Fiber Photometry Project Notes

[weiglszonja]

Fiber photometry

https://doi.org/10.1101/2023.12.09.570945

We used fiber photometry and the GRABDA dopamine sensor (AddGene #140554) to measure
dopamine activity during the task. AAV9-hsyn-GRAB DA2h was injected into the NAcc. To control for motion artifacts, mCherry (AAV1-CB7-CI-mCherry-WPRE-RBG, AddGene #105544) was also expressed because it is constitutively active. 60 nl of equal parts GRABDA and mCherry were delivered in each injection. Chronically implantable optic fibers (Thor labs) with 400 μm core, 0.5 NA fiber optics were implanted unilaterally over the injection site (DV -6.7). Doric Lenses hardware and software (Doric Neuroscience Studio) were used to record fluorescence. Two-channel motion artifact correction (TMAC) was used to correct for movement artifacts, with mCherry as the activity-independent channel.

Doric Acquisition

user manual
Doric Neuroscience Studio software was used to control the Doric Lenses hardware that recorded the fluorescence signals (activity-dependent, activity-independent channels) from two fibers [TODO: confirm if it is always two fibers, left and right hemisphere).

Doric File

The software can save data to .doric format (HDF5 based) or .csv. We have data for both examples.

.doric example structure

Channels Types

From the .doric file we can extract the timestamps for the fluosrescence signals using the "Time" field.
We can also retrieve the raw and isosbestic signals from the two fibers using the "AnalogIn" channels.
There is a field called "Username" that corresponds to each channel such as:

• AIN01: cordA-mCherry-raw
• AIN02: cordA-green-raw
• AIN03: cordB-mCherry-raw
• AIN04: cordB-green-raw
  Therefore cordA could correspond to ch1 and cordB to ch2 in the processed data.

However, we also have channels in "LockInAOUT" fields, namely:

• LockInAOUT01
  • AIN02: cordA-isos
  • AIN04: cordB-isos
• LockInAOUT02
  • AIN02: cordA-gfp
  • AIN04: cordB-gfp
• LockInAOUT03
  • AIN01: cordA-mCherry
• LockInAOUT04
  • AIN03: cordB-mCherry

The Lock-In mode can detect fluorescence signals embedded in strong noise (e.g. Isosbestic and a fluorophore) or separate multiple signals from a single input during fiber photometry.

So these are the demodulated and downsampled signals which are used for processing.