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[New Format]: Inscopix #707

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CodyCBakerPhD opened this issue Jan 16, 2024 · 8 comments · May be fixed by #714
Open
2 tasks done

[New Format]: Inscopix #707

CodyCBakerPhD opened this issue Jan 16, 2024 · 8 comments · May be fixed by #714
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@bendichter
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data interfaces enhancement

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@CodyCBakerPhD
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What format would you like to see added to NeuroConv?

Inscopix finally releases an open API

Does the format have any documentation?

Not as far as I can tell, but could be inferred from some of the source code at https://github.com/inscopix/py_isx/blob/main/isx/__init__.py

Existing APIs for format

https://github.com/inscopix/py_isx

Do you have any example files you are willing to share?

Test files found with releases: https://github.com/inscopix/py_isx/releases

Do you have any interest in helping implement the feature?

Yes.

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@bendichter
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@CodyCBakerPhD see test data addition PR here: https://gin.g-node.org/CatalystNeuro/ophys_testing_data/pulls/19

@bendichter
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blocked by catalystneuro/roiextractors#274

@CodyCBakerPhD
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You mean blocked by inscopix/pyisx#45?

@CodyCBakerPhD
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Oh I see, catalystneuro/roiextractors#274 blocked by inscopix/pyisx#45 as a chain

@bendichter
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I'm thinking about it as a chain of dependencies. This is blocked by catalystneuro/roiextractors#274 and catalystneuro/roiextractors#274 is blocked by inscopix/pyisx#45, so effectively this is blocked by inscopix/pyisx#45. I wish GitHub offered a better way to express this formally.

@CodyCBakerPhD
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Do they not even have a static FPS attributed to the files? Exact timestamps technically aren't necessary for instantiating the SegmentationExtractor

@bendichter
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Yes but it looks like they have not exposed that attribute yet in a non-private method

@sg-s
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sg-s commented Jan 23, 2024

also docs, are available here: https://inscopix.github.io/py_isx/

@bendichter bendichter linked a pull request Jan 24, 2024 that will close this issue
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add inscopixdatainterface.py catalystneuro/neuroconv
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@bendichter @sg-s @CodyCBakerPhD