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Merged
jburel merged 8 commits into from
Apr 8, 2026
Merged

livingobjects #63

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ed3ea9a
livingobjects
pwalczysko Apr 7, 2026
11182f1
Fix v0.4 and add idr0044 to url
pwalczysko Apr 7, 2026
490b906
Fix the url to the idr0044 image also in 2 .py scripts
pwalczysko Apr 7, 2026
99acd79
fix build
pwalczysko Apr 7, 2026
0332cb6
try
pwalczysko Apr 7, 2026
0f841aa
Change the micromamba setup action
pwalczysko Apr 7, 2026
28ca806
update env packages
pwalczysko Apr 7, 2026
a5e6812
Update also distributed
pwalczysko Apr 7, 2026
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6 changes: 3 additions & 3 deletions .github/workflows/build.yml
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Original file line number Diff line number Diff line change
Expand Up @@ -13,15 +13,15 @@ jobs:
build:
strategy:
matrix:
os: [ubuntu-latest, windows-latest, macos-latest]
os: [ubuntu-24.04, windows-latest, macos-latest]
runs-on: ${{ matrix.os }}
steps:
- uses: actions/checkout@v4
- uses: actions/setup-python@v5
with:
python-version: '3.9'
python-version: '3.12'
- name: Install Conda environment with Micromamba
uses: mamba-org/provision-with-micromamba@v15
uses: mamba-org/setup-micromamba@v3
with:
environment-file: binder/environment.yml
environment-name: binder
14 changes: 7 additions & 7 deletions binder/environment.yml
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Expand Up @@ -2,20 +2,20 @@ name: omero-guide-python
channels:
- conda-forge
dependencies:
- python==3.9.*
- python==3.12.*
- conda-forge::zeroc-ice==3.6.5
- distributed==2022.2.0
- distributed==2026.3.0
- pip
- pip:
- matplotlib==3.8.4
- pooch==1.8.1
- omero-py==5.19.2
- omero-py==5.22.1
- scikit-image==0.22.0
- pandas==2.2.2
- pandas==3.0.2
- jupyter==1.0.0
- ome-zarr==0.8.3
- ome-zarr==0.14.0
- dask-image==2023.8.1
- cellpose==3.0.7
- geojson==3.1.0
- geojson==3.2.0
# dependency used to convert the OMERO masks into numpy array
- omero-cli-zarr==0.5.5
- omero-cli-zarr==0.8.0
4 changes: 2 additions & 2 deletions notebooks/idr0044_zarr_segmentation_parallel.ipynb
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Expand Up @@ -90,8 +90,8 @@
"outputs": [],
"source": [
"def load_binary_from_s3(id, resolution='4'):\n",
" endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'\n",
" root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)\n",
" endpoint_url = 'https://livingobjects.ebi.ac.uk/'\n",
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@will-moore will-moore Apr 7, 2026 •
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As on a previous PR, this attempts to load 4007801.zarr from https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/4007801.zarr

But this image hasn't been migrated to livingobjects.

Instead you need to use:
https://livingobjects.ebi.ac.uk/idr/zarr/v0.4/idr0044A/4007801.zarr

So, either add the extra idr0044A to the line below,

root = 'idr/zarr/v0.4/idr0044/%s.zarr/%s/' % (id, resolution)\n",

or just update v0.4 here and add idr0044 where the function is called

load_binary_from_s3("idr0044/4007801", resolution)

" root = 'idr/zarr/v0.4/idr0044/%s.zarr/%s/' % (id, resolution)\n",
" return da.from_zarr(endpoint_url + root)"
]
},
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2 changes: 1 addition & 1 deletion notebooks/idr0062_prediction_zarr_public_s3.ipynb
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Expand Up @@ -76,7 +76,7 @@
"metadata": {},
"outputs": [],
"source": [
"ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'"
"ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'"
]
},
{
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2 changes: 1 addition & 1 deletion notebooks/zarr-public-s3-multiscale.ipynb
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Expand Up @@ -62,7 +62,7 @@
"# imageid = 9822151\n",
"imageid = 9822152\n",
"\n",
"endpoint = 'https://uk1s3.embassy.ebi.ac.uk'\n",
"endpoint = 'https://livingobjects.ebi.ac.uk'\n",
"imagepath = f'idr/zarr/v0.1/{imageid}.zarr'"
]
},
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4 changes: 2 additions & 2 deletions scripts/idr0044_zarr_segmentation_cluster.py
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Expand Up @@ -46,8 +46,8 @@

# Load-binary
def load_binary_from_s3(id, resolution='4'):
endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'
root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)
endpoint_url = 'https://livingobjects.ebi.ac.uk/'
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@will-moore will-moore Apr 7, 2026

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As elsewhere, need to use /v0.4/idr0044/%s.zarr/%s/ below and in idr0044_zarr_segmentation_parallel.py and idr0044_zarr_segmentation_parallel.ipynb‎

root = 'idr/zarr/v0.4/iddr0044/%s.zarr/%s/' % (id, resolution)
return da.from_zarr(endpoint_url + root)


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4 changes: 2 additions & 2 deletions scripts/idr0044_zarr_segmentation_parallel.py
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Expand Up @@ -45,8 +45,8 @@

# Load-binary
def load_binary_from_s3(id, resolution='4'):
endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'
root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)
endpoint_url = 'https://livingobjects.ebi.ac.uk/'
root = 'idr/zarr/v0.4/iddr0044/%s.zarr/%s/' % (id, resolution)
return da.from_zarr(endpoint_url + root)


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