Testing data for registration

[jburel]

Sample data that we have evaluated the registration workflows

Testing workflow & data for metadata/register.py script.

For Images, create a Dataset and use the ID as --target below:

OME-Zarr v0.4

Embassy image - duplicate:

python register.py --target 21520 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0101A/13457227.zarr
python register.py --target 21520 --endpoint https://uk1s3.embassy.ebi.ac.uk/ --nosignrequest s3://idr/zarr/v0.4/idr0101A/13457227.zarr

AWS images - first 2 are duplicates:

python register.py --target 21520 https://s3.us-east-1.amazonaws.com/gs-public-zarr-archive/CMU-1.ome.zarr/0
python register.py --target 21520 --endpoint https://s3.us-east-1.amazonaws.com/ s3://gs-public-zarr-archive/CMU-1.ome.zarr/0 --nosignrequest
python register.py --target 21520 https://data.source.coop/joshmoore/idr-ome-ngff-samples/v0.4/idr0062A/6001240.zarr

Google cloud - bioformats2raw.layout - 3 images

python register.py --target 21520 https://storage.googleapis.com/jax-public-ngff/example_v2/LacZ_ctrl.zarr

bioformats2raw.layout (single image)

python register.py --target 21520 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0048A/9846151.zarr/

plate from idr0011 (48 Wells, 1 field):

python register.py https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/S-BIAD866/7f95aba3-cfbf-4ae8-a106-edaa36f5b07f/7f95aba3-cfbf-4ae8-a106-edaa36f5b07f.zarr/

plate from idr0001 (96 Wells, 6 fields - 6 acquisitions):

python register.py https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr

Test rendering settings (image also has labels)

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/

Others

• https://s3.embl.de/spatialdata/spatialdata-sandbox/mcmicro_io.zarr/labels/exemplar-001_cell/
• https://files.cryoetdataportal.cziscience.com/10162/ycw2012-03-12-3/Reconstructions/VoxelSpacing15.480/Tomograms/100/ycw2012-03-12-3.zarr
• https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/EMPIAR-10094/IM1/IM1.zarr/0 (unint32)
• https://uk1s3.embassy.ebi.ac.uk/idr/share/microscopynodes/20250730/FIBSEM_dino_masks.zarr/ (rnd settings issue)

OME-Zarr v0.5

NB: register.py script works, but images are not yet viewable with omero-zarr-pixel-buffer)

Embassy image (with labels):

python register.py --target 21520 https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/0.0.5/6001240_labels.zarr

bioformats2raw.layout

python register.py --target 21520 https://uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0066/ExpB_whole_cns_MIP.ome.zarr

Plate

python register.py https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.5/idr0010/76-45.ome.zarr