Ca2+) and negatively charged (Cl-) ions. Electrons are negatively charged particles in our electrodes and wires (i.e., metal).

+

All charged particles exert an electric force on other charged particles. Coulomb’s law (Eq 1) describes that this force will have both magnitude (it will be bigger if the charges are larger or closer together) and direction (it will either attract or repel, depending on whether the charges have different or the same polarity).

+
+\[F= k\frac{q1q2}{r^2}\]
+

Equation 1: F = electric force, k = Coulomb constant, q1 + q2 = charges, r = distance of separation

+
+Representation of a positive and negative charge being attracted towards each other, and two positive charges being repelled from each other. +
+

Figure 1: The magnitude of electric force between charges depends on their charge and the distance between them.#

+
+
+

We often represent electric force using electric field lines surrounding the particle. These lines show that charges in the vicinity of the particle will be influenced by its force, and that this influence has a particular direction.

+
+A single positive charge represented as a circle, surrounded by a gradient (which is darkest close to the charge) representing the strength of the electric force, and electric field lines radiating out from the charge. +
+

Figure 2: Electric field lines show the direction of the force on a positive charge. Colour intensity represents electric potential#

+
+
+

If a charged particle is free to move and placed within an electric field, then the electric forces acting on it will cause it to move in a certain direction. An example is an ion in the cytoplasm; if not bound to a membrane, this ion will be moved by electric forces it experiences.

+
+
+

Currents are moving charges#

+

Moving charges create a current (I) measured in amperes. The current tells us how much charge is moving per second.

+
+\[I = \frac{Q}{t}\]
+

Equation 2: Current (I) is equal to charge (Q) over time (t).

+

By convention, the direction of this current is always the direction of positive charge movement. When currents are generated by a negatively charged ion, such as chloride, we describe them as a positive current moving in the opposite direction to the chloride ion.

+
+
+

Electric Potential Difference#

+

Figure 3 shows a negative and positive charge that are held in a certain position in space. These large charges are not allowed to move, but still exert an attracting force on each other. If we let them, they would move towards each other. We can see that their electric forces will interact.

+
+../../../_images/electric_potential.png +
+

Figure 3: Electric potential mapped around a positive and negative charge#

+
+

© 2010 Geek3 /CC BY-SA 4.0

+
+
+
+

Each point in this image has a value that describes the electric potential at that point, represented by colour. If free to do so, positive charges will move from areas of higher potential to areas of lower potential. Just as a difference in gravitational potential energy can cause a river to flow down a mountain, a difference in electric potential can cause charged particles to flow from a region of higher potential towards a region of lower potential until the charges no longer experience a net electrical driving force. In an electric circuit, the driving force is therefore a difference in electric potential between two points.

+
+

+
+

The bigger the difference in electric potential between A and B, the higher the driving force on the charges. If there is no difference in electric potential, no net charges will move (no current). Our driving force is therefore the Electric Potential Difference between two points, measured in volts and often referred to as ‘voltage’.

+
+

+
+

If we placed a +1 ‘test’ charge at any point in this space, it would experience a net electric force; some influence from the + charge, some influence from the negative charge. The vector description of the magnitude and direction of that force is the electric field, and is shown as field lines on Figure 3.

+
+

+
+

The electric potential is different to the electric field. While the electric field has both magnitude and direction, the electric potential only has magnitude, and is represented as colour in Figure 3. High, (orange) positive electric potential surrounds our positive charge, and low (blue) negative potential surrounds our negative charge.

+
+

+
+

If we placed our positive +1 test charge at an area of high potential, like point ‘A’, it would follow the gradient of the electric potential until it reached the negative particle at point ‘B’. The difference in electric potential between point A and B therefore generated a current (a moving charge). We could use that converted potential energy to power something else.

+
+

+
+

In contrast, to move the same particle from point B to point A, we would need to provide additional energy to counteract the repelling force generated by the positive point charge. The difference in electric potential between two points tells us how much energy we need to move a charge from one place to another. If we were to add more point charges (that are not allowed to move) to this image, their generated forces will sum, giving a more complex map of electric potentials at every point in space.

+
+

+
+

Because it is defined as a difference between two points, voltage always has to be measured between two points. When we do extracellular recordings, we measure the electric potential difference between the tip of our electrode and our ground or reference point.

+
+

Where is 0 volts?#

+

To describe the height of a mountain, there is no such thing as absolute altitude; instead, we use ‘sea level’ as our point 0 and measure from there. A similar thing goes for voltage. We pick a point to call ‘0 V’ and compare the rest of the circuit to that. This point can be the negative terminal of a battery, the extracellular fluid, or a point at infinity, far from all sources of electric potential (Einevoll et al., 2013).

+
+

+
+

The terms ground, reference, and earth are often used interchangeably, but are not quite the same thing.

+

Reference: A point in the circuit that you labelled 0V, so that you can measure the other values from there.

+

Ground: Often used as a reference point and considered 0V, but has the additional capacity to provide (source) or get rid of (sink) a lot of current, without its own potential changing.

+

Earth: The actual planet earth is the best ground we have. Metal poles in the earth are used to sink current from lightning bolts because the sheer size of the earth means that such a tiny bit of extra current is not a problem, and won’t change the potential of the earth.

+
+
+
+

Resistance#

+

Resistance opposes current flow. The electric potential difference (V) drives a current (I) from point A to B across a resistance (R). A resistance can be measured between any two points A and B; it may be so high as to be infinite in which case we consider the points isolated from each other. The resistance may be very low, such as in a wire, in which case we consider the two points short circuited.

+

This is described by Ohm’s law:

+
+\[I = V/R\]
+

Equation 3: Current (I) is equal to voltage (V) over resistance (R).

+
+
+

Capacitance#

+

Capacitors for use in electronics are made of two conducting plates, separated by a thin layer of insulating material that prevents the plates from touching. When a capacitor is connected to a voltage source, such as a battery, charges collect on one of the plates. The charges cannot move through the insulating layer, but they can exert a force through it. This electric force pushes away similar charges on the opposite plate. This movement of charge is what gives us current flow in the circuit, even though charges cannot flow directly through the capacitor.

+
+\[Q = C * V\]
+

Equation 4: The amount of charge (Q) a capacitor can separate depends on is its capacitance (C, measured in farads) and the voltage (V) across the capacitor.

+
+two capacitors are represented as vertical lines. The left capacitor is uncharged, and has balanced positive and negative charges on each side represented as circles with +1 or -1 charge. The capacitor on the right has been charged; a voltage has been applied and now the positive charges are aligned on one side of the plate, and the negative charges on the other. +
+

Figure 4: An uncharged capacitor has no net charge on either plate (left). A charged capacitor separates charges with positive charges on one plate, and negative charges on the other (right).#

+
+
+

In a direct current circuit, current will flow while the capacitor charges, as charge is pushed or pulled on either plate. Current flow will stop once the capacitor is fully charged. This electric charge can be discharged (and, for instance, used to power something) by providing a path that connects the positive and negative charges of the capacitor.

+
+
+

Impedance#

+

A battery provides a positive current flow in a single direction. In contrast, neuronal currents can move both towards and away from our measuring electrode. After all, Na+ ions can both enter and exit the cell. Neuronal signals are therefore alternating signals. The frequency of an alternating signal tells us how often the direction of flow changes. The power supply in buildings is also alternating: the current direction switches at a fixed frequency, producing a sinewave (the notorious 50/60Hz frequency noise in ephys recordings).

+

For alternating signals, we need to use impedance (Z) to describe opposition to current flow, instead of using resistance. The impedance represents opposition to current flow measured in both magnitude and phase, which allows us to describe the relationship between voltage and current for time-varying signals. We can measure the impedance of a component at different frequencies, so that we understand both the magnitude and phase relationship between V and I over a broad frequency range (from 1 Hz to 10 kHz). Let’s examine the response of resistors and capacitors to an applied sinusoidal voltage (an alternating signal).

+
+

Impedance: Resistors#

+

For resistors, the impedance magnitude (Z) is constant and does not vary with the frequency of signal applied. The impedance follows Ohm’s Law (V = IR), which doesn’t take the frequency of the signal into account.

+
+
+

Impedance: Capacitors#

+

In contrast, for a capacitor, the magnitude of impedance decreases as the frequency increases (see Eq 5). We can therefore only describe the impedance of a capacitor at a specific frequency. A second component of impedance is phase offset; in capacitors, the current is 90° out of phase with the voltage. This second aspect of impedance is not within the scope of this course.

+
+\[Zc = \frac{1}{2 \pi fC}\]
+

Equation 5: The magnitude of impedance of a capacitor (Zc) will decrease with increasing frequency (f). The larger the capacitance (C), the lower the impedance at a specific frequency.

+
+
+
+
+

Equivalent circuits in the brain#

+

Let’s apply the electronics concepts above to our neuronal tissue. Neuronal activity relies mainly on ions such as Na+, K+ and Ca2+. Whenever these charges flow, we have a current. In neurons, our resistance to current flow is largely formed by the permeability of the cell membrane to our ion, and changed by opening or closing ion channels in the membrane. When more channels open, the resistance to a certain ion is lowered, and the charge is able to flow in or out of the cell.

+

The driving force in this scenario is the membrane potential, i.e. the difference in electric potential between the inside of the cell membrane and the extracellular fluid. A neuron typically has a resting membrane potential of around -70 mV compared to the extracellular fluid, if we decide that the extracellular fluid has 0 V.

+

In addition to electric forces, ions in neurons are affected by a second driving force; concentration gradients. Ions will tend to diffuse away from areas where there is a high concentration of the ion, to areas with a lower concentration. The interaction of the concentration and electrical driving forces is the electrochemical gradient and this balance is described by the Nernst equation. This will not be covered in this course, but Wright 2004 provides a clear refresher on this, and to understand how the -70mV is maintained by the cell.

+
+

Neuronal output: Action Potentials#

+

Input signals to the neuron can trigger the opening of voltage-dependent Na+ ion channels, greatly reducing membrane resistance to Na+. This allows Na+ to follow its concentration and electrical gradient, an travel from outside the cell, where the Na+ concentration is high, to the inside of the cell, where Na+ concentration is low and the intracellular medium has a lower potential (Kandel, Schwartz, & Jessel, 2000). In neurons, voltage-sensitive Na+ channels are usually concentrated at the initial segment of the axon, and it is therefore more likely that an action potential will be generated there, rather than in other regions of the cell. The subsequent opening of K+ channels begins the process of returning the membrane potential to resting conditions (Hodgkin and Huxley, 1939).

+
+
+

Neuronal input: Postsynaptic potentials#

+

Slower frequencies in extracellular recordings are the focus of the LFP or EEG. These are thought to be largely generated by postsynaptic potentials, as these occur over slower timescales (10s of ms) than the action potential (1-2 ms), so there is more opportunity for signals from multiple cells to summate and result in larger signals. When activated, AMPA and NMDA synapses mediate excitatory currents as Na+ and Ca2+ enter the cell.

+
+
+

Capacitors in the brain#

+

The definition of a capacitor was described above. This configuration of two conducting materials separated by a thin, insulating layer, does not only happen in specifically designed electronics components, but can occur anywhere. One example is the neuron, where both the intracellular and extracellular medium are conductive, but the cell membrane is not. The cell membrane is therefore also a capacitor, and charge can be separated along the membrane depending on the potential difference between the inside and the outside of the cell.

