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[Feature]: Suite2p multiple optical channels #234

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tuanpham96 opened this issue Jul 24, 2023 · 1 comment · Fixed by #242
Closed
4 tasks done

[Feature]: Suite2p multiple optical channels #234

tuanpham96 opened this issue Jul 24, 2023 · 1 comment · Fixed by #242
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enhancement New feature or request

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@tuanpham96
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What would you like to see added to ROI Extractors?

What would you like to see added to NeuroConv?

Some datasets might have multiple optical channels, for example a second channel with certain genetic tags. The F.npy and Fneu.py would have additional files called F_chan2.npy and Fneu_chan2.npy. No spks_chan2.npy as far as I know.

Here's an example sample dataset: https://gitlab.com/fleischmann-lab/calcium-imaging/calimag/-/tree/master/data/v2021_05-2p-Simon/suite2p

A "trimmed" version can be found here: https://gitlab.com/fleischmann-lab/calcium-imaging/calimag/-/tree/master/data/v2021_05-2p-Simon/suite2p_trim

suite2p
├── plane0
│   ├── F.npy
│   ├── F_chan2.npy
│   ├── Fneu.npy
│   ├── Fneu_chan2.npy
│   ├── iscell.npy
│   ├── ops.npy
│   ├── redcell.npy
│   ├── spks.npy
│   └── stat.npy
├── plane1
│   ├── F.npy
│   ├── F_chan2.npy
│   ├── Fneu.npy
│   ├── Fneu_chan2.npy
│   ├── iscell.npy
│   ├── ops.npy
│   ├── redcell.npy
│   ├── spks.npy
│   └── stat.npy
└── plane2
    ├── F.npy
    ├── F_chan2.npy
    ├── Fneu.npy
    ├── Fneu_chan2.npy
    ├── iscell.npy
    ├── ops.npy
    ├── redcell.npy
    ├── spks.npy
    └── stat.npy

Is your feature request related to a problem?

No response

Do you have any interest in helping implement the feature?

Yes, but I would need guidance.

Code of Conduct

Do you have any interest in helping implement the feature?

Yes, but I would need guidance.

Code of Conduct

@weiglszonja
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@CodyCBakerPhD I can work on this, this is relevant for the Pinto conversion as well.

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