Skip to content

Integrator #5

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
pwalczysko wants to merge 6 commits into
base: main
Choose a base branch
from
+5 −5
Open

Integrator #5

Show file tree
Hide file tree
Changes from all commits
Commits
Show all changes
6 commits
Select commit Hold shift + click to select a range
2771c12
Update endpoint to livingobjects
jburel Apr 2, 2026
9e3c7d4
Update endpoint
jburel Apr 2, 2026
096495b
Update Cellpose_parallel.ipynb
jburel Apr 2, 2026
c9cac53
Fix bia-integrator-data -> bioimaging-integrator-data
pwalczysko Apr 13, 2026
1f89227
Update Cellpose_parallel.ipynb
pwalczysko Apr 13, 2026
1329d95
One more bia -> bioimaging
pwalczysko Apr 13, 2026
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions Cellpose_parallel.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -89,7 +89,7 @@
"metadata": {},
"outputs": [],
"source": [
"ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'"
"ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'"
]
},
{
Expand Down Expand Up @@ -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/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)"
]
},
{
Expand All @@ -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/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."
]
},
{
Expand All @@ -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-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0'\n",
"data = load_binary_from_s3(name)"
]
},
Expand Down
2 changes: 1 addition & 1 deletion Reading_zarr_images.ipynb
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -113,7 +113,7 @@
"metadata": {},
"outputs": [],
"source": [
"ENPOINT_URL = 'https://uk1s3.embassy.ebi.ac.uk/'"
"ENPOINT_URL = 'https://livingobjects.ebi.ac.uk/'"
]
},
{
Expand Down