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Add functionality to remove labels/views etc. from zarr file and MoBIE dataset #24

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imagejan opened this issue Apr 5, 2023 · 1 comment
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@imagejan
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imagejan commented Apr 5, 2023

Use case while developing an image analysis solution:

  • run some segmentation on ome-zarr data, save into labels/<some_id> and add as segmentation view into some MoBIE project;
  • after trying out multiple approaches (possibly in several subgroups of labels/ in each well group of the ome-zarr dataset, we'd like to remove previous segmentation trials while keeping both the zarr file and the MoBIE dataset intact:
    • remove the labels/<some_id> folder from each subgroup of the zarr file
    • (possibly) remove labels entries from .zattrs (listing of labels subgroup is not yet in the ngff spec)
    • remove the corresponding sources and views from the MoBIE dataset.
@imagejan
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For MoBIE, we have remove_source to remove single sources, but we'll have to still get the (merged grid) view and iterate over its sources (and check if the sources are used somewhere else) before finally removing the mergedGrid from the sourceTransforms.

Also, this functionality would possibly fit upstream into mobie-utils-python.

@tibuch tibuch added this to the Code cleanup milestone Oct 9, 2023
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