+

Remember that:

+
+\[Q = C * V\]
+

The amount of charge (Q) a capacitor can separate depends on is its capacitance (C, measured in farads) and the voltage (V) across the capacitor. That means that when the voltage across the cell membrane is reduced (i.e. the cell depolarises), the ability for the membrane to store charge is also reduced. These charges are released from the membrane and generate capacitive currents (see Fig 5 below).

+

Importantly for acquisition systems, cables are capacitors too; imagine a cable containing two wires. These wires are conductive, and are separated by a thin layer of insulation. These wires will separate and release charge depending on the electric potential difference between them.

+
+
+

Extracellular measurements#

+

When we perform extracellular recordings, we are measuring the electric potential induced at the electrode (Velectrodeor Vec ) by these currents. The effect on the induced electric potential depends on the magnitude, sign and location of the current sources, and on the conductivity of the extracellular medium (Buzsaki et al., 2012; Nunez and Srinivasan, 2006). The effect of these currents diminishes with distance, depending on how well the extracellular fluid conducts electricity. The extracellular potential Vec at position re and time t, with respect to a point at infinity, can be computed with the following equation (Einevoll et al., 2013; Nunez and Srinivasan, 2006):

+
+../../../_images/point_source_equation.png +
+

Equation 6: The point source equation#

+
+
+

Conceptually, this point-source equation (Equation 6) is key for computing the extracellular potential in response to any transmembrane current (Buzsaki et al., 2012). In(t) represents the nth point current source and re – rn represents the distance between the point source and the position of measurement, with n = 1…N, where N is the number of individual point sources and ρ is the extracellular conductivity. If the extracellular medium is considered homogeneous and isotropic, we can use a constant conductivity value for the extracellular fluid (Einevoll et al., 2013).

+
+

+
+

Extracellular action potential waveforms usually last on the order of 1-2 ms, and are in the range of tens to hundreds of microvolts in amplitude, with the largest potential deflections being detected close to the soma of a neuron. These stereotypical temporal deflections of the electric potential in the extracellular space are called action potentials or spikes. The model in Fig 5 below illustrates how the electric potential varies depending on electrode location relative to a spiking neuron.

+
+

+
+

Fig 5 depicts the (modelled) time-varying extracellular potential measured at 3 different locations close to a neuron. Each extracellular waveform results from the superposition of ionic and capacitive transmembrane currents. The peaks in the potential waveforms correspond to the current (right column) that is dominant at that time-point: the first positive peak of the waveform is attributed to the positive capacitive current resulting from the strong Na+ current entering the axon initial segment; the main negative peak is attributed to the influx of Na+; and finally, the second positive peak results from repolarising K+ current flowing out of the cell (Gold et al., 2006). As the effect of a current decreases with distance, the relative position of the electrode determines the relative contribution of each current and therefore the net overall current shape (left column). For instance, if the electrode is close to the axon initial segment (where many voltage-dependent Na+ channels are), the Na+ current will be larger.

+
+../../../_images/electric_potential_spike.png +
+

Figure 5: Electric potential generated by current sources in a conductive volume.#

+
+
+
+

Note

+

Electric potential generated by current sources in a conductive volume. The extracellular potentials and currents are adapted from Gold et al., 2006. The shape of the extracellular potential waveforms at various spatial positions ‘re’ (marked with black dots) are simulated for a CA1 pyramidal neuron.

+

Currents: simulated net membrane current (first column) across the soma and proximal dendrites that best estimates the extracellular potential waveform and membrane current components in terms of Na+, K+ and capacitive currents (second column). In the soma, the positive capacitive current coincides with the larger Na+ current. At locations along the apical trunk, the initial capacitive peak becomes visible. In dendritic compartments the membrane depolarisation is initially driven by Na+ current from the soma, until local Na+ currents are activated and the action potential regenerates. In the brief time before the local Na+ currents activate, the positive capacitive current is the dominant membrane current and a capacitive-dominant phase is visible in the net current (Gold et al., 2006, adapted by Joana Neto).

+
+
+
+
+

What does an acquisition system do?#

+

There are several things that any extracellular acquisition system has to be able to do. Here is a quick overview so that you can start to imagine what the acquisition system does, but don’t worry if they don’t make sense yet. We will go through each of these points carefully during the course.

+

The extracellular electrophysiology techniques in Table 1 all share the same major goal: to measure activity occurring in biological tissue. They do that by detecting changes in electric potential due to cellular activity, compared to a reference or ground point, and by faithfully shuttling these signals to an output where the experimenter can view or record them. In most cases this output will be a computer where we can visualise and store our data.

+

The signal at the electrode is measured in volts (V) and is very small, in the microvolt range. This is tiny compared to the voltages we encounter elsewhere in the lab: for instance, a battery is around 3V, and the building main power supply 120 or 230V. The world, and your lab, is also an electrically noisy place, which you will know if you have done any ephys before. Electrical equipment, communications devices, but also just walking around (static electricity) creates electric potential differences many orders of magnitude larger than the biological signal you are trying to measure. The acquisition system needs to be designed so that it can detect our tiny signals even in the face of surrounding noise signals generated by other sources.

+
+An extracellular voltage beside a neuron is detected by an electrode. The signal coming out of the electrode is Vin. This goes into a recording system, and the output of that system is called Vout. +
+

Figure 6: The voltage at the electrode tip (Vec), the voltage after the electrode (Vin) and the voltage we read out (Vout). We can only read Vout, and must design our acquisition system so that it is as similar to Vec as possible.#

+
+
+

To know what is going on in our cells, we need as much as possible of the signal at the electrode tip (Vec) to make it through the electrode (Vin) and acquisition system and arrive at our output (Vout). If we lose signal magnitude, or lose certain frequencies because of the way our acquisition system is designed, we may miss important data or come to wrong conclusions about our cells. We therefore have to design our acquisition system to pass on signals as faithfully as possible, losing little signal to the environment.

+

An acquisition system must therefore:

+
    +

  • Detect changes in electric potential difference

    • +

  • Faithfully transfer this signal to our acquisition system output

    • +

  • Distinguish interesting biological signals from other sources of electrical noise

    • +
+
+
+

The electrode detects changes in electric potential#

+

Getting from neuronal activity (Vec) to the input to the recording system (Vin) relies first on the interface between the electrode and the extracellular space. Extracellular microelectrodes are usually made from metallic conductors. A thin insulated metal wire with an exposed tip is the most basic, and still widely used, device for in vivo extracellular recording from brains. Metals such as platinum, gold, tungsten, iridium, titanium nitride, stainless steel, iridium, iridium oxide, and alloys, nickel-chrome, platinum-iridium and platinum-tungsten have all been used in neural electrodes.

+

The transition from ion flow in the extracellular space (due to neural activity) to electron flow in the electrode is made through the double layer interface. When a metal is placed in a saline solution two phenomena occur: water dipoles close to the metal surface become oriented, and assuming the metal surface is negatively charged, the solution close to the metal surface become depleted of negative ions (anions), leaving behind a cloud of positive ions (cations). This cloud of cations screens the electric field caused by the excess of charge on the metal. Electroneutrality across the interface requires that the charge on the metal is always equal and opposite to the total charge on the solution side of the interface (Musa et al., 2012). The resulting charge distribution - two narrow regions of equal and opposite charge - is known as the electrical double layer (EDL). The double layer region (represented in pink in the schematics) has the ability to separate charges on both sides, and therefore a capacitance ‘Ce’. The double layer also opposes the direct flow of current across it, and therefore has a resistance ‘Re’.

+
+Depicts cartoon of metal and solution touching (electrode and extracellular fluid respectively). Negative ions within the metal are attracted to positive charges in the solution. +
+

Figure 7: The double layer interface between an electrode and the extracellular fluid#

+
+
+

We can describe the electrical behaviour of electrodes by making an ‘equivalent circuit’, getting rid of the specific shape or material and just representing the electrical properties of the double layer interface:

+
+The components of the double layer interface abstracted as electrical components, where the metal electrode is a resistance called Rm, the double layer interface is a capacitor and resistor in parallel called Re and Ce, and the extracellular solution is a resistance named Rs. +
+

Figure 8: The equivalent circuit describes the electrical properties of the double-layer interface between electrode and extracellular fluid#

+
+
+

In the above figure, the double layer interface between the solution and the electrode is represented by a parallel resistance and capacitance, in combination with resistances Rm (metal) and Rs (solution) in series.

+
    +

  • Re represents leakage resistance of the electrode; the charge transfer due to charge carriers crossing the electrical double layer.

    • +

  • Ce is the capacitance of the electrical double layer at the interface of the exposed metal and the solution.

    • +

  • Rm (metal) is the resistance within the electrode itself, which depends on what the electrode is made of.

    • +

  • Rs (solution) is the resistance of the fluid surrounding the electrode.

    • +
+

Because the resistance of the extracellular fluid Rs is small and independent of the electrode or acquisition system, we often simplify our equivalent circuits by leaving this value out.

+

The ratio between Ce and Re determines how current can flow. If Re is relatively small, this low resistance allows individual charges to travel directly across the electrode-solution interface, transferring between the electrode and the extracellular fluid. This current over the small Re bypasses the capacitor Ce, which we can then ignore. Electrodes with this property are called ‘non-polarised’ electrodes.

+

In contrast, if Re is very large, ions cannot cross the double layer directly. Instead, charge transfer relies on the capacitive properties Ce of the double layer. The double layer will separate charges, with negative charges inside the electrode and positive charges on the side of the extracellular fluid holding each other in place. When cellular activity causes a redistribution of ions in the extracellular fluid, the resulting increase or decrease in attractive force will recruit or release electrons in the electrode. Either direction, a current will flow inside the electrode. Electrodes with a large Re are called ‘polarised’ electrodes.

+
+

Non-polarised electrodes#

+

The silver-silver chloride (Ag-AgCl) electrode approaches the ideal nonpolarisable type. In these ‘charge transfer’ electrodes, surface-confined species are oxidized and reduced (Bard & Faulkner, 2001, Merrill et al., 2005). Non-polarisable electrodes have a small Re. This low resistance allows individual charges to travel directly across the electrode-solution interface, transferring between the electrode and the extracellular fluid. This current over the small Re bypasses the capacitor Ce, thus providing a direct path for the measurement of steady potential levels.

+
+
+

Polarised electrodes#

+

The tungsten microelectrode is considered a polarised electrode. Polarised electrodes have large Re values, in the order of several megaOhms, and so charges cannot cross the double layer. Instead, the transition from ion flow in the solution to electron flow in the electrode is capacitive. The double layer will separate charges, with negative charges inside the electrode and positive charges on the side of the extracellular fluid holding each other in place. When cellular activity causes a redistribution of ions in the extracellular fluid, the resulting increase or decrease in attractive force will recruit or release electrons in the electrode. Either direction, a current will flow inside the electrode.

+

Therefore, processes in polarisable electrodes are purely electrostatic and caused by the charging and discharging of the double layer capacitance. Although charge does not cross the interface, currents inside the recording system can flow when the potential or solution composition changes (Cooper, 1971).

+

To give an example of a polarised electrode, a tungsten microelectrode like the one used by Hubel and Wiesel in the 1950’s and 60’s has:

+
    +

  • Ce ~ 0.2 pF / um2 ~ 10 - 20 pF (unplated)

    • +

  • Re ~ 10 to 100 MOhm.

