SpikeInterface / SpikeInterface/spikeinterface
unable to detect channels outside of brain with `detect_bad_channels`
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 847
- Forks
- 280
- Avg merge
- 3d 9h
- Merged PRs (30d)
- 29
Description
Hi,
I tried to remove bad channels of my neuropixels 1.0 data, and the detect_bad_channels function could not detect any channels outside of brain no matter parameters...
key questions:
- since i shifted 48 channels to bank 1, channel 0-47 are actually at the top. in this case, what should i do with
outside_channels_location? - should i do this step on raw or highpass filtered data? with raw data, it can detect noise channels, but not on highpass filtered one. and yet by eye you can see those noisy channels that are outside of the brain:
ps. running spikeinterface v0.101.0 on linux fedora 39
Thanks!
Contributor guide
No contributing guide indexed for this repository
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 the detect_bad_channels entry point and reproduce the behavior using the reported Neuropixels 1.0 data, comparing raw and highpass-filtered inputs and the outside_channels_location setting. Done means the channel-location and filtering behavior is clarified, with a confirmed fix or documented limitation and relevant regression coverage.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100