Migrate uk1s3.embassy to livingobjects everywhere

[will-moore]

#32 fixes URLs in this repo, but we need to update ALL our repos with the same change!

The idr bucket name is unchanged, but other bia buckets are being renamed:

Embassy	LivingObjects
bia-apps	bioimaging-01-pub/bia-apps
bia-empiar-integration	bioimaging-01-pub/bia-empiar-integration
bia-empiar-manifests	bioimaging-01-pub/bia-empiar-manifests
bia-idr-integration	bioimaging-idr-integration
bia-integrator-data	bioimaging-integrator-data
bia-zarr-test	bioimaging-01-pub/bia-zarr-test
ebi-ngff-challenge-2024	bioimaging-01-pub/ebi-ngff-challenge-2024
testbucket-bia	bioimaging-sandbox/testbucket-bia
testbucket-empiar-bia	bioimaging-sandbox/testbucket-empiar-bia

Listing repos to get an idea of what's needed and keep track. Start by searching for uk1s3.embassy across all ome and IDR repos...

• Petr https://github.com/ome/napari-ome-zarr · README.md the PR is livingobjects ome/napari-ome-zarr#148
• Petr https://github.com/ome/ngff · resources/data/index.md the PR is livingobjects ome/ngff#497
• Petr https://github.com/ome/ome2024-ngff-challenge · dev1/resave.py the PR is replace all uk1s3.embassy with livingobjects ome/ome2024-ngff-challenge#107
• Petr https://github.com/ome/www.openmicroscopy.org · build.sh PR is Replace with livingobjects ome/www.openmicroscopy.org#862
• Petr https://github.com/ome/omero-ms-zarr · src/scripts/fetch-ms-zarr.py the PR is livingobjects ome/omero-ms-zarr#129
• https://github.com/ome/omero-analysis-desktop · napari_s3.ipynb
• Will: Fix New livingobjects location not correct for some samples ome/ome2024-ngff-challenge#109 (comment) PR is Fix livingobjects ebi-ngff-challenge-2024 links ome/ome2024-ngff-challenge#111
• Petr omero-guide-fiji view_mobie_zarr.rst -> PR is livingobjects ome/omero-guide-fiji#35
• https://github.com/ome/ome_zarr_test_suite · sources.yml
• Petr -won't fix, images were not migrated, repo not maintainable https://github.com/ome/EMBL-EBI-imaging-course-05-2022 · Day_4/Solutions_0_Python_API.ipynb - PR is livingobjects 2nd batch ome/EMBL-EBI-imaging-course-05-2022#13
• Petr https://github.com/ome/presentations · 2025/Woods_Hole/viewing_omezarr/index.html PR is livingobjects ome/presentations#188
• Petr https://github.com/ome/EMBL-EBI-imaging-course-04-2024 · Day_5/S3minio.ipynb -> PR is livingobjects ome/EMBL-EBI-imaging-course-04-2024#17
• https://github.com/ome/ZarrReader · README.md
• Petr https://github.com/ome/omero-guide-python · scripts/idr0044_zarr_segmentation_cluster.py PR is livingobjects ome/omero-guide-python#63
• https://github.com/ome/ome-ngff-prototypes · workflows/mobie-example/create_mobie_ome_zarr_example_project.py
• https://github.com/ome/ome-ngff-tools · docs/_data/features.yml
• Petr https://github.com/ome/EMBL-EBI-imaging-course-04-2025 · Reading_zarr_images.ipynb the PR is livingobjects ome/EMBL-EBI-imaging-course-04-2025#12
• Petr https://github.com/ome/ABIS-GBI-imaging-course-07-2023 · notebooks/Cellpose_parallel.ipynb the PR is livingobjects ome/ABIS-GBI-imaging-course-07-2023#4
• https://github.com/ome/napari-ome-zarr · .napari/DESCRIPTION.md PR is livingobjects ome/napari-ome-zarr#148
• Petr https://github.com/ome/EMBO-Practical-Course-2023 · 5_Cloud_Bash.ipynb PR is livingobjects ome/EMBO-Practical-Course-2023#2
• https://github.com/ome/ome-zarr-catalog · public/zarr_samples.csv
• Jmarie and Petr Cellpose_parallel.ipynb](Update endpoint ome/EMBL-EBI-imaging-course-03-2026#4) the PRs are Update endpoint ome/EMBL-EBI-imaging-course-03-2026#4 and Integrator ome/EMBL-EBI-imaging-course-03-2026#5
• https://github.com/ome/ome-zarr-catalog · public/csv_examples/url_only.csv
• Petr https://github.com/ome/omero-guide-ilastik · notebooks/idr0062_pixel_classification_zarr.ipynb the PR is livingobjects ome/omero-guide-ilastik#41
• https://github.com/ome/ome-zarr-catalog · public/csv_examples/idr_study.csv
• Petr https://github.com/ome/www.openmicroscopy.org · _posts/2021-12-16-ome-ngff.md the PR is Replace with livingobjects ome/www.openmicroscopy.org#862
• Petr https://github.com/ome/www.openmicroscopy.org · _posts/2020-12-01-zarr-hcs.md the PR is Replace with livingobjects ome/www.openmicroscopy.org#862
• Petr https://github.com/ome/www.openmicroscopy.org · _posts/2020-11-04-zarr-data.md the PR is Replace with livingobjects ome/www.openmicroscopy.org#862
• Petr https://github.com/ome/ome2024-ngff-challenge · samples/other_samples.csv the PR is replace all uk1s3.embassy with livingobjects ome/ome2024-ngff-challenge#107
  • Petr LOTs of others from the challenge - not listing all here! the PR is replace all uk1s3.embassy with livingobjects ome/ome2024-ngff-challenge#107
  • Petr https://github.com/ome/ome2024-ngff-challenge-metadata · uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/0.0.5/6001240.zarr/zarr.json the PR is replace with livingobjects ome/ome2024-ngff-challenge-metadata#1
  • Petr Also https://github.com/ome/ome2024-ngff-challenge-metadata · raw.githubusercontent.com/will-moore/ome2024-ngff-challenge/samples_viewer/samples/other_samples.csv etc the PR is replace with livingobjects ome/ome2024-ngff-challenge-metadata#1
  • Petr https://github.com/ome/ome2024-ngff-challenge-metadata · uk1s3.embassy.ebi.ac.uk/idr/share/ome2024-ngff-challenge/idr0048/9846151_3D_chunks.zarr/0/zarr.json the PR is replace with livingobjects ome/ome2024-ngff-challenge-metadata#1
• Petr https://github.com/ome/napari-ome-zarr · napari_ome_zarr/_reader.py PR is livingobjects ome/napari-ome-zarr#148
• Petr https://github.com/ome/omero-guide-fiji · scripts/groovy/mobie_ome_zarr.groovy the PR is livingobjects ome/omero-guide-fiji#35
• Petr https://github.com/ome/ngff · rfc/6/index.md PR is livingobjects ome/ngff#497
• Petr https://github.com/ome/omero-guide-python · scripts/idr0044_zarr_segmentation_parallel.py the PR is livingobjects ome/omero-guide-python#63
• Petr https://github.com/ome/EMBL-EBI-imaging-course-05-2023 · Day_5/Cellpose_parallel.ipynb the PR is Fix S3 urls, update tests ome/EMBL-EBI-imaging-course-05-2023#18

