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convert2nwbEcephysPyNpx
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Martynas Dervinis 7a560fbbbe Update 'README.md' 1 year ago
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convert2nwb.py b61de047ec Fixed minor issues in localFunctions 2 years ago
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README.md

convert2nwbEcephysPyNpx

Python functions to convert extracellular electrophysiology recordings and associated behavioural data to Neurodata Without Borders (NWB) file format: Neuropixels example.

In order to download this repository, you will have to install GIN client. You can find the installation instructions here.

To download the repository execute the following lines in your command line:

gin get dervinism/convert2nwbEcephysPyNpx
cd convert2nwbEcephysPyNpx
gin get-content

Alternatively, you can download the repository through the web browser. In this case, large files may require to be downloaded individually.

PyNWB installation instructions are available here. Other dependencies include h5py, numpy, scipy, pathlib, os, re, datetime, dateutil which often come preinstalled.

Once you have downloaded and installed all the required dependencies you can execute convert2nwb script in Python. This should convert the example data into NWB format and store it inside the npx_derived_data_nwb folder. If you want to adapt the code for your own puprposes, have a look at the code and the comments inside Python scritps.

Keywords: Neurodata Without Borders; NWB; pynwb; extracellular electrophysiology; ecephys; Neuropixels; silicone probe; extracellular electrode; spiking; FAIR principles; open science.