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Add OmeZarr v0.4 metadata support #32

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bogovicj opened this issue Mar 15, 2022 · 3 comments
Open

Add OmeZarr v0.4 metadata support #32

bogovicj opened this issue Mar 15, 2022 · 3 comments

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@bogovicj
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I hope that it will be possible to incorporate mobie/mobie-viewer-fiji#596 by @KateMoreva
(and, if necessary, other parts of https://github.com/mobie/mobie-viewer-fiji) to achieve this.

@tischi @constantinpape

@constantinpape
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constantinpape commented Mar 15, 2022

Hi @bogovicj,
thanks for following up on this. We are still very interested in doing this. We (to be more precise @KateMoreva and @K-Meech who did the actual work ;)) were just very busy with finishing the MoBIE release for intial ome.zarr v0.4 support.
This is done since yesterday, so this is on the agenda now and we will reach out as soon as there is more to discuss :).

@bogovicj
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Summary of the discussion with @KateMoreva and @constantinpape today.

Action items

Long(er) term

  • Decide what class(es) should store these image data (SourceAndConverter, Source ?)
    • how does this affect other code using the metadata (e.g. in n5-ij could we make an ImagePlus (or imageJ2 Dataset) from a Source)?
    • deprecate redundant classes (e.g. N5Source)
  • Consider moving some of this into the ome group. Need to talk to @joshmoore

@tischi
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tischi commented May 18, 2022

  • how does this affect other code using the metadata (e.g. in n5-ij could we make an ImagePlus (or imageJ2 Dataset) from a Source)?

Not sure this is the right place to discuss this but with @tpietzsch we talked about having an ImageDataSet class that would hold on to the data and then have methods such as asImagePlus() or asSourceAndConverter(), or maybe rather implements SourceAndConverter.

This could serve as a place to start thinking about this: https://github.com/imaris/imglib2-imaris-bridge/blob/master/src/main/java/com/bitplane/xt/ImarisDataset.java

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