    • +

  • Rm ~ 10 to 100 Ohm (Rm= (resistivity x length)/ cross sectional area)

    • +
+
+
+
+

References#

+

Bard, A. J., & Faulkner, L. R. (2001). Electrochemical methods Fundamentals and Applications. Molecular Biology (Second, Vol. 8). John Wiley & Sons, Inc.

+

Buzsaki, G., Anastassiou, C.A., and Koch, C. (2012). The origin of extracellular fields and currents - EEG, ECoG, LFP and spikes. Nat Rev Neurosci 13, 407–420.

+

Defelipe, J., Alonso-Nanclares, L., and Arellano, J. (2002). Microstructure of the neocortex: Comparative aspects. Journal of Neurocytology 31, 299–316.

+

Einevoll, G.T., Kayser, C., Logothetis, N.K., and Panzeri, S. (2013). Modelling and analysis of local field potentials for studying the function of cortical circuits. Nature Reviews Neuroscience 14, 770–785.

+

Gold, C., Henze, D.A., Koch, C., and Buzsáki, G. (2006). On the Origin of the Extracellular Action Potential Waveform: A Modeling Study. Journal of Neurophysiology 95, 3113–3128.

+

Herculano-Houzel, S. (2009). The human brain in numbers: a linearly scaled-up primate brain. Front. Hum. Neurosci. 3.

+

Hodgkin, A.L., and Huxley, A.F. (1939). Action Potentials Recorded from Inside a Nerve Fibre. Nature 144, 710–711.

+

Kandel, E.R., Schwartz, J.H., and Jessel, T.M. (1991). Principles of neural science.

+

Markram, H., Muller, E., Ramaswamy, S., Reimann, M.W., Abdellah, M., Sanchez, C.A., Ailamaki, A., Alonso-Nanclares, L., Antille, N., Arsever, S., et al. (2015). Reconstruction and Simulation of Neocortical Microcircuitry. Cell 163, 456–492.

+

Merrill, D.R., Bikson, M., and Jefferys, J.G.R. (2005). Electrical stimulation of excitable tissue: design of efficacious and safe protocols. Journal of Neuroscience Methods 141, 171–198.

+

Meyer, A.C., and Moser, T. (2010). Structure and function of cochlear afferent innervation. Curr Opin Otolaryngol Head Neck Surg 18, 441–446.

+

Musa, R. (2011). Design, fabrication and characterization of a neural probe for deep brain stimulation and recording.

+

Musa, S., Rand, D.R., Cott, D.J., Loo, J., Bartic, C., Eberle, W., Nuttin, B., and Borghs, G. (2012). Bottom-Up SiO2 Embedded Carbon Nanotube Electrodes with Superior Performance for Integration in Implantable Neural Microsystems. ACS Nano 6, 4615–4628.

+

Nelson, M.J., Bosch, C., Venance, L., and Pouget, P. (2013). Microscale Inhomogeneity of Brain Tissue Distorts Electrical Signal Propagation. J. Neurosci. 33, 2821–2827.

+

Nunez, P.L., and Srinivasan, R. (2006). Electric fields of the brain: the neurophysics of EEG (Oxford ; New York: Oxford University Press).

+

Obien, M.E.J., Deligkaris, K., Bullmann, T., Bakkum, D.J., and Frey, U. (2015). Revealing neuronal function through microelectrode array recordings. Front. Neurosci. 8.

+

Ray Cooper. (1971). Recording Changes in Electrical Properties in the Brain in Methods of Psychobiology. (R. D. Myers, Ed.) (Volume 1). London and New York: Academic Press.

+

Wright, S. (2004). Generation of resting membrane potential. Adv Physiol Educ. 28: 139-142.

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Theory Day 2#

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Yesterday, we said that an acquisition system must:

+
    +

  • Detect changes in electric potential difference

    • +

  • Faithfully *transfer* this signal to our acquisition system output

    • +

  • Distinguish interesting biological signals from other sources of electrical noise

    • +
+
+

Impedance ratios determine signal transmission#

+
+../../../_images/black_box_recording_system.png +
+

The signal Vec (V electrode) is measured at the electrode tip. Vin is the voltage that enters the acquisition system. Vout is the signal output of the acquisition system. Faithfully transferring the signal means not losing (much) signal between Vec, Vin, and Vout. This is all based on the idea of voltage dividers; that the voltage between two impedances in series will be determined by the ratio of their impedances.

+
+

+
+
+
+

Why is impedance important?#

+

The figure below includes the equivalent circuit of the electrode, as discussed yesterday. The signal Vec must travel through the electrode, to Vin, the voltage before the acquisition system itself. From there, currents coming from our neurons travel to ground. They can do so either by passing through our acquisition system, or (in parallel) they can be lost to ground through shunt impedance. Shunt impedance is primarily capacitive (see section below) and represented as (Cs). Shunt capacitances are created by cables or the sides of electrodes; they are accidental but unavoidable capacitances in the system.

+
+equivalent circuit of the electrode, with a subsequent capacitance to ground representing shunt capacitance +
+

We can replace these components with a representation of the impedance (Z) they provide.

+
+equivalent circuit of electrode, shunt capacitance and acquisition system with each component represented as an impedance. +
+

The impedance of the shunt capacitance, Zcs and the impedance of the acquisition system Za are impedances in parallel. +We can simplify our circuit by combining their impedances and calling it Za’.

+
+The electrode impedance and the shunt+amplifier impedance in series, showing how these two parts form a voltage divider. +
+

This gives us a voltage divider, similar to the one we built before, where:

+
+\[Vin = \frac{Za'}{Za'+Ze} Vec\]
+

The ratio of Ze and Za’ therefore determines how much of our electrode tip voltage Vec reaches Vin.

+

To get more of our voltage Vec into our recording system, we want to keep electrode impedance Ze low, and system input impedance Za’ very high.

+

If Za’ is not substantially greater than Ze, Vin will be much lower than Vec. To have high Za’, we need amplifiers with high input impedance and high shunt impedance.

+
+
+

Electrode Impedance#

+

The impedance of an electrode is a measure of its ability to resist the flow of charge across the electrode-solution interface (i.e., across the electronic conductor (metal) and ionic conductor (extracellular fluid)). It is the impedance of the whole electrode equivalent circuit we built yesterday, consisting of the resistance of the electrode metal (Rm) and the resistance (Re) and capacitance (Ce) of the double layer at the electrode-solution interface.

+
+../../../_images/circuit_double_layer_interface.png +
+

In polarized electrodes, the large Re prevents much current from taking this route. Therefore, in practice, the electrode is primarily the double-layer capacitor Ce in series with Rm and Rs (Robinson, 1968).

+

So far, we know that the impedance magnitude of a capacitor decreases with increased capacitance, and that electrode impedance is dominated by double layer capacitor, Ce. Therefore, to decrease our electrode impedance, we need to increase the electrode capacitance Ce. +How can we increase the value of Ce?

+
+\[C = \frac{\epsilon A}{d}\]
+

The capacitance of a capacitor (C, in Farads), is proportional to the area of the capacitor plates (A) divided by the distance (d) between them. ε is the electrostatic constant.

+

To make C bigger, we can increase the surface area (A) of the electrode, for instance by electroplating a thin layer of gold on to an electrode. We can also coat electrodes with materials complemented with pseudo-capacitance, such as conducting polymers or transition metal oxide films, such as IrOx (Green, Lovell, Wallace, & Poole-Warren, 2008; Musa, 2011).

+

Electrode impedance magnitude is usually measured at 1 kHz, before and after electrode coating, allowing us to see an impedance decrease of up to 10-fold (Neto et al., 2018).

+

By increasing the capacitance (Ce) of our electrode, the electrode impedance (Ze) will be smaller, preserving more of our signal amplitude at Vin.

+
+
+

Shunt Impedance#

+

Shunt impedance is the total impedance of shunt capacitance Cs and shunt resistance Rsh. These are both routes to ground outside of the intended acquisition system. At the high frequencies (1kHz) we are interested in, the capacitive component will have relatively low impedance. It will therefore have more effect than the resistive component, so Rsh is often ignored.

+

Remember that any two conducting surfaces, with a non-conducting layer in between, is a capacitor. Shunt capacitance arises mainly from the capacitance across the thin insulation layer isolating an electrode and the surrounding electrolyte, as well as the cumulative capacitance along cables and connectors (Robinson, 1968).

+

The shunt capacitance for a tungsten wire (~50 to 100 pF) is usually higher than for a silicon probe (5-20 pF/cm). (Why? Think of what makes a capacitor, and the relative shape and conductances of these electrodes).

+
+

Try it yourself

+

Here is a model of the electrode with shunt capacitance, resistance, and amplifier in parallel to ground. You should see that either decreasing electrode impedance or increasing shunt impedance gives you a larger output voltage.

+

https://tinyurl.com/yepsdold

+
+

We want a large shunt impedance, to prevent current from flowing down this route. Being capacitive, the impedance decreases with signal frequency (Nelson et al., 2008). Therefore, to create a large shunt impedance, the shunt capacitance should be small:

+
+\[Z = \frac{1}{2 \pi fC}\]
+

However, some shunt capacitance is inevitable and often there is not much we can do about it. Because the shunt impedance is in parallel with the impedance of the acquisition system, we can focus on increasing the acquisition system impedance to give us a large Za’.

+
+
+
+

Amplifiers#

+
+

Amplifiers in the headstage prevent current being drawn#

+

A perfect 5V voltage source would always provide exactly 5 Volts, no matter what the rest of the circuit looks like. If we put a lot of high impedance components in the rest of the circuit, less current will flow, and if we put low impedance components we will get a high current.

+

A real voltage source has a bit of output impedance, which means it acts as a voltage source in series with an impedance. This is modelled here (click to view high-quality version in the simulator):

+
+voltage sources passing a resistance to ground. Real and ideal voltage sources are compared, where real voltage sources act as a perfect voltage source in series with a small resistance. +
+

That invisible, small series resistance creates a voltage divider. Though the actual source voltage is the same 5V, the apparent voltage of the source varies depending on the ratio between the output impedance of the source, and the impedance of the rest of the circuit. The lower the impedance of the components used in the rest of the circuit, the higher the relative influence of the source output impedance, and the lower the apparent source voltage (the voltage droops).

+

In our acquisition system, the voltage source is the potential changes in the extracellular fluid (Vec). The resistive and capacitive properties of the electrode create an output resistance. The relative impedance of the circuit before and after Vin influences the magnitude of the signal at Vin. If we allow a lot of current to flow from our electrode to ground, we have a low impedance circuit, which will distort our signal. We therefore need something with a very high impedance to stop current being drawn from our Vec. Amplifiers do exactly this: their high input impedance prevents current flow from the electrodes, and amplifiers provide the necessary current for the rest of the circuit from a separate source.

+
+
+

The operational amplifier#

+

The operational amplifier or op-amp is a crucial building block of our acquisition system. The amplifier has two inputs (+ and -), one output, and two power rails (e.g. a 3 and -3V power rail).

+
+an amplifier is represented as a triangle pointing towards the right. It has two inputs (+ and -) and one output. +
+
+
+

Amplifiers have high input impedance#

+

The amplifier input impedance, Zais very high. The circuit acts as though the current has to cross a very high resistor to actually enter the amplifier. The current flow therefore becomes very low (Ferree et al., 2001), preventing us from drawing much current from the electrode to ground.

