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will-moore wants to merge 7 commits into from
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Support for import of labels up to 5D #7

will-moore wants to merge 7 commits into from

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@will-moore
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@will-moore will-moore commented Jun 26, 2025 •
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Add support for importing OME-Zarr labels as regular OMERO Masks, with binary data in the DB.

Based on code from https://github.com/IDR/idr0156-szabo-tadcnd/blob/main/scripts/create_rois.py

Use --labels argument to include labels.

Screenshot shows colours and Shape text values read from Labels exported with omero-cli-zarr:

Screenshot 2025-06-26 at 15 09 15

@will-moore will-moore mentioned this pull request Jun 26, 2025
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jburel commented Jun 26, 2025 •
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Do you have some 5D examples?
We have https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.2/6001240.zarr but version 0.2 is not supported by the pixel buffer
The "registration" does not work with labels, It works without
i.e.

s3://idr/zarr/v0.2/6001240.zarr/labels/0/.zattrs
Traceback (most recent call last):
  File "/home/omero/register.py", line 705, in <module>
    main()
  File "/home/omero/register.py", line 702, in main
    register_image(conn, uri, args.name, transport_params, endpoint=endpoint, uri_parameters=params, do_labels=args.labels)
  File "/home/omero/register.py", line 497, in register_image
    image, rnd_def = create_image(conn, img_attrs, uri, image_name, families, models, transport_params, endpoint, uri_parameters, do_labels)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omero/register.py", line 362, in create_image
    create_labels(conn, image, f"{labels_url}{labels_path}/", transport_params=transport_params)
  File "/home/omero/register.py", line 312, in create_labels
    axes = label_image["multiscales"][0]["axes"]
           ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^^^^^^
KeyError: 'axes'

We need to decide which version we support.
e.g 0.4+ similar to zarr-pixel-buffer

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jburel commented Jul 18, 2025 •
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Note that the PR introduced the need for new dependencies
Easiest option is to install ome-zarr and omero-rois

Attempting to import the image https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr

python register.py https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr --labels
leads to

labels_attrs {'labels': ['0']}
Traceback (most recent call last):
  File "/home/omero/register.py", line 760, in <module>
    main()
  File "/home/omero/register.py", line 754, in main
    obj = register_image(conn, uri, args.name, transport_params, endpoint=endpoint, uri_parameters=params, do_labels=args.labels)
          ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omero/register.py", line 500, in register_image
    image, rnd_def = create_image(conn, img_attrs, uri, image_name, families, models, transport_params, endpoint, uri_parameters, do_labels)
                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omero/register.py", line 363, in create_image
    create_labels(conn, image, f"{labels_url}{labels_path}/", transport_params=transport_params)
  File "/home/omero/register.py", line 320, in create_labels
    labels_nd = da.from_zarr(array_path)
                ^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.11/site-packages/dask/array/core.py", line 3796, in from_zarr
    z = zarr.open_array(store=store, path=component, **kwargs)
        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.11/site-packages/zarr/creation.py", line 645, in open_array
    init_array(
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.11/site-packages/zarr/storage.py", line 455, in init_array
    _init_array_metadata(
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.11/site-packages/zarr/storage.py", line 536, in _init_array_metadata
    shape = normalize_shape(shape) + dtype.shape
            ^^^^^^^^^^^^^^^^^^^^^^
  File "/home/omero/workspace/OMERO-server/.venv3/lib64/python3.11/site-packages/zarr/util.py", line 84, in normalize_shape
    raise TypeError("shape is None")

Same issue when issuing directly the uri (which makes sense) i.e.

python register.py s3://idr/zarr/v0.4/idr0062A/6001240.zarr --endpoint https://uk1s3.embassy.ebi.ac.uk --nosignrequest --labels

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jburel commented Jul 21, 2025

Tested independently of this work
The approach taken to "read the labels" does not yet work for v4 with labels

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jburel commented Jul 22, 2025

also tested with
https://uk1s3.embassy.ebi.ac.uk/bia-idr-integration/S-BIAD1961/experimentA/RP-TMA/RP-TMA-3_ROI01_multichannel.zarr/experimentA_backup/RP-TMA/RP-TMA-3_ROI01_multichannel.zarr/

@will-moore
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will-moore commented Jul 31, 2025 •
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Merged origin/main in...

Test with e.g:

$ python register.py --target 21520 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr --labels

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will-moore commented Jul 31, 2025 •
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With example above:

$ python register.py --target 21520 https://uk1s3.embassy.ebi.ac.uk/bia-idr-integration/S-BIAD1961/experimentA/RP-TMA/RP-TMA-3_ROI01_multichannel.zarr/experimentA_backup/RP-TMA/RP-TMA-3_ROI01_multichannel.zarr/ --labels

Gives error:

/Users/wmoore/Desktop/BIONGFF/omero-import-utils/metadata/register.py:116: RuntimeWarning: overflow encountered in scalar add
  for i in range(1, labels_nd.max() + 1):

The label data ( in that example looks like

labels_data [[[[[  0   0   0 ...   0   0   0]
    [  0   0   0 ...   0   0   0]
    [  0   0   0 ...   0   0   0]
    ...
    [  0   0   0 ... 255 255 255]
    [  0   0   0 ... 255 255 255]
    [  0   0   0 ... 255 255 255]]]]]

@dominikl
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dominikl commented Sep 2, 2025

This would actually be really useful to have for https://github.com/IDR/idr0173-breiter-alphasynuclein. Could we port that to omero-cli-zarr too?

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will-moore commented Sep 10, 2025

Moved to ome/omero-cli-zarr#180

@will-moore will-moore closed this Sep 10, 2025
@jburel jburel mentioned this pull request Sep 15, 2025
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@will-moore @jburel @dominikl