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ome / omero-cli-zarr

https://pypi.org/project/omero-cli-zarr/
GNU General Public License v2.0
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Export dataset #88

Closed will-moore closed 2 years ago

will-moore commented 2 years ago

This PR replaces https://github.com/ome/omero-cli-zarr/pull/83 for export of a Dataset from OMERO:

$ omero zarr export Dataset:1

This will create a top-level group, named after the Dataset ID: 1.zarr The group metadata lists images using their name as a path:

"collection": {
  "images": {
    "image_name1.tiff": {},
    "image_name2.tiff": {}
  }
}

NB: as noted on PR above, some characters in image names break this, e.g. /, [, ] so need to handle them.

Recent test export using commit 8dc4707 below is hosted at https://minio-dev.openmicroscopy.org/idr/v0.3/datasets/idr0043/13901.zarr and can be viewed in vizarr but it not very reliable (see https://github.com/hms-dbmi/vizarr/pull/124#issuecomment-934226522)

Screenshot 2021-10-05 at 10 43 49

joshmoore commented 2 years ago

I assume this is closed waiting on https://github.com/ome/ngff/pull/67? It might be interesting to try the strategy here with the OME-XML from https://github.com/ome/ngff/issues/104

will-moore commented 2 years ago

Try an OME-XML strategy from the bioformats2raw export? Or generate OME-XML via python? Not sure what "the strategy" means here?

joshmoore commented 2 years ago

I meant generate OME-XML from this plugin to match the specs in 104 which tie multiple images together into a single collection.