spikeline_cloud

Spike sorting pipeline for generating consensus units from neuropixel recordings. Much of this repo has been moved to https://github.com/esutlie/data_transfer as part of a holistic post-processing pipeline. Please reference that repo.

About The Project

This is the postprocessing pipeline used by the Shuler lab to extract spike times from ephys recordings collected with Neuropixel Probes. It uses Spike Interface to run multiple sorting algorithms and find consensus units.

Installation

Requirements

• Spike Interface (https://github.com/SpikeInterface)
• Kilosort 2.5 (https://github.com/MouseLand/Kilosort/releases/tag/v2.5)
• Kilosort 3 (https://github.com/MouseLand/Kilosort)

Follow install and requirements instructions from the Spike Interface and Kilosort Readme files.

Clone the repo

git clone https://github.com/esutlie/spikeline_cloud.git

Change the directories to point to your installations of Kilosort 2.5 and Kilosort3

os.environ['KILOSORT3_PATH'] = os.path.join('PATH', 'TO', 'Kilosort3')
os.environ['KILOSORT2_5_PATH'] = os.path.join('PATH', 'TO', 'Kilosort2_5')

Change the path variable to point to the folder containing your recording data

if __name__ == '__main__':
    path = os.path.join('PATH', 'TO', 'RECORDINGS')
    batch_sort(path)

License

Distributed under the MIT License. See LICENSE.txt for more information.

Contact

Elissa Sutlief - [email protected]

Project Link: https://github.com/esutlie/spikeline_cloud

Acknowledgments

• https://github.com/SpikeInterface
• https://github.com/MouseLand/Kilosort

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