+

Here is the amplifier added into our circuit diagram:

+
+../../../_images/circuit_electrode_shunt_amp.png +
+
+
+

Amplifiers have low output impedance#

+

The output impedance of amplifiers is very low, which means that a lot of current can flow from the amplifier. This current enables the driving of the signal through all the subsequent circuits (e.g., interconnect lines, multiplexer, and ADC). By placing an amplifier in our circuit, we make sure that the rest of our recording circuit is driven by current provided by the amplifier, not by current provided by the electrode tip.

+
+
+

Amplifiers output a voltage#

+

The amplifier outputs the voltage difference between the voltages at its two inputs.

+
+../../../_images/op-amp-basic.png +
+

How does it do that?

+

If the difference between its two inputs is positive, the amplifier connects its output to the positive ‘power rail’, giving a positive output voltage. If the positive power rail is 3V, the amplifier will output (pretty much) that.

+

If the difference between the two inputs is negative, the amplifier will connect its output to the negative rail, outputting -3V. While doing that, the operational amplifier draws basically no current on its inputs.

+

In this configuration, the amplifier does not distinguish between small or large differences in voltage across its inputs; it will only every output the most negative or most positive voltage it can. Another way to say that, is that it amplifies the difference between its inputs with a huge factor, also called ‘gain’. This gain is so large that the amplifier always saturates, providing either the maximum or minimum voltage it can.

+
+
+

Negative feedback prevents saturation#

+
+an amplifier with the output and negative terminal connected +
+

If we connect the output of the operational amplifier to the - input, then the following happens:

+
    +

  • Initially, if + is higher than -, the operational amplifier will output a high voltage.

    • +

  • If we connect the output back to -, the amplifier will continue to output a high voltage, but now this voltage starts to increase the value of -, bringing the value of the inputs closer together. This behaviour will keep the voltages at its + and - inputs the same.

    • +

  • Now, the - input is always actively driven to follow the voltage on the + input. This means that whatever voltage we connect to the + input can be measured just by looking at the - input (which is connected to / the same as the output). Increasing + will induce a difference between + and -, but the corresponding change in the amount of output voltage will bring - back up.

    • +
+

We can measure the voltage that at + by just measuring the output of the operational amplifier, BUT because the + input draws almost no current at all (in other words, very high input impedance), we can now measure weak signals. The output of the operational amplifier on the other hand side has very low output impedance. In other words, we can draw a lot of current from it and it will keep its voltage.

+

You can run this example in the simulator (click the image above), and see if what we said about the operational amplifier makes sense.

+
+
+

An op-amp as a headstage#

+

Our electrodes will be attached to a headstage, which contains an amplifier. This amplification step performs several functions:

+
    +

  • Prevents us from drawing current and allows to drive current to ADC and computer

    • +

  • Rejects common mode noise

    • +

  • Increases the range of the signal to fit the dynamic range of our digitizer

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Theory Day 3#

+ +
+

+
+

An acquisition system must:

+
    +

  • Detect changes in electric potential difference

    • +

  • Faithfully transfer this signal to our acquisition system output

    • +

  • Distinguish interesting biological signals from other sources of electrical noise

    • +
+
+

Differential amplifiers remove common noise#

+
+

Referencing#

+

We live in an (electrically) very noisy world. To get rid of some of this noise from our recording, we can use a reference point. This can be another electrode in the brain or a screw in the animal’s skull. The choice you make here is very important for your recording: the amplifier will output the difference between your recording electrode and your reference point. That means that the amplifier will do its best to get rid of any signal that the two share. If the recording electrode is picking up 50 Hz noise generated by the mains power supply in the walls, you want the amplifier to get rid of it, so it’s best to use a reference point that will also pick up this noise. However, if your reference is picking up signals that you are interested in, the amplifier will get rid of those too. To choose an appropriate reference, you have to decide what qualifies as noise in your experiment.

+
+
+

Differential Amplifiers#

+
+
+

Talk#

+

The amplification of the potential difference between the measuring electrode and the reference electrode (in the order of microvolts) is a crucial step. This is accomplished with differential amplifiers that amplify the difference and rejecting the ‘common-mode’ noise (i.e., noise identical in the recording and reference electrodes typically caused by motion artifacts and capacitive coupling of the body and electrode lead with power line fields (Nunez & Srinivasan, 2009)).

+
+
+
+

Instrumentation amplifiers#

+
+

Talk#

+
+
+
+
+

Why do we need instrumentation amps?#

+

Why can’t we just use 1 operational amplifier to get a nice signal?

+
+../../../_images/op_amp_spikes_ref.png +
+

To make this circuit differential, we need voltage dividers. But these are connecting our fragile signal to ground! Plus, any mismatch in the input impedances between ‘+’ and ‘-’ messes up the signal if there is a lot of common mode noise. In practical terms, there is always going to be a mismatch between these resistors, they simply cannot be produced in a way that makes them exactly equal.

+

Why? Because this resistor is also your electrode. If you work with electrodes, have you measured their impedances? How similar are they? If you made these resistors as different as your electrodes are variable, this circuit will not work to eliminate common mode noise and amplify our spikes.

+

The solution is to use three op-amps:

+
+../../../_images/three_op_amps.png +
+
+

+
+

Here it is in the simulator: +|

+
+two operational amplifiers with negative feedback receive the measurement and reference electrode, respectively. Their outputs are fed into a third operation amplifier with negative feedback to form an instrumentation amplifier. +
+
+

Gain resistor#

+

The voltages on either side of the gain resistor are fixed, because the op-amps are keeping them in place. If we have the same V and lower RGain = more current must travel through the resistor, and therefore more current through the feedback resistors of the two buffer op-amps. Those are fixed resistors: now we have a higher I for same R and therefore a higher voltage drop across these resistors. Both buffer op-amps now have to work harder to overcome this voltage drop and will output more extreme voltages. By decreasing the value of RGain, we are basically making the inputs to the final op-amp more different to each other, and therefore increasing the gain of the instrumentation amp.

+
+
+
+

Common mode rejection ratio (CMRR)#

+

When the input impedances of the differential amplifier weren’t matched, part of the input signal that was common to both inputs, and thus should be cancelled out, actually appeared in the output. A common way to model how well an amplifier subtracts one input to the other is the following: +We define each input (+ and -) to be a sum of an individual voltage (V1 or V2) plus a voltage common to both. In our arms, or the brain of an animal, this common voltage (Vc) could be electrical noise or muscle activity we are not interested in and want to discard. In this case, the inputs would be:

+
+\[V+ = V1 + Vc\]
+
+\[V- = V2 + Vc\]
+

(In some examples of a differential amplifier, V2 is ground 0V, which is a perfectly valid value). In an ideal differential amplifier, the output should be the difference of both amplified by a factor:

+
+\[Vout = Ad (V+ - V-)\]
+
+\[= Ad ((V1+Vc)-(V2+Vc))\]
+
+\[= Ad (V1-V2)\]
+

Where Ad is the differential gain, the factor by which the differential signal is amplified. +Here, the unwanted, common signals cancel out and only the signal we are interested in is amplified.

+

A real amplifier, however, acts in a different way. As we’ve seen, small imperfections can lead to part of the common voltages being amplified as well. In this case, the output of a real amplifier ends up being:

+
+\[Vout = Ad (V1 - V2 ) + Ac * Vc\]
+

In addition to the differential gain, a new term ‘Ac’, or common gain, appears. This amplifies the signal common to both inputs. Of course, we want an amplifier to have a differential gain as high as possible and a common gain as low as possible (ideally, Ac would be 0). The relation between these two gains tells us how good an amplifier is at amplifying only the differential signals. This is called the Common Mode Rejection Ratio, or CMRR, simply defined as

+
+\[CMRR = \frac{Ad}{Ac}\]
+

or

+
+\[CMRR = 20log\frac{Ad}{Ac}\]
+

if measured in decibels.

+

The higher the CMRR, the better the amplifier is at cancelling out the signals common to both inputs. +Instrumentation amplifiers are not completely immune to common input noise. They are real circuits and, as such, there are multiple ways for these common signals to bleed out into the output. They have, however, a very high CMRR. Comparing the two devices we’ve been using, the operational amplifier LM358 has a CMRR of 80dB while the instrumentation amplifier has a CMRR of 120dB, 100 times higher! (Sounds underwhelming? Remember decibels are logarithmic; the difference between 80 and 120 dB in terms of sound is the difference between a toilet flushing and a jet engine).

+
+
+
+

Why do we need a ground electrode?#

+

When we build our EMG circuit, we will use three electrodes: measurement (+), reference (-), and ground. Why do we have a ground electrode (or ground pin or screw) when we already have ‘+’ and ‘-’ inputs? This is a bit tricky, and there’s multiple ways to understand it.

+
+
+
+

Imagine you just walked across a carpet and you’re charged to 10kV. Now you want to do a differential measurement of EMG (or EEG). In theory, as far as we’ve really talked about until now, this should work via the magic of common-mode rejection. However, remember the circuit that is inside the instrumentation amp:

+
+../../../_images/instrumentation_amp_simulator.png +
+

The ‘-’ inputs of the two input op-amps are connected to ground, via a bunch of resistors. If you are charged to 10kV compared to Ground, we’re asking these op-amps to deal with very high differences in voltage, and they will saturate. Even if here we did not include rails in the simulation, remember that each op-amp can only go as high or low as its voltage rails (3V in our case, so with a 100x gain, a 0.03V input saturates the amplifier).

+
+

+
+

Remember the common mode rejection ratio. If our amplifier is good at rejecting 99.99% of the common mode, but 0.01% makes it through, in the range of volts, this could still be enough to prevent us from resolving microvolt spikes.

+
+

+
+

Attaching a ground electrode to ourselves, and then connecting this to the ground of our acquisition system, brings our body to 0V from the perspective of the acquisition system. The remaining noise fluctuations are still there, but the voltage difference is not as big anymore. We will still have residual 50 or 60Hz noise from the mains supply, plus other muscles, electrostatic charge, bodies moving through the fields in the room and so on, but these can all be handled by the amplifier.

+
+

+
+

The last, related, issue is that the output of the whole thing is relative to ground. At some point you want to connect this to a PC, which sits at ground level.

+
+

+
+

Practically, all this means that we want to ground our subjects as well as possible. For tetrode recordings in mice, we use a large ‘ground screw’ with low impedance to ground, so that we can effectively discharge the mouse.

+
+

+
+

One more detail: Ground is not (always) earth, in many cases it is just a certain circuit we treat as 0 that can provide or sink a lot of current. That circuit can have noise on it, just like any other circuit. If the ground has a lot of 50/60Hz noise, we’ll be charging and discharging the animal (any animal is also a capacitor) constantly through the ground connection. If the ground screw/electrode is low enough impedance and close to our recording site, we’ll manage to keep the animal’s voltage equal to the changing GND level and we won’t notice this noise. However, if we put the ground screw/electrode too far away from where we record, e.g. we put the ground connection on the tail (extreme example), then the head of the animal won’t be sufficiently charged/discharged and we’ll encounter what will look like 50/60Hz noise in our tetrode recordings.

