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
Provides
Requires
License
MIT
Changelog
* Mon May 05 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.28-1
- Update to 0.2.28 (close RHBZ#2364054)
* Mon May 05 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.27-1
- Update to 0.2.27 (close RHBZ#2364031)
* Mon May 05 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.26-3
- F41+: Use the provisional pyproject declarative buildsystem
* Wed Mar 12 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.26-2
- Add a weak dependency on python3-jsonschema
- Remove testing workaround for formerly-missing JSON schema file
* Wed Mar 12 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.26-1
- Update to 0.2.26 (close RHBZ#2351534)
* Fri Feb 07 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.25-2
- Conditionalize Zarr BuildRequires and associated tests
* Fri Feb 07 2025 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.25-1
- Update to 0.2.25 (close RHBZ#2344205)
* Sat Jan 18 2025 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.24-2
- Rebuilt for https://fedoraproject.org/wiki/Fedora_42_Mass_Rebuild
* Fri Sep 06 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.24-1
- Update to 0.2.24 (close RHBZ#2310398)
* Thu Jul 18 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.23-1
- Update to 0.2.23 (close RHBZ#2298480)
* Mon Jul 15 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.22-1
- Update to 0.2.22 (close RHBZ#2297975)
* Mon Jun 17 2024 Python Maint <python-maint@redhat.com> - 0.2.21-3
- Rebuilt for Python 3.13
* Mon Feb 05 2024 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.21-1
- Update to 0.2.21 (close RHBZ#2262778)
* Fri Jan 26 2024 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.20-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
* Mon Jan 22 2024 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.20-3
- Rebuilt for https://fedoraproject.org/wiki/Fedora_40_Mass_Rebuild
* Mon Dec 18 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.20-2
- Assert that %pyproject_files contains a license file
* Tue Dec 12 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.20-1
- Update to 0.2.20 (close RHBZ#2254044)
* Thu Nov 02 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.19-1
- Update to 0.2.19
* Tue Oct 31 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.18-1
- Update to 0.2.18 (close RHBZ#2247108)
* Fri Jul 21 2023 Fedora Release Engineering <releng@fedoraproject.org> - 0.2.17-4
- Rebuilt for https://fedoraproject.org/wiki/Fedora_39_Mass_Rebuild
* Wed Jul 12 2023 Benjamin A. Beasley <code@musicinmybrain.net> - 0.2.17-3
- Use trailing slashes for directories in files lists
* Wed Jun 28 2023 Python Maint <python-maint@redhat.com> - 0.2.17-2