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Fix the IBL Cbin extractor so that it works with 4 split shanks as well#4567

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rai-pranav wants to merge 1 commit intoSpikeInterface:mainfrom
int-brain-lab:fix/cbin-ibl-4-split-shanks
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Fix the IBL Cbin extractor so that it works with 4 split shanks as well#4567
rai-pranav wants to merge 1 commit intoSpikeInterface:mainfrom
int-brain-lab:fix/cbin-ibl-4-split-shanks

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@rai-pranav
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The .meta file that is produced when converting the Np2 probes to 4 individual shanks does not contain the ~ sign in front of the fileds which are lists, and hence the read_meta_file function from neo.rawio.spikeglxrawio fails. So I have written some functions which can handle this version of the meta file.

I am taking the latest way of getting the sample shifts during the merge conflit.
@rai-pranav
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Hi @alejoe91
I have created this PR to fix some IBL specific loading of the Np2 4 shanks dataset.
Some of the windows OS tests are failing which I don't think are related to the my changes. Any hints on how to resolve them?

@chrishalcrow
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Hello, I think the test failure was related to a downstream cache test failure here: https://github.com/SpikeInterface/spikeinterface/actions/runs/24997078165
I reran the caching successfully here: https://github.com/SpikeInterface/spikeinterface/actions/runs/25054593823
Which seems to have fixed the git-annex install here.
I'm not sure how to make this more robust, but at least the tests are passing now!

@rai-pranav
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I cannot directly assign reviewers to this PR.
Can someone please review this PR ? @chrishalcrow @alejoe91 🙏

@chrishalcrow
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Hi @rai-pranav , I think that all the probe reading logic should be handled by ProbeInterface instead of SpikeInterface.

I don't quite understand the problem. Does SpikeGLX produce these .meta files, or do you make them yourself when you convert your 4-shank recording into 4 1-shank recordings? If SpikeGLX makes them, we should update this function

https://github.com/SpikeInterface/probeinterface/blob/6c94c35dbdadc703ee38359fcd16d39bcf34aad6/src/probeinterface/neuropixels_tools.py#L875

to work with your data.

Could you share your .meta files? Would help me understand the issue better :)

@rai-pranav
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Hi @chrishalcrow
Thanks for your reply.

I have uploaded an example .meta file here

These meta files are produced when we convert the NP 2.4 probes to 4 1 shank probes. So I think this is very IBL specific, and that is why I was thinking including it inside cbin_ibl.py file would restrict it to the IBL data.

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2 participants