+
+
+

Low and High pass filtering#

+

Filters are used to remove certain frequencies from our data. We can do this in hardware or in software. Usually hardware filtering (implemented in the amplifier circuit) is used to increase (apparent) signal to noise ratio by rejecting unwanted frequencies and to prevent signal aliasing (e.g., bandpass between 0.5 and 2 kHz). +Remember the exercise where we measured the voltage across our fingers with the oscilloscope, and saw very high values. Even with a differential amplifier, we usually have a decent amount of slow (~<10Hz or so) voltages that are simply too big for the amplifier or ADC (analog to digital converter). Any voltages above or below the amplifier rails (or above/below the input range of the digitizer) will be ‘clipped’ and all we’ll see is a constant value. +The solution is to remove the large amplitude slow components, so we can fit the lower amplitude, faster, interesting components into our dynamic range.

+
+The analog to digital converter cannot detect signals that cross over its +3 high rail. If the true signal is more than +3 V, this will still be represented as +3, resulting in a flat line for all values over +3, however high they may truly be. +
+

Therefore, high-pass filters first remove the large DC offsets present at the electrode-extracellular interface, along with any undesired low-frequency signals (e.g., movement artefacts). Additionally, low-pass filters must be configured to less than half of the ADC frequency sampling rate (Nyquist limit) to prevent aliasing, and may also be used to block undesired high-frequency signals and artefacts. For instance, if our sampling frequency is 30 kHz, the low pass filter should be ~15 kHz. Below is an example of the Intan headstage circuit.

+
+The intan chip used in many headstages contains high pass analog filters and a differential amplifier for each ephys channel. +
+
+

Low-pass filters#

+

These filters block high frequencies. This is basically another voltage divider, with a frequency-dependent component. You’ve already seen one of these when you charged/discharged a capacitor! The exponential decay of the capacitor gets convolved with our signal. Remember that the impedance of our capacitor decreases as the signal frequency increases. At low frequencies, the high impedance of the capacitor means we get a large voltage drop over the capacitor, and more of our input signal can reach our Vout.

+
+a resistor with capacitor to ground forms a low-pass filter +
+
+
+

High-pass filters#

+

This is the same idea. +With increasing signal frequency, the impedance of the capacitor decreases (day 1), reducing the voltage drop over the capacitor and sending more signal to the output.

+
+a capacitor with resistor to ground forms a low-pass filter +
+

These are called RC filters because they’re built from a resistor (R) and a capacitor (C). Because there’s only one of each, we call them ‘single pole’. In real life, filters are built from more than one pair in order to get specific characteristics. This goes beyond the scope of this course but there are entire classes on this topic.

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+ Last updated on Aug 02, 2024. +
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+ + \ No newline at end of file diff --git a/courses/open-ephys/theory-day-4/index.html b/courses/open-ephys/theory-day-4/index.html new file mode 100644 index 00000000..8f25339b --- /dev/null +++ b/courses/open-ephys/theory-day-4/index.html @@ -0,0 +1,822 @@ + + + + + + + + + + + Theory Day 4 — upsidedownlabs.github.io documentation + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +
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Theory Day 4#

+ +
+

Digitization#

+

The purpose of digitization is to convert amplified signals into digital values. Why do we digitize neural signals? To protect them from noise, and so that we can process and store them. +First, the output of the amplifier (Vout) should match the digitizer dynamic range. Your analog signal should ‘occupy’ as much as possible, i.e. all discrete values in the digitization range. In other words, digitization range should match maximum analog signal. If the dynamic range is too small the signal will saturate, and if it is too large it will decrease effective signal resolution.

+
+../../../_images/3bitADC.png +
+

If you have a voltage divider and an open-loop op-amp (comparator) you can already build a circuit that checks if your analog signal is above or below a certain value. Now instead of one voltage divider, you could have a whole ‘ladder’, creating intermediate values, and compare to these. This is an incredibly inefficient way to make an ADC.

+

Here’s what this may look like:

+
+../../../_images/comparator_ladder.png +
+

In practice, many ADCs still use the same basic idea of using op-amps as comparators, but instead of comparing millions of values to obtain a precise measurement, they generate a reference voltage from an internal DAC and adjust that until it matches the input voltage, or use some other clever tricks.

+
+../../../_images/2vs3bitresolution.png +
+

Typically AD converters have 12 to 16 bit resolution (4096 to 65536 discrete values) for neural signals, which is usually enough because of the size of the signals we want (spikes etc), and because the thermal noise floor of typical electrodes is similar to the achievable resolution anyway: better digitizers would just measure more of that noise. If you want to read more about that, have a look here.

+
+
+

Talk: Acquisition and Synchronization#

+

One of the most common pitfalls in Neuroscience is correctly synchronizing multiple datastreams. How do you know whether your imaging and electrophysiology are aligned in time? How many different clocks do you have on your set up, and which of those can you trust?

+
+
+

The code for the exercises Filipe shows is available on google drive if you want to try it out yourself.

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+ Last updated on Aug 02, 2024. +
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+ + \ No newline at end of file diff --git a/diy-neuroscience-kit-basic.pdf b/diy-neuroscience-kit-basic.pdf new file mode 100644 index 00000000..b720bca1 Binary files /dev/null and b/diy-neuroscience-kit-basic.pdf differ diff --git a/diy-neuroscience-kit-pro.pdf b/diy-neuroscience-kit-pro.pdf new file mode 100644 index 00000000..8331ac2c Binary files /dev/null and b/diy-neuroscience-kit-pro.pdf differ diff --git a/experiments/index.html b/experiments/index.html index eb6667a7..d150b061 100644 --- a/experiments/index.html +++ b/experiments/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@ + +
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    • @@ -737,7 +751,10 @@

    Step 4: Wipe off the gel

    Warning

    -

    Close your eyes while using the alcohol swabs for EOG recording else it may cause eye redness & irritation.

    +
      +

    • Using alcohol swabs can dry out the skin, so don’t use them if your skin is already dry.

      • +

    • Close your eyes while using the alcohol swabs for EOG recording else it may cause eye redness & irritation.

      • +

    @@ -912,7 +929,7 @@

    Using BioAmp bands

    - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

    diff --git a/guides/usage-guides/using-bioamp-bands/index.html b/guides/usage-guides/using-bioamp-bands/index.html index 185ff089..48f98263 100644 --- a/guides/usage-guides/using-bioamp-bands/index.html +++ b/guides/usage-guides/using-bioamp-bands/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@     + +
  • + + Courses + +
    • +
    • + +
  • + + Courses + +
    • +

    • Types of BioAmp Bands#

    There are 3 types of BioAmp Bands and all these bands offer targeted and efficient solutions for recording biopotential signals from the muscles, heart, and brain, making them versatile tools for a wide range of HCI/BCI applications.

    -

    1) Muscle BioAmp Band#

    +

    1. Muscle BioAmp Band#

    Muscle BioAmp Band (EMG Band) is a stretchable band that can be connected to any of our Muscle BioAmp Hardware or any EXG sensor using a BioAmp Cable. It allows you to record your muscle signals hassle-free.

    ../../../_images/muscle-bioamp-band.png @@ -691,7 +705,7 @@

    1) Muscle BioAmp Band

    -

    2) Heart BioAmp Band#

    +

    2. Heart BioAmp Band#

    Heart BioAmp Band (ECG Band) is a stretchable band that can be connected to any of our Heart BioAmp Hardware or any EXG sensor using BioAmp Cable. It allows you to record your ECG signals hassle-free.

    ../../../_images/heart-bioamp-band.png @@ -726,7 +740,7 @@

    2) Heart BioAmp Band -

    3) Brain BioAmp Band#

    +

    3. Brain BioAmp Band#

    Brain BioAmp Band (EEG Band) is a stretchable band that can be connected to any of our Brain BioAmp Hardware or any EXG sensor using BioAmp Cable to record signals from the brain hassle-free.

    @@ -783,7 +797,7 @@

    Assembly
    ../../../_images/emg-band-assembly-1.gif
    -
      +

      1. Take the other end of the band and insert it in the buckle.

      @@ -799,7 +813,7 @@

      Assembly

      Skin Preparation#

      Apply Nuprep Skin Preparation Gel on the skin surface where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.

      -

      For more information, please check out detailed step by step skin preparation guide.

      +

      For more information, please check out detailed step by step Skin Preparation Guide.

      Measure EMG#

      @@ -809,7 +823,7 @@

      Measure EMG ../../../_images/connecting-cable.gif

      -
        +

        1. Flip the band again and wear it on your arm in such a way that IN+ and IN- are placed on the arm near the ulnar nerve and REF (reference) on the far side of the band.

        @@ -839,10 +853,10 @@

        Using Heart BioAmp Band

        Skin Preparation#

        Apply Nuprep Skin Preparation Gel on your chest where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.

        -

        For more information, please check out detailed step by step skin preparation guide.

        +

        For more information, please check out detailed step by step Skin Preparation Guide.

        -
        -

        Assembly#

        +
        +

        Assembly#

        1. Take your Heart BioAmp Band and wrap the band around your chest in such a way that the pointy part of the snap touches your chest and the flat part is on the outer side.

        @@ -888,8 +902,8 @@

        Measure ECG

        Using Brain BioAmp Band#

        -
        -

        Assembly#

        +
        +

        Assembly#

        You get the band in two parts - the longer part consists of buckles at both ends and the shorter one has loose ends on both sides.

        1. Hold one end of the longer band and align the top part of the buckle with the flat surface of the snap.

          2. @@ -898,10 +912,10 @@

          Assembly#

        2. Your band is now ready to use. You can also adjust the size of the band according to your head size.

        -
        -

        Skin Preparation#

        +
        +

        Skin Preparation#

        Apply Nuprep Skin Preparation Gel on your targeted area (visual cortex or prefrontal cortex) where dry electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.

        -

        For more information, please check out detailed step by step skin preparation guide.

        +

        For more information, please check out detailed step by step Skin Preparation Guide.

        Measure 1-channel EEG#

        @@ -986,9 +1000,9 @@

        Measure 1-channel EEGOverview
      1. Why use BioAmp Bands?
      2. Types of BioAmp Bands

        3. What makes it different?#

        @@ -724,11 +740,15 @@

        Software requirements

      3. Before you start using the kit, please download Arduino IDE v1.8.19 (legacy IDE). Using this you’ll be able to upload the arduino sketches in your development board and visualise the data on your laptop.

        4. +
        ../../../_images/arduino-ide.png +

        • Download Backyard Brains’ Spike Recorder according to the operating system you are using (Windows, OSX, Linux).

        +
        ../../../_images/byb.png +

        Using the Hardware#

        @@ -736,11 +756,17 @@

        Using the Hardware

        Step 1: Solder Connectors#

        Insert the provided BioAmp cable’s JST PH connector and header pins from top as shown in the image and solder them from below.

        -
        +
        ../../../_images/assembly-step1.png +
        +

        Soldering the connector & header pins on BioAmp EXG Pill#

        +
        -
        +
        ../../../_images/bioamp-exg-pill-soldered.png +
        +

        After soldering, BioAmp EXG Pill should look like this#

        +

        @@ -757,8 +783,8 @@

        Step 2 (optional): Configure for ECG/EMG

        Step 3: Connect MCU/ADC#

        Connect your BioAmp EXG Pill to your MCU/ADC as per the connection table shown below:

        -

    - +
    BioAmp to MCU/ADC connection#
    + @@ -777,8 +803,11 @@

    Step 3: Connect MCU/ADC

    BioAmp to MCU/ADC connection#

    BioAmp

    MCU/ADC

    For all the examples provided, we are using the A0 pin of Arduino UNO R3. Connect your BioAmp to your MCU/ADC via jumper cables provided in the kit. If you are connecting OUT pin of BioAmp to any other analog pin (A0-A5) of Arduino UNO board, then you will have to change the INPUT PIN in the Arduino sketch accordingly.

