https://bugzilla.redhat.com/show_bug.cgi?id=2012917
Bug ID: 2012917
Summary: Review Request: python-probeinterface - Handles probe
layout, geometry, and wiring to device
Product: Fedora
Version: rawhide
Hardware: All
OS: Linux
Status: NEW
Component: Package Review
Severity: medium
Priority: medium
Assignee: [email protected]
Reporter: [email protected]
QA Contact: [email protected]
CC: [email protected]
Target Milestone: ---
Classification: Fedora
Spec URL: https://music.fedorapeople.org/python-probeinterface.spec
SRPM URL:
https://music.fedorapeople.org/python-probeinterface-0.2.5-1.fc34.src.rpm
Description:
A Python package to handle the layout, geometry, and wiring of silicon probes
for extracellular electrophysiology experiments.
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/project:
• spikeinterface team: integrate this into spikeextractor for channel
location
• neo team: handle array_annotations for AnalogSignal
• spikeforest team: use this package for plotting 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
Fedora Account System Username: music
Koji scratch builds:
F36: https://koji.fedoraproject.org/koji/taskinfo?taskID=77076410
F35: https://koji.fedoraproject.org/koji/taskinfo?taskID=77076411
F34: https://koji.fedoraproject.org/koji/taskinfo?taskID=77076413
F33: https://koji.fedoraproject.org/koji/taskinfo?taskID=77076414
This is a dependency for python-spikeinterface
(https://pagure.io/neuro-sig/NeuroFedora/issue/473), and @neuro-sig will have
commit privileges.
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