From 2771c12c92df5273fb3145a1aa9f6bf77f5b27bc Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 2 Apr 2026 11:05:13 +0100 Subject: [PATCH 1/6] Update endpoint to livingobjects --- Cellpose_parallel.ipynb | 2 +- Reading_zarr_images.ipynb | 2 +- 2 files changed, 2 insertions(+), 2 deletions(-) diff --git a/Cellpose_parallel.ipynb b/Cellpose_parallel.ipynb index 7e3f479..49b0899 100644 --- a/Cellpose_parallel.ipynb +++ b/Cellpose_parallel.ipynb @@ -89,7 +89,7 @@ "metadata": {}, "outputs": [], "source": [ - "ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'" + "ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'" ] }, { diff --git a/Reading_zarr_images.ipynb b/Reading_zarr_images.ipynb index 9d273fb..e1ad3fc 100644 --- a/Reading_zarr_images.ipynb +++ b/Reading_zarr_images.ipynb @@ -113,7 +113,7 @@ "metadata": {}, "outputs": [], "source": [ - "ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'" + "ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'" ] }, { From 9e3c7d48d9c75e7d4f8d3435200877d74f067f7c Mon Sep 17 00:00:00 2001 From: Jean-Marie Burel Date: Thu, 2 Apr 2026 11:10:53 +0100 Subject: [PATCH 2/6] Update endpoint --- Cellpose_parallel.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cellpose_parallel.ipynb b/Cellpose_parallel.ipynb index 49b0899..717ebff 100644 --- a/Cellpose_parallel.ipynb +++ b/Cellpose_parallel.ipynb @@ -434,7 +434,7 @@ "## Cellpose and BIA data\n", "\n", "Using ome-zarr for both IDR and BIA allows us to use the same analytical pipeline on data stored in two different resources.\n", - "We will run Cellpose against an [image](https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html) in BIA associated with the study with accession number [S-BIAD338]( https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD338)" + "We will run Cellpose against an [image](https://livingobjects.ebi.ac.uk/.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html) in BIA associated with the study with accession number [S-BIAD338]( https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD338)" ] }, { @@ -444,7 +444,7 @@ "source": [ "### Lazy Loading of data\n", "\n", - "To find the name, go to https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html. Click on ``Copy S3 URI to clipboard``, paste it here or into a text editor and remove the endpoint, i.e. the https://uk1s3.embassy.ebi.ac.uk." + "To find the name, go to https://livingobjects.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html. Click on ``Copy S3 URI to clipboard``, paste it here or into a text editor and remove the endpoint, i.e. the https://livingobjects.ebi.ac.uk." ] }, { From 096495b17175cf012942a38ef7c62357f1462859 Mon Sep 17 00:00:00 2001 From: jean-marie burel Date: Thu, 2 Apr 2026 13:58:43 +0100 Subject: [PATCH 3/6] Update Cellpose_parallel.ipynb Co-authored-by: pwalczysko --- Cellpose_parallel.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cellpose_parallel.ipynb b/Cellpose_parallel.ipynb index 717ebff..3a31467 100644 --- a/Cellpose_parallel.ipynb +++ b/Cellpose_parallel.ipynb @@ -434,7 +434,7 @@ "## Cellpose and BIA data\n", "\n", "Using ome-zarr for both IDR and BIA allows us to use the same analytical pipeline on data stored in two different resources.\n", - "We will run Cellpose against an [image](https://livingobjects.ebi.ac.uk/.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html) in BIA associated with the study with accession number [S-BIAD338]( https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD338)" + "We will run Cellpose against an [image](https://livingobjects.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html) in BIA associated with the study with accession number [S-BIAD338]( https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD338)" ] }, { From c9cac53b2e78428436822667d4834b2e38b57645 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Mon, 13 Apr 2026 14:51:58 +0100 Subject: [PATCH 4/6] Fix bia-integrator-data -> bioimaging-integrator-data --- Cellpose_parallel.ipynb | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/Cellpose_parallel.ipynb b/Cellpose_parallel.ipynb index 3a31467..633dc2b 100644 --- a/Cellpose_parallel.ipynb +++ b/Cellpose_parallel.ipynb @@ -444,7 +444,7 @@ "source": [ "### Lazy Loading of data\n", "\n", - "To find the name, go to https://livingobjects.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html. Click on ``Copy S3 URI to clipboard``, paste it here or into a text editor and remove the endpoint, i.e. the https://livingobjects.ebi.ac.uk." + "To find the name, go to https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html. Click on ``Copy S3 URI to clipboard``, paste it here or into a text editor and remove the endpoint, i.e. the https://livingobjects.ebi.ac.uk." ] }, { @@ -464,7 +464,7 @@ ], "source": [ "%%time \n", - "name = 'bia-integrator-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0'\n", + "name = 'bioimaging-integrator-dataor-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0'\n", "data = load_binary_from_s3(name)" ] }, From 1f892270c2de8d1f7861ccbccd13fb617a379746 Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Mon, 13 Apr 2026 16:20:23 +0100 Subject: [PATCH 5/6] Update Cellpose_parallel.ipynb Co-authored-by: jean-marie burel --- Cellpose_parallel.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cellpose_parallel.ipynb b/Cellpose_parallel.ipynb index 633dc2b..4f70f50 100644 --- a/Cellpose_parallel.ipynb +++ b/Cellpose_parallel.ipynb @@ -464,7 +464,7 @@ ], "source": [ "%%time \n", - "name = 'bioimaging-integrator-dataor-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0'\n", + "name = 'bioimaging-integrator-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0'\n", "data = load_binary_from_s3(name)" ] }, From 1329d9537ecc45d10c94a091b8a2f2fe451e665e Mon Sep 17 00:00:00 2001 From: pwalczysko Date: Mon, 13 Apr 2026 16:26:59 +0100 Subject: [PATCH 6/6] One more bia -> bioimaging --- Cellpose_parallel.ipynb | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/Cellpose_parallel.ipynb b/Cellpose_parallel.ipynb index 4f70f50..b9b1c77 100644 --- a/Cellpose_parallel.ipynb +++ b/Cellpose_parallel.ipynb @@ -434,7 +434,7 @@ "## Cellpose and BIA data\n", "\n", "Using ome-zarr for both IDR and BIA allows us to use the same analytical pipeline on data stored in two different resources.\n", - "We will run Cellpose against an [image](https://livingobjects.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html) in BIA associated with the study with accession number [S-BIAD338]( https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD338)" + "We will run Cellpose against an [image](https://livingobjects.ebi.ac.uk/bioimaging-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html) in BIA associated with the study with accession number [S-BIAD338]( https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD338)" ] }, {