Python package to handle probe layout, geometry and wiring to device.
Project description
probeinterface
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
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