BioNGFF

• Will: https://github.com/BioNGFF/biongff-viewer · README.md PR is Update uk1s3.embassy to livingobjects BioNGFF/biongff-viewer#48
• Will: https://github.com/BioNGFF/ome-zarr.js · docs/luts.md
  • Lots of others from ome-zarr.js - PR is update bia urls to livingobjects BioNGFF/ome-zarr.js#32
• Will: https://github.com/BioNGFF/vizarr · python/notebooks/IDR_example.ipynb PR is Update uk1s3.embassy URLs to livingobjects BioNGFF/vizarr#77
• Will: https://github.com/BioNGFF/vizarr · [fixtures/6001240_labels.yaml] (https://github.com/BioNGFF/vizarr/blob/33c04109b008d9612fee755f2313debf2633d36f/fixtures/6001240_labels.yaml#L3) PR is Update uk1s3.embassy URLs to livingobjects BioNGFF/vizarr#77
• https://github.com/BioNGFF/omero-import-utils · metadata/test_register.sh

gists

• will-moore / OMERO.figure_NGFF_demo.json
• will-moore / ngff_images_figure.json
• dominikl / list_submissions.py

Others:

• Update uk1s3.embassy URLs to livingobjects hms-dbmi/vizarr#346
• Update uk1s3.embassy links to livingobjects ome/omero-cli-zarr#194 (don't know why this didn't show up in search above?)
• Update uk1s3.embassy urls to livingobjects ome/ome-ngff-validator#72
• https://github.com/mobie/mouse-embryo-spatial-transcriptomics-project/blob/c4a9f52496b5f0cd0fae3c6027788e867cf8e5f0/add_idr_links.py#L10 https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0138A/TimEmbryos-120919/HybCycle_29

[will-moore]

@joshmoore Trying to decide what under "share" on the idr bucket needs to be kept/migrated and what can be deleted?
Checked items have been copied to livingobjects:
E.g.

./rclone sync embassy:/idr/share/microscopynodes livingobjects:/idr/share/microscopynodes --progress --transfers=16 --checkers=16 --s3-chunk-size=64M --s3-upload-concurrency=8

• share/2021-Q1-3D (13 GB)
• share/biohackeu20 (1.944 KiB)
• share/community-bioc (208 GB)
• share/community-call-2020-10-29 (154 GiB)
• share/esa-sentinel (217 GB)
• share/gbi2022 (564 MiB)
• share/i2k2020 (159 GB)
• share/idr0106-ome-tiff (39 GB)
• share/microscopynodes (done ?)
• share/ome2024-ngff-challenge (lots!)
• share/spatialdata-2023 (133 MiB)
• share/zarr-demo (1.828 KiB)