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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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