From ed3ea9abcbcd60a3d8aa58bdfa2aa4a0c94bc827 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 15:26:32 +0100 Subject: [PATCH 1/8] livingobjects --- notebooks/idr0044_zarr_segmentation_parallel.ipynb | 2 +- notebooks/idr0062_prediction_zarr_public_s3.ipynb | 2 +- notebooks/zarr-public-s3-multiscale.ipynb | 2 +- scripts/idr0044_zarr_segmentation_cluster.py | 2 +- scripts/idr0044_zarr_segmentation_parallel.py | 2 +- 5 files changed, 5 insertions(+), 5 deletions(-) diff --git a/notebooks/idr0044_zarr_segmentation_parallel.ipynb b/notebooks/idr0044_zarr_segmentation_parallel.ipynb index a3fcd2e..d774932 100644 --- a/notebooks/idr0044_zarr_segmentation_parallel.ipynb +++ b/notebooks/idr0044_zarr_segmentation_parallel.ipynb @@ -90,7 +90,7 @@ "outputs": [], "source": [ "def load_binary_from_s3(id, resolution='4'):\n", - " endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/'\n", + " endpoint_url = 'https://livingobjects.ebi.ac.uk/'\n", " root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)\n", " return da.from_zarr(endpoint_url + root)" ] diff --git a/notebooks/idr0062_prediction_zarr_public_s3.ipynb b/notebooks/idr0062_prediction_zarr_public_s3.ipynb index 202ff73..90a4ae3 100644 --- a/notebooks/idr0062_prediction_zarr_public_s3.ipynb +++ b/notebooks/idr0062_prediction_zarr_public_s3.ipynb @@ -76,7 +76,7 @@ "metadata": {}, "outputs": [], "source": [ - "ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'" + "ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'" ] }, { diff --git a/notebooks/zarr-public-s3-multiscale.ipynb b/notebooks/zarr-public-s3-multiscale.ipynb index bc57719..748311e 100644 --- a/notebooks/zarr-public-s3-multiscale.ipynb +++ b/notebooks/zarr-public-s3-multiscale.ipynb @@ -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'" ] }, diff --git a/scripts/idr0044_zarr_segmentation_cluster.py b/scripts/idr0044_zarr_segmentation_cluster.py index 2110457..54731a8 100644 --- a/scripts/idr0044_zarr_segmentation_cluster.py +++ b/scripts/idr0044_zarr_segmentation_cluster.py @@ -46,7 +46,7 @@ # Load-binary def load_binary_from_s3(id, resolution='4'): - endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/' + endpoint_url = 'https://livingobjects.ebi.ac.uk/' root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution) return da.from_zarr(endpoint_url + root) diff --git a/scripts/idr0044_zarr_segmentation_parallel.py b/scripts/idr0044_zarr_segmentation_parallel.py index 6a84f98..cec2533 100644 --- a/scripts/idr0044_zarr_segmentation_parallel.py +++ b/scripts/idr0044_zarr_segmentation_parallel.py @@ -45,7 +45,7 @@ # Load-binary def load_binary_from_s3(id, resolution='4'): - endpoint_url = 'https://uk1s3.embassy.ebi.ac.uk/' + endpoint_url = 'https://livingobjects.ebi.ac.uk/' root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution) return da.from_zarr(endpoint_url + root) From 11182f1f1370725a18b23a32250589140e715af3 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:27:00 +0100 Subject: [PATCH 2/8] Fix v0.4 and add idr0044 to url --- notebooks/idr0044_zarr_segmentation_parallel.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/notebooks/idr0044_zarr_segmentation_parallel.ipynb b/notebooks/idr0044_zarr_segmentation_parallel.ipynb index d774932..e86f4c4 100644 --- a/notebooks/idr0044_zarr_segmentation_parallel.ipynb +++ b/notebooks/idr0044_zarr_segmentation_parallel.ipynb @@ -91,7 +91,7 @@ "source": [ "def load_binary_from_s3(id, resolution='4'):\n", " endpoint_url = 'https://livingobjects.ebi.ac.uk/'\n", - " root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution)\n", + " root = 'idr/zarr/v0.4/idr0044/%s.zarr/%s/' % (id, resolution)\n", " return da.from_zarr(endpoint_url + root)" ] }, From 490b90680b8acdbbaed5f139c36133f91b42f926 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:37:56 +0100 Subject: [PATCH 3/8] Fix the url to the