SpikeInterface / SpikeInterface/probeinterface
State of Neuropixels support in SpikeGadgets/Trodes
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- Dominant language
- Python
- Stars
- 85
- Forks
- 49
- Avg merge
- 13h 47m
- Merged PRs (30d)
- 3
Description
With #441 (NP2.0 support, currently in review), read_spikegadgets_neuropixels covers three of the seven (device, deviceSubType) pairs Trodes recognises (configuration.cpp:5246-5291):
(device, deviceSubType) |
Status |
|---|---|
("neuropixels1", "10") |
supported (NP1.0 standard) |
("neuropixels2", "1_SHANK") |
supported via #441 (extrapolated, not yet fixture-verified) |
("neuropixels2", "4_SHANK") |
supported via #441 (fixture-verified) |
("neuropixels1", "HD") |
missing (NP1.0 High Density) |
("neuropixels1", "NHP_SHORT") |
missing |
("neuropixels1", "NHP_MEDIUM") |
missing |
("neuropixels1", "NHP_LONG") |
missing |
("neuropixelsNRIC", ...) |
missing (different device, separate dispatch path) |
The bottleneck for the missing variants is that SpikeGadgets .rec files do not record the IMEC probe part number, so we can only resolve down to a family ((device, deviceSubType)) rather than to a specific SKU. If SpikeGadgets surfaced the part number from the probe's EEPROM the way SpikeGLX and the Open Ephys neuropixels-pxi plugin already do, several of the missing variants would land automatically as one-line dispatch entries.
In the meanwhile, we could read the Trodes source and implement similar remappings. But I would like to wait for users who have a real recording or an XML companion they can share as test data; without one I do not want to extrapolate, since each variant has enough edges to make a from-source-only implementation likely to be subtly wrong. Please leave a comment with the variant you record on and we can take it from there.
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start with read_spikegadgets_neuropixels and the device mappings in configuration.cpp:5246-5291, then compare the NP2.0 work in #441 and the corresponding Trodes source. Done means the missing variants have validated remappings backed by a real recording or XML companion fixture, rather than source-only extrapolation.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 45/100