SpikeInterface / SpikeInterface/spikeinterface
Loading SpikeGLX survey mode recordings
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- Python
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Description
Hello,
SpikeGLX has a Survey mode (https://vimeo.com/783581937) to map the activity of all the banks on a neuropixels probe. It would be very useful to load these sessions in spikeinterface to compute some metrics on the entire probe. I imagine one way would be to aggregate the channels of the different bank recordings into one recording as if they were recorded simultaneously.
Here is some code from Jennifer Colonell that loads such recording in Matlab: https://github.com/jenniferColonell/SpikeGLX_Datafile_Tools/blob/main/MATLAB/SGLX_readMeta.m, function svyBankTimes.
The main difference with a normal recording is the addition of the field ~svySBTT in the metadata, indicating the start sample for each shank/bank. I am unsure what the two sample numbers for each bank correspond to. My guess is that the first sample is when the recording changes bank and the second is when the amplifiers have settled.
I am including a file with such survey mode recording. Note that there is nothing interesting in this recording as it's just a probe in the air with a survey of only 5s per bank.
Onedrive link to the compressed recording
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Research direction
Start by comparing the MATLAB SGLX_readMeta.m function svyBankTimes with the SpikeGLX recording-loading path, focusing on the ~svySBTT metadata field and its two sample values. Done means a supplied Survey mode recording can be loaded and its bank channels represented as one recording with the correct timing.
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Assessment
- Tech stack
- python
- Domain
- data
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100