idr0044 image also in 2 .py scripts --- scripts/idr0044_zarr_segmentation_cluster.py | 2 +- scripts/idr0044_zarr_segmentation_parallel.py | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/scripts/idr0044_zarr_segmentation_cluster.py b/scripts/idr0044_zarr_segmentation_cluster.py index 54731a8..3008923 100644 --- a/scripts/idr0044_zarr_segmentation_cluster.py +++ b/scripts/idr0044_zarr_segmentation_cluster.py @@ -47,7 +47,7 @@ # Load-binary def load_binary_from_s3(id, resolution='4'): endpoint_url = 'https://livingobjects.ebi.ac.uk/' - root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution) + root = 'idr/zarr/v0.4/iddr0044/%s.zarr/%s/' % (id, resolution) return da.from_zarr(endpoint_url + root) diff --git a/scripts/idr0044_zarr_segmentation_parallel.py b/scripts/idr0044_zarr_segmentation_parallel.py index cec2533..a2b9cc8 100644 --- a/scripts/idr0044_zarr_segmentation_parallel.py +++ b/scripts/idr0044_zarr_segmentation_parallel.py @@ -46,7 +46,7 @@ # Load-binary def load_binary_from_s3(id, resolution='4'): endpoint_url = 'https://livingobjects.ebi.ac.uk/' - root = 'idr/zarr/v0.1/%s.zarr/%s/' % (id, resolution) + root = 'idr/zarr/v0.4/iddr0044/%s.zarr/%s/' % (id, resolution) return da.from_zarr(endpoint_url + root) From 99acd79a80824b521806dd39a2ece16d7c57cd36 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:42:42 +0100 Subject: [PATCH 4/8] fix build --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index d78b0d9..aca0b3d 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,13 +13,13 @@ 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 with: From 0332cb667d73a9dd2db7edf5caafa0cc141bcf6e Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:43:53 +0100 Subject: [PATCH 5/8] try --- .github/workflows/build.yml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index aca0b3d..2d06dd5 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,13 +13,13 @@ jobs: build: strategy: matrix: - os: [ubuntu-24.04, windows-latest, macos-latest] + os: [ubuntu-22.04, windows-latest, macos-latest] runs-on: ${{ matrix.os }} steps: - uses: actions/checkout@v4 - uses: actions/setup-python@v5 with: - python-version: '3.12' + python-version: '3.9' - name: Install Conda environment with Micromamba uses: mamba-org/provision-with-micromamba@v15 with: From 0f841aafcaecfe52bce2ed731117c4a01a25cce3 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:48:54 +0100 Subject: [PATCH 6/8] Change the micromamba setup action --- .github/workflows/build.yml | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/.github/workflows/build.yml b/.github/workflows/build.yml index 2d06dd5..b807f8f 100644 --- a/.github/workflows/build.yml +++ b/.github/workflows/build.yml @@ -13,15 +13,15 @@ jobs: build: strategy: matrix: - os: [ubuntu-22.04, 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 From 28ca806814ae3af8c22817260c09e8a75b2ae03d Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:54:52 +0100 Subject: [PATCH 7/8] update env packages --- binder/environment.yml | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/binder/environment.yml b/binder/environment.yml index 8394bd9..6f1da24 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -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 - 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 From a5e68127be1df146ddfe1e65da0e5252bc12d453 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Tue, 7 Apr 2026 16:57:06 +0100 Subject: [PATCH 8/8] Update also distributed --- binder/environment.yml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/binder/environment.yml b/binder/environment.yml index 6f1da24..6aaa93d 100644 --- a/binder/environment.yml +++ b/binder/environment.yml @@ -4,7 +4,7 @@ channels: dependencies: - python==3.12.* - conda-forge::zeroc-ice==3.6.5 - - distributed==2022.2.0 + - distributed==2026.3.0 - pip - pip: - matplotlib==3.8.4