    -
    +
    ../../../_images/connections-with-arduino.png +
    +

    Connections with Arduino UNO R3#

    +

    Warning

    @@ -788,7 +817,12 @@

    Step 3: Connect MCU/ADC

    Step 4: Connecting electrode cable#

    Connect the BioAmp cable to BioAmp EXG Pill by inserting the cable end in the JST PH connector as shown in the graphic below.

    +
    ../../../_images/connection-with-cable.png +
    +

    Connections with BioAmp Cable v3#

    +
    +

    Step 5: Skin Preparation#

    @@ -814,19 +848,24 @@

    Electrodes placement

    Peel the plastic backing from electrodes

  • Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.

    • +
    ../../../_images/emg.png +

    • Using Muscle BioAmp Band:

    -
      +

      1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.

        2. -

      2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

        -

        Tutorial on how to use the band:

        -
        3. +

      3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

      +
      +

      Tip

      +

      Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

      +

      Tutorial on how to use the band:

      +
      +

      Note

      In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

      @@ -834,23 +873,25 @@

      Electrodes placement

      Uploading the code#

      Connect the Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste any one of the Arduino Sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:

      -

      EMG Filter: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      -

      EMG Envelope: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      -

      Go to tools from the menu bar, select “board” option then select Arduino UNO. In the same menu, +

      EMG Filter

      +

      EMG Envelope

      +

      Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize the EMG signals.

      After opening the serial plotter make sure to select the baud rate to 115200.

      -
      -

      Warning

      +
      +

      Important

      Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.

    Visualizing the EMG signals#

    Now flex your arm to visualize the muscle signals in real time on your laptop.

    +
    ../../../_images/EMGEnvelop.jpg +
    @@ -872,7 +913,9 @@

    Electrodes placement ../../../_images/ecg.png +

    • Using Heart BioAmp Band:

    @@ -881,28 +924,35 @@

    Electrodes placement +

    Tip

    +

    Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

    Tutorial on how to use the band:

    + +

    Uploading the code#

    Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:

    -

    ECG Filter: upsidedownlabs/Heart-BioAmp-Arduino-Firmware

    -

    Go to tools from the menu bar, select “board” option then select Arduino UNO. In the same menu, +

    ECG Filter

    +

    Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize the signals.

    After opening the serial plotter make sure to select the baud rate to 115200.

    -
    -

    Warning

    +
    +

    Important

    Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.

    Visualizing the ECG signals#

    +

    Sit back, relax and see your ECG signals in real time on your laptop.

    +
    ../../../_images/bioamp-Exg-Pill-ECG.jpg +
    @@ -922,7 +972,9 @@

    Electrodes placement

  • Horizontal EOG recording:

    • +
    ../../../_images/eog-horizontal.png +

    1. Connect the BioAmp cable to gel electrodes.

    2. Peel the plastic backing from electrodes.

      3. @@ -931,7 +983,9 @@

      Electrodes placement

    3. Vertical EOG recording:

      4. +
      ../../../_images/eog-vertical.png +

      1. Connect the BioAmp cable to gel electrodes.

      2. Peel the plastic backing from electrodes.

        3. @@ -941,21 +995,24 @@

        Electrodes placement

        Uploading the code#

        Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:

        -

        EOG Filter: upsidedownlabs/Eye-BioAmp-Arduino-Firmware

        -

        Go to tools from the menu bar, select “board” option then select Arduino UNO. In the same menu, +

        EOG Filter

        +

        Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code, & open the serial plotter from the tools menu to visualize the signals.

        After opening the serial plotter make sure to select the baud rate to 115200.

        -
        -

        Warning

        +
        +

        Important

        Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.

    Visualizing the EOG signals#

    +

    Move your eyes up-down or left-right to see your EOG signals in real time on your laptop.

    +
    ../../../_images/bioamp-exg-pill-eog.jpg +
    @@ -968,14 +1025,18 @@

    Step 8: Measuring Electroencephalography (EEG)International 10-20 system for recording EEG.

    -../../../_images/10-20-system.png +
    +../../../_images/10-20-system.png +

    Electrodes placement#

    We have 2 options to measure the EEG signals, either using the gel electrodes or using dry electrode based Brain BioAmp Band. You can try both of them one by one.

    • Using gel electrodes to record from prefrontal cortex part of brain:

    +
    ../../../_images/eeg.png +

    1. Connect the BioAmp cable to gel electrodes.

    2. Peel the plastic backing from electrodes.

      3. @@ -989,24 +1050,28 @@

      Electrodes placement +

      Tip

      +

      Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

      +

      Tutorial on how to use the band:

      +
      +

      Note

      Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same.

      -

      Tutorial on how to use the band:

      -
      -

    +

    Uploading the code#

    Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:

    -

    Spike recorder arduino code

    -

    Go to tools from the menu bar, select “board” option then select Arduino UNO. In the same menu, +

    Spike recorder arduino code

    +

    Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your development board is connected. To find out the right COM port, screen disconnect your board and reopen the menu. The entry that disappears should be the right COM port. Now upload the code.

    -
    -

    Warning

    +
    +

    Important

    Make sure your laptop is not connected to a charger and sit 5m away from any AC appliances for best signal acquisition.

    @@ -1014,14 +1079,22 @@

    Uploading the code#

    Open the Spike Recorder software. When the Spike Recorder starts, it will start recording from your microphone. To change that, go to the settings by clicking the first icon on the top left corner of the screen, select the COM port on which your Arduino UNO is connected and click on connect.

    -
    +
    ../../../_images/spike-recorder-configurations.jpg +
    +

    Spike Recorder settings#

    +

    Mute the speakers and apply the 50Hz notch filter by clicking on the checkbox as shown in the screenshot above. You should set the low band pass filter to 1Hz and high bandpass filter to 40Hz as we are only recording the EEG signals which range between these frequencies.

    Now everything is configured and connected. So close the settings window and start recording EEG signals.

    +
    ../../../_images/bioamp-exg-pill-eeg.png +
    +

    EEG signals being visualised in Spike Recorder#

    +
    +

    The signals that you can see on the screen right now are originating from prefrontal cortex part of your brain and propagating through all the layers to the surface of your skin.

    To record these EEG signals, you have placed the electrodes on the forehead (Fp1 & Fp2), then BioAmp EXG Pill is amplifying those signals so that we can detect it and finally sending it to the ADC (Analog to Digital Convertor) of your Arduino Uno. Ultimately the signals are being visualized in Spike Recorder software.

    We hope everything is clear now and you understand how the signals are propagating from your brain to the screen of the laptop.

    @@ -1086,17 +1159,41 @@

    Project ideas & tutorials
    -Detecting heart beats
    +Controlling video game using brainwaves (EEG)
    -     +
    -Measuring heart rate
    +Visualising electrical impulses from eyes (EOG)
    +
    +
    + +
    +
    +
    +
    +Recording EEG from visual cortex
    +
    +
    +
    +
    +
    +
    +
    +Recording EEG from prefrontal cortex
    +
    +
    +
    +
    +
    +
    +
    +Eye blink detection
    -
    +
    @@ -1104,23 +1201,47 @@

    Project ideas & tutorials Creating a drowsiness detector

    - + + +
    +
    +
    +
    +Record publication-grade ECG
    +
    +
    +
    +
    +
    +
    +
    +Measuring heart rate
    +
    +
    +
    +
    +
    +
    +
    +Detecting heart beats
    +
    +
    -Detecting eye blinks
    +Record publication-grade EMG
    -
    +
    -Record EEG from visual cortex part of brain
    +Detecting up and down movement of eyes
    -
    + @@ -1276,7 +1397,6 @@

    Software tutorials - Download PDF @@ -1293,6 +1413,10 @@

    Software tutorials

    - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

    diff --git a/hardware/bioamp/bioamp-v1.5/index.html b/hardware/bioamp/bioamp-v1.5/index.html index b8548443..b49529fa 100644 --- a/hardware/bioamp/bioamp-v1.5/index.html +++ b/hardware/bioamp/bioamp-v1.5/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@     + +
  • + + Courses + +
    • +
    • + +
  • + + Courses + +
    • +

  • Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.

    • +
    ../../../_images/bioamp-v1-5-emg.png +

    Using Muscle BioAmp Band#

    @@ -909,14 +919,19 @@

    Using Muscle BioAmp Band

    Tip

    -

    In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

    +

    Step 4: Connecting 9V battery#

    Connect any 9V battery to BioAmp v1.5 using the 9V snap cable. Now activate the board by flipping ON the power switch, and you’ll notice an LED light up, showing that the board is ready to use.

    +
    ../../../_images/9v-battery.png +

    Step 5: Listen to your muscle signals#

    @@ -928,7 +943,9 @@

    Using speakers ../../../_images/listening-emg-2.png +

    Using wired earphones/headphones#

    @@ -937,7 +954,9 @@

    Using wired earphones/headphones +
    +../../../_images/listening-emg-3.png +

    @@ -950,7 +969,9 @@

    Using Phone Recorder app +
    +../../../_images/emg-in-mobile-2.png +

    Using Backyard Brains’ Spike Recorder mobile app#

    @@ -959,13 +980,17 @@

    Using Backyard Brains’ Spike Recorder mobile app

    Open the app, click the setting icon on the top right corner and set the recording type to EMG.

  • Apply the 50Hz or 60Hz notch filter depending on the country you are living in. For example if you are in India then the AC current oscillates at a frequency of 50Hz but it oscillates at 60Hz frequency in USA. This AC current acts as a noise in the signals so we have to remove it by applying this notch filter.

    • -    ../../../_images/spike-recorder-mobile.jpg +
    +../../../_images/spike-recorder-mobile.jpg +

    1. Again click on the setting icon to close it and you are ready.

    2. Flex your muscles to be able to visualize the muscle signals (EMG).

    3. You can record the EMG data as a .wav file by pressing the record button on the top right corner of the app and then convert it in any other format as per your project requirements.

    -../../../_images/emg-in-mobile.png +
    +../../../_images/emg-in-mobile.png +

    @@ -978,13 +1003,17 @@

    Using Backyard Brains’ Spike Recorder ../../../_images/spike-recorder-laptop.png +

    1. Again click on the setting icon to close it and you are ready.

    2. Flex your muscles to be able to visualize the muscle signals (EMG)

    3. You can record the EMG data as a .wav file by pressing the record button on the top right corner of the app and then convert it in any other format as per your project requirements.

    +
    ../../../_images/emg-in-laptop.png +

    Using Audacity#

    @@ -994,7 +1023,9 @@

    Using Audacity ../../../_images/emg-in-audacity.png +

    @@ -1110,7 +1141,6 @@

    Using Audacity Download PDF @@ -1125,6 +1155,10 @@

    Using Audacity

    - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

    diff --git a/hardware/bioamp/muscle-bioamp-biscute/index.html b/hardware/bioamp/muscle-bioamp-biscute/index.html index b3d8bbdf..5140f290 100644 --- a/hardware/bioamp/muscle-bioamp-biscute/index.html +++ b/hardware/bioamp/muscle-bioamp-biscute/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@     + +
  • + + Courses + +
    • +
    • + +
  • + + Courses + +
    • +

  • Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.

    • +
    ../../../_images/biscute-emg.png +

    • Using Muscle BioAmp Band:

    -
      +

      1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.

