hernan-lab-to-nwb

This package converts neurophysiology data to NWB and it prompts the user to interact with excel files to fill out metadata information!

Development information:

• Validated on MAC silicon M2 - only use on mac devices!
• Early testing and development on PC underway
• Supports Neuralynx, UCLA miniscope, Pinnacle
  • Neuralynx handles .ncs, .ntt, .nvt, .nev files
  • UCLA Miniscope handles .avi and .json files
  • Pinnacle handles multiple, simultaneously recorded animals if relevant. No inputs required.

Workflow:

• Define your directory in terminal python shell
• Interact with excel sheets

Relevant notebook:

• .../tests/fulltest.ipynb

Current supported formats:

1. Neuralynx:
   • Must have data from one session in a unique folder
2. UCLA Miniscope:
   • Must have data from one session in a unique folder. In the subfolder with name "miniscope", you must have all recorded movies in that folder from that session! So 0.avi, 1.avi, 2.avi, 3.avi.
   • This code works by loading each file separately, then adding that file to the NWB File. To avoid loading the fullfile to memory, the nwbfile is loaded lazily, then the next movie is added.
3. Pinnacle:
   • Can have as many animals as you want in a unique folder. Handles multiple simultanoeous recordings across animals

Download

1. Download anaconda3 and git.
2. Run the lines below in your terminal (mac) or conda terminal (pc)

conda create -n my_env python=3.9
conda activate my_env
git clone https://github.com/JohnStout/hernan-lab-to-nwb 
cd hernan-lab-to-nwb
pip install -e .

Close terminal and re-open upon first installation

Converting data in terminal:

1. Open terminal (if on mac, normal terminal. If on PC, open conda terminal).
2. Enter the greyed out lines below in your terminal:

Activate your environment

conda activate my_env

Start python

python

Import package

from hernan_lab_to_nwb.converters import convert

Enter directory

dir = r' your directory '

IF MINISCOPE:

convert(dir).miniscope()

IF NEURALYNX:

convert(dir).neuralynx()

IF PINNACLE:

convert(dir).pinnacle()

Interface with Terminal

mov1.mov

Follow Terminal Instructions

mov2.mov

Interact with Excel to fill out NWB metadata

mov3.mov

Use Excel to define metadata about recording devices

mov4.mov

Watch Terminal window to monitor progress

mov5.mov

Important Details Regarding Credit

These packages/sources were used directly or modified. Neuralynx .nvt file reader from Ben Dichters CatalystNeuro team.

• neo: https://github.com/NeuralEnsemble/python-neo
• CatalystNeuro: https://github.com/catalystneuro