probeinterface

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A Python package to handle the layout, geometry, and wiring of silicon probes for extracellular electrophysiology experiments.

Documentation : https://probeinterface.readthedocs.io/

Goals

Make a lightweight package to handle:

• probe contact geometry (both 2D and 3D layouts)
• probe shape (contour of the probe, shape of channel contact, ...)
• probe wiring to device (the physical layout often doesn't match the channel ordering)
• combining several probes into a device with global geometry + global wiring
• exporting probe geometry data into JSON files
• loading existing probe geometry files (Neuronexus, imec, Cambridge Neurotech...) Started here

Bonus :

• optional plotting (based on matplotlib)
• load/save geometry using common formats (PRB, CSV, NWB, ...)
• handle SI length units correctly um/mm/...

Target users/projet :

• spikeinterface team : integrate this into spikeextractor for channel location
• neo team : handle array_annotations for AnalogSignal
• spikeforest team : use this package for ploting probe activity
• phy team: integrate for probe display
• spyking-circus team : handle probe with this package
• kilosort team : handle probe with this package
• tridesclous team : handle probe with this package
• open ephys team : automatically generate channel map configuration files

Author: Samuel Garcia