AllenNeuralDynamics / AllenNeuralDynamics/aind-smartspim-stitch

Channel organization and OME-Zarr

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#29 コメント 4 件 リアクション 1 件 担当者 1 名 @camilolaiton が担当を希望しています GitHub で見る
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Python
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4
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2
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4日 4時間
マージ済み PR(30日)
1

説明

I wanted to start a discussion about how we organize data and how it conforms to the OME-Zarr specification. Namely, I wanted to ask "should our spectral channels continue to be independent zarr files, or should they be on the [`c` axis ](https://ngff.openmicroscopy.org/latest/#image-layout)of a single NGFF spec file?"

This, of course, doesn't need to be a priority, but I think the discussion is worthwhile. I can foresee the following pros/cons of consolidating the volume in this way:

Pros:
- Better presentation in neuroglancer (brightness/contrast for each channel in one place, as opposed to treating each as a separate image) (I think?)
- Better discovery of available channels with data processing and analysis scripts. Is this true? Right now I would do a `glob('*Ex*.zarr')` type of search within a parent folder and parse the file name for channel identity, as opposed to looking within the metadata of the file to get channel identities.
- Follows the NGFF specification

Cons:
- Data organization is less human-readable, I guess. Channels will be in `0, 1, 2, . . .` folders instead of `Ex_488_Em_525.zarr, . . .` folders.
- This will take a (perhaps not small) amount of work within the capsule

I think that @dyf may have an opinion about the data organization/packaging aspects and @camilolaiton would have insight into the complexity of implementation.

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