        2. -

      2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

        -

        Tutorial on how to use the band:

        -
        3. +

      3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

      +
      +

      Tip

      +

      Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

      +

      Tutorial on how to use the band:

      +
      +

      Note

      In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

      @@ -937,8 +964,8 @@

      Electrodes placement

      Uploading the code#

      Connect your Arduino UNO to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:

      -

      EMG Filter: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      -

      EMG Envelope: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      +

      EMG Filter

      +

      EMG Envelope

      Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the @@ -953,7 +980,9 @@

      Uploading the code

      Visualizing the EMG signals#

      Now flex your arm to visualize the muscle signals in real time on your laptop.

      +
      ../../../_images/using-biscute.png +

      Video tutorial:

      +
      +

      Note

      In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

      @@ -824,8 +842,8 @@

      Using Muscle BioAmp Band

      Step 7: Uploading the code#

      Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:

      -

      EMG Filter: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      -

      EMG Envelope: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      +

      EMG Filter

      +

      EMG Envelope

      Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the @@ -840,7 +858,9 @@

      Step 7: Uploading the code

      Step 8: Visualizing the EMG signals#

      Now flex your arm to visualize the muscle signals in real time on your laptop.

      +
      ../../../_images/emg-recording.png +

      Footnotes

    +
    ../../../_images/candy-emg.png +

    • Using Muscle BioAmp Band:

    -
      +

      1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.

        2. -

      2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

        -

        Tutorial on how to use the band:

        -
        3. +

      3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

      +
      +

      Tip

      +

      Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

      +

      Tutorial on how to use the band:

      +
      +

      Note

      In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

      @@ -813,8 +868,8 @@

      Electrodes placement

      Uploading the code#

      Connect your Arduino UNO R3 to your laptop using the USB cable (Type A to Type B). Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:

      -

      EMG Filter: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      -

      EMG Envelope: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      +

      EMG Filter

      +

      EMG Envelope

      Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the @@ -829,7 +884,9 @@

      Uploading the code

      Visualizing the EMG signals#

      Now flex your arm to visualize the muscle signals in real time on your laptop.

      +
      ../../../_images/using-candy.png +

      Video tutorial:

      Software requirements#

      Before you start using the kit, please download Arduino IDE v1.8.19 (legacy IDE). Using this you’ll be able to upload the arduino sketches on your development board and visualise the data on your laptop.

      +
      ../../../_images/arduino-ide.png +
      +

      Download Arduino IDE v1.8.19#

      +
      +

      Assembling the Kit#

      @@ -779,194 +801,194 @@

      Assembling the Kit
      -
      +
      ../../../_images/01_Bare_Board.jpg
      -

      Step 1 - Bare Board#

      +

      Step 1 - Bare Board#

      -
      +
      ../../../_images/02_1M_Resistors.jpg
      -

      Step 2 - 1M Resistors#

      +

      Step 2 - 1M Resistors#

      -
      +
      ../../../_images/03_330R_Resistors.jpg
      -

      Step 3 - 330R Resistors#

      +

      Step 3 - 330R Resistors#

      -
      +
      ../../../_images/04_10K_Resistors.jpg
      -

      Step 4 - 10K Resistors#

      +

      Step 4 - 10K Resistors#

      -
      +
      ../../../_images/05_22K_Resistors.jpg
      -

      Step 5 - 22K Resistors#

      +

      Step 5 - 22K Resistors#

      -
      +
      ../../../_images/06_1K_Resistors.jpg
      -

      Step 6 - 1K Resistors#

      +

      Step 6 - 1K Resistors#

      -
      +
      ../../../_images/07_220K_Resistors.jpg
      -

      Step 7 - 220K Resistors#

      +

      Step 7 - 220K Resistors#

      -
      +
      ../../../_images/08_1nF_Capacitors.jpg
      -

      Step 8 - 1nF Capacitors#

      +

      Step 8 - 1nF Capacitors#

      -
      +
      ../../../_images/09_100nF_Capacitors.jpg
      -

      Step 9 - 100nF Capacitors#

      +

      Step 9 - 100nF Capacitors#

      -
      +
      ../../../_images/10_100pF_Capacitors.jpg
      -

      Step 10 - 100pF Capacitors#

      +

      Step 10 - 100pF Capacitors#

      -
      +
      ../../../_images/11_Angled_Header_Pins.jpg
      -

      Step 11 - Angled Header Pins#

      +

      Step 11 - Angled Header Pins#

      -
      +
      ../../../_images/12_5x5mm_Buttons.jpg
      -

      Step 12 - 5x5mm Buttons#

      +

      Step 12 - 5x5mm Buttons#

      -
      +
      ../../../_images/13_OptoIsolator.jpg
      -

      Step 13 - OptoIsolator#

      +

      Step 13 - OptoIsolator#

      -
      +
      ../../../_images/14_JST_PH_Angled_Connectors.jpg
      -

      Step 14 - JST PH Angled Connectors#

      +

      Step 14 - JST PH Angled Connectors#

      -
      +
      ../../../_images/15_JST_PH_Straight_Connectors.jpg
      -

      Step 15 - JST PH Straight Connectors#

      +

      Step 15 - JST PH Straight Connectors#

      -
      +
      ../../../_images/16_IC_Socket.jpg
      -

      Step 16 - IC Socket#

      +

      Step 16 - IC Socket#

      -
      +
      ../../../_images/17_IC.jpg
      -

      Step 17 - IC#

      +

      Step 17 - IC#

      -
      +
      ../../../_images/18_LEDs.jpg
      -

      Step 18 - LEDs#

      +

      Step 18 - LEDs#

      -
      +
      ../../../_images/19_3.5mm_Headphone_Jack.jpg
      -

      Step 19 - 3.5mm Headphone Jack#

      +

      Step 19 - 3.5mm Headphone Jack#

      -
      +
      ../../../_images/20_2.2uF_Capacitor.jpg
      -

      Step 20 - 2.2uF Capacitor#

      +

      Step 20 - 2.2uF Capacitor#

      -
      +
      ../../../_images/21_1uF_Capacitor.jpg
      -

      Step 21 - 1uF Capacitor#

      +

      Step 21 - 1uF Capacitor#

      -
      +
      ../../../_images/22_470uF_Capacitor.jpg
      -

      Step 22 - 470uF Capacitor#

      +

      Step 22 - 470uF Capacitor#

      -
      +
      ../../../_images/23_Header_Pins.jpg
      -

      Step 23 - Header Pins#

      +

      Step 23 - Header Pins#

      -
      +
      ../../../_images/24_Assembled.jpg
      -

      Step 24 - Assembled Shield#

      +

      Step 24 - Assembled Shield#

      @@ -1013,15 +1035,18 @@

      Using gel electrodes

      Using Muscle BioAmp Band#

      -
        +

        1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.

          2. -

        2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

          -

          Tutorial on how to use the band:

          -
          3. +

        3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

        +
        +

        Tip

        +

        Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

        +

        Tutorial on how to use the band:

        +
        +

        Note

        In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

        @@ -1041,10 +1066,8 @@

        Step 5: Connect Arduino UNO to your laptop

        Step 6: Visualise EMG signals on laptop#

        Copy paste any one of the arduino sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:

        -
        -
        +

        EMG Filter

        +

        EMG Envelope

        Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, disconnect your board and reopen the menu. The entry that disappears should be the @@ -1059,9 +1082,7 @@

        Step 6: Visualise EMG signals on laptop

        Step 7: Visualise EMG signals on LEDs#

        Copy paste the Arduino Sketch given below in Arduino IDE:

        -
        -
        +

        LED Bar Graph

        Make sure you have selected the right board and COM port. Now upload the code, and flex your arm. You’ll see the LED bar going up. More strength you apply, more the LED bar goes up.

        ../../../_images/led-graph.gif @@ -1097,9 +1118,7 @@

        Listening EMG on a wired earphones/headphones#

        Connect the servo claw to Muscle BioAmp Shield.

        Copy paste the Arduino Sketch given below in Arduino IDE:

        -
        -
        +

        Servo Controller

        Make sure you have selected the right board and COM port. Now upload the code, and flex your arm to control the servo claw in real time.

        ../../../_images/servo-control.gif @@ -1109,9 +1128,7 @@

        Step 9: Controlling a servo motor#

        Connect the servo claw to Muscle BioAmp Shield.

        Copy paste the Arduino Sketch given below in Arduino IDE:

        -
        -
        +

        Claw Controller

        Make sure you have selected the right board and COM port. Now upload the code, and flex your arm to control the servo claw in real time.

        ../../../_images/claw-control.gif @@ -1278,11 +1295,14 @@

        Using user buttons Download PDF + + + +

      @@ -1323,7 +1343,7 @@

      Using user buttons

      - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

      diff --git a/hardware/index.html b/hardware/index.html index f8c156cc..230625f0 100644 --- a/hardware/index.html +++ b/hardware/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@       + +
    1. + + Courses + +
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      9. @@ -748,7 +765,7 @@

      Overview of BioAmp Hardware

      - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

      diff --git a/kits/diy-neuroscience/basic/index.html b/kits/diy-neuroscience/basic/index.html index fdcb12d3..f74c648c 100644 --- a/kits/diy-neuroscience/basic/index.html +++ b/kits/diy-neuroscience/basic/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@       + +
    9. + + Courses + +
      10. +
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    11. + + Courses + +
      12. +

    13. Place the IN+ and IN- cables on the arm near the ulnar nerve & REF (reference) at the back of your hand as shown in the connection diagram.

    +
    ../../../_images/emg1.png +

    • Using Muscle BioAmp Band:

    -
      +

      1. Connect the BioAmp cable to Muscle BioAmp Band in a way such that IN+ and IN- are placed on the arm near the ulnar nerve & REF (reference) on the far side of the band.

        2. -

      2. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

        -

        Tutorial on how to use the band:

        -
        3. +

      3. Now put a small drop of electrode gel between the skin and metallic part of BioAmp cable to get the best results.

      +
      +

      Tip

      +

      Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

      +

      Tutorial on how to use the band:

      +
      +

      Note

      In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

      @@ -734,8 +769,8 @@

      Electrodes placement

      Uploading the code#

      Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste any one of the Arduino Sketches given below in Arduino IDE v1.8.19 that you downloaded earlier:

      -

      EMG Filter: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      -

      EMG Envelope: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

      +

      EMG Filter

      +

      EMG Envelope

      Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Maker Uno is connected. To find out the right COM port, disconnect your Maker UNO board and reopen the menu. The entry that disappears should be the @@ -750,7 +785,9 @@

      Uploading the code

      Visualizing the EMG signals#

      Now flex your arm to visualize the muscle signals in real time on your laptop.

      +
      ../../../_images/EMGEnvelop1.jpg +
      @@ -766,7 +803,9 @@

      Electrodes placement ../../../_images/ecg1.png +

      • Using Heart BioAmp Band:

      @@ -775,14 +814,18 @@

      Electrodes placement +

      Tip

      +

      Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

      Tutorial on how to use the band:

      + +

      Uploading the code#

      Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:

      -

      ECG Filter: upsidedownlabs/Heart-BioAmp-Arduino-Firmware

      +

      ECG Filter

      Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Maker Uno is connected. To find out the right COM port, disconnect your Maker UNO board and reopen the menu. The entry that disappears should be the @@ -796,7 +839,9 @@

      Uploading the code

      Visualizing the ECG signals#

      +
      ../../../_images/bioamp-Exg-Pill-ECG1.jpg +

      @@ -807,7 +852,9 @@

      Electrodes placement

    1. Horizontal EOG recording:

      2. +
      ../../../_images/eog-horizontal1.png +

      1. Connect the BioAmp cable to gel electrodes.

      2. Peel the plastic backing from electrodes.

        3. @@ -816,7 +863,9 @@

        Electrodes placement

      3. Vertical EOG recording:

        4. +
        ../../../_images/eog-vertical1.png +

        1. Connect the BioAmp cable to gel electrodes.

        2. Peel the plastic backing from electrodes.

          3. @@ -826,7 +875,7 @@

          Electrodes placement

          Uploading the code#

          Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:

          -

          EOG Filter: upsidedownlabs/Eye-BioAmp-Arduino-Firmware

          +

          EOG Filter

          Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Maker Uno is connected. To find out the right COM port, disconnect your Maker UNO board and reopen the menu. The entry that disappears should be the @@ -840,21 +889,27 @@

          Uploading the code

          Visualizing the EOG signals#

          +
          ../../../_images/bioamp-exg-pill-eog1.jpg +

      Step 8: Measuring EEG (ElectroEncephaloGraphy)#

      Let’s understand the electrode placements before moving forward in this project. For recording EEG from different parts of the brain, you have to place the electrodes according to the International 10-20 system for recording EEG.

      +
      ../../../_images/10-20-system.png +

      Electrodes placement#

      We have 2 options to measure the EEG signals, either using the gel electrodes or using dry electrode based Brain BioAmp Band. You can try both of them one by one.

      • Using gel electrodes to record from prefrontal cortex part of brain:

      +
      ../../../_images/eeg1.png +

      1. Connect the BioAmp cable to gel electrodes.

      2. Peel the plastic backing from electrodes.

        3. @@ -872,10 +927,14 @@

        Electrodes placementNote

        Similarly you can use the band to record EEG signals from the visual cortex part of brain by placing the dry electrodes on O1 and O2 instead of Fp1 and Fp2. Everything else will remain the same.

        +
        +

        Tip

        +

        Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

        Tutorial on how to use the band:

      + +

      Uploading the code#

      Connect the Maker Uno to your laptop using the USB cable (Type A to Type B). Copy paste the Arduino Sketch given below in Arduino IDE v1.8.19 that you downloaded earlier:

      @@ -893,15 +952,18 @@

      Uploading the code#

      Open up your BackyardBrains Spike Recorder software. At first, it will monitor signals from your microphone. To change that, go to the settings by clicking the icon on the top left corner of the screen, select the COM port on which the Maker UNO is connected and click on connect.

      -
      +
      ../../../_images/spike-recorder-configurations.jpg

      Mute the speakers and apply the 50Hz notch filter by clicking on the checkbox as shown in the screenshot above. You should set the low band pass filter to 1Hz and high bandpass filter to 40Hz as we are only recording the EEG signals which range between these frequencies.

      Now everything is configured and connected. So close the settings window and start recording EEG signals.

      -
      -../../../_images/bioamp-exg-pill-eeg.png +
      +Recording EEG from pre-frontal cortex part of brain +
      +

      Recording EEG signals from pre-frontal cortex#

      +

      The signals that you can see on the screen right now are originating from prefrontal cortex part of your brain and propagating through all the layers to the surface of your skin.

      To record these EEG signals, you have placed the electrodes on the forehead (Fp1 & Fp2), then BioAmp EXG Pill is amplifying those signals so that we can detect it and finally sending it to the ADC (Analog to Digital Convertor) of your Maker Uno. Ultimately the signals are being visualized in Spike Recorder software.

      @@ -1093,6 +1155,30 @@

      Some Project Ideas + + + + + + + + + + + + + + + + + + + Download PDF + + + + @@ -1131,7 +1217,7 @@

      Some Project Ideas

      - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

      diff --git a/kits/diy-neuroscience/pro/index.html b/kits/diy-neuroscience/pro/index.html index 010f07e4..85c5ed26 100644 --- a/kits/diy-neuroscience/pro/index.html +++ b/kits/diy-neuroscience/pro/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@       + +
    2. + + Courses + +
      3. +
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    4. + + Courses + +
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      6. @@ -703,7 +721,9 @@

      Software requirements

      Spike Recorder

    6. Arduino IDE v1.8.19 (legacy IDE)

      7. +
      ../../../_images/arduino-ide.png +

      Using the kit#

      @@ -724,7 +744,7 @@

      Step 1: Using BioAmp EXG Pill

      Note

      -

      Checkout the complete documentation on BioAmp EXG Pill which includes how to use the sensor, record various biopotential signals from your body (ECG, EMG, EOG, EEG) and make different HCI/BCI projects using it.

      +

      Checkout the complete documentation on BioAmp EXG Pill which includes how to use the sensor, record various biopotential signals from your body (ECG, EMG, EOG, EEG) and make different HCI/BCI projects using it.

      @@ -738,7 +758,7 @@

      Step 2: Using Muscle BioAmp Shield

      Note

      -

      Checkout the complete documentation on Muscle BioAmp Shield which includes how to use the sensor, record/visualise/listen muscle signals and make different HCI projects using it.

      +

      Checkout the complete documentation on Muscle BioAmp Shield which includes how to use the sensor, record/visualise/listen muscle signals and make different HCI projects using it.

      @@ -756,8 +776,11 @@

      a. Connecting Muscle BioAmp Shield to MCU/ADC

      b. Configure for ECG/EMG (optional)#

      BioAmp EXG Pill is by default configured for recording EEG or EOG but if you want to record good quality ECG or EMG, then it is recommended to configure it by making a solder joint as shown in the image.

      -
      +
      ../../../_images/assembly-step2.png +
      +

      Configure BioAmp EXG Pill for EMG/ECG#

      +

      Note

      @@ -800,7 +823,7 @@

      d. Connecting electrode cables#

      We’ll create a 2-channel EMG acquisition system and to do so, we’ll be using both the sensors to record EMG signals from the ulnar nerve of both the hands, Thus, prepare the skin accordingly.

      Apply Nuprep Skin Preparation Gel on the skin surface where electrodes would be placed to remove dead skin cells and clean the skin from dirt. After rubbing the skin surface thoroughly, clean it with an alcohol wipe or a wet wipe.

      -

      For more information, please check out detailed step by step skin preparation guide.

      +

      For more information, please check out detailed step by step Skin Preparation Guide.

      f. Electrodes placement#

      @@ -838,14 +861,17 @@
      Using Muscle BioAmp Band ../../../_images/bioamp-band-connection.gif -
        -

      1. Now put a small drop of electrode gel between the skin and metallic parts of BioAmp Cables to get the best results.

        -

        Tutorial on how to use the band:

        -
        2. +
          +

        1. Now put a small drop of electrode gel between the skin and metallic parts of BioAmp Cables to get the best results.

        +
        +

        Tip

        +

        Visit the complete documentation on how to assemble and use the BioAmp Bands or follow the youtube video given below.

        +

        Tutorial on how to use the band:

        +
        +

        Note

        In this demonstration we are recording EMG signals from the ulnar nerve, but you can record EMG from other areas as well (biceps, triceps, legs, jaw etc) as per your project requirements. Just make sure to place the IN+, IN- electrodes on the targeted muscle and REF on a bony part.

        @@ -854,7 +880,7 @@
        Using Muscle BioAmp Band

        g. Uploading the code#

        Connect Arduino Uno to your laptop using the USB cable (Type A to Type B). Download the github repository given below:

        -

        Muscle BioAmp Arduino Firmware: upsidedownlabs/Muscle-BioAmp-Arduino-Firmware

        +

        Muscle BioAmp Arduino Firmware

        Go to the folder 8_EMGScrolling, open the arduino sketch 8_EMGScrolling.ino in Arduino IDE.

        Go to tools from the menu bar, select board option then select Arduino UNO. In the same menu, select the COM port on which your Arduino Uno is connected. To find out the right COM port, @@ -875,7 +901,7 @@

        h. Testing the connections

        i. Running python script#

        -

        Open Visual Studio Code, click on File < Open folder to open the folder 8_EMGScrolling.

        +

        Open Visual Studio Code, click on File > Open folder to open the folder 8_EMGScrolling.

        Open the terminal, and ensure that the path is configured to the location of the requirement.txt file.

        To install all the modules that are required to run the Python script, write the given command in the terminal:

        pip install -r requirements.txt
@@ -893,6 +919,7 @@ 
        i. Running python script
 
        j. Scrolling using EMG signals#
        
+
        Press the SW1 button on Muscle BioAmp Shield again.
        
 
        In the terminal, you will see Move Now prompt. When you flex your right arm, you’ll see UP in the terminal. Similarly, when you move your left arm, you’ll see DOWN in the terminal.
        
 
        
 ../../../_images/demo-1.gif
@@ -909,11 +936,11 @@ 
        j. Scrolling using EMG signals
 
        k. Calibrating the code#
        
 
        Changes in Arduino Sketch
        
-
        Modify the threshold values on lines 73 and 74. Threshold 1 is for the EMG signals recorded from the Muscle BioAmp Shield, and threshold 2 is for the EMG signals recorded from the BioAmp EXG Pill.
        
+
        Modify the threshold values on lines 73 and 74. Threshold 1 is for the EMG signals recorded from the Muscle BioAmp Shield, and threshold 2 is for the EMG signals recorded from the BioAmp EXG Pill.
        
 
        Uncomment line 71 in the Arduino code and navigate to Tools > Serial Plotter. You’ll see two plots showing the EMG signals of both of your arms. Flex your right arm and observe the peak value on the y-axis. If the peak value is around 240, you can set threshold 1 anywhere between 150 to 200. The lower the threshold value, the easier it is to trigger the output as UP or DOWN, and vice versa. Repeat the process to determine the threshold 2 value for your left arm.
        
 
        After setting the thresholds, comment out line 71.
        
 
        Changes in Python script
        
-
        Adjust the latency value on line 51. A higher latency value will make the output less responsive, requiring you to flex and hold longer to scroll through the screen. A lower latency value will make the output more responsive, allowing you to scroll through the screen more easily.
        
+
        Adjust the latency value on line 51. A higher latency value will make the output less responsive, requiring you to flex and hold longer to scroll through the screen. A lower latency value will make the output more responsive, allowing you to scroll through the screen more easily.

      l. Conclusion#

      @@ -1036,7 +1063,7 @@

      1. Projects made using BioAmp EXG Pill -

      2. Projects made using Muscle BioAmp Shield#

      +

      1. Projects made using Muscle BioAmp Shield#

      @@ -1083,7 +1110,7 @@

      2. Projects made using Muscle BioAmp Shield -

      3. Projects made using the sensors together#

      +

      1. Projects made using the sensors together#

      @@ -1184,8 +1211,8 @@

      3. Projects made using the sensors togetherSome project ideas @@ -1214,6 +1241,30 @@

      3. Projects made using the sensors together Show Source

      +
      + +
      + + + + + + + + + + + + + + + + + Download PDF + + + +
      @@ -1254,7 +1305,7 @@

      3. Projects made using the sensors together

      - Last updated on Jun 28, 2024. + Last updated on Aug 02, 2024.

      diff --git a/kits/index.html b/kits/index.html index ad66ab91..813a7eef 100644 --- a/kits/index.html +++ b/kits/index.html @@ -53,7 +53,7 @@ - + @@ -184,6 +184,13 @@       + +
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