Update endpoint

[jburel]

Update endpoint to livingobjects

[pwalczysko]

Notebook:
Cellpose_parallel.ipynb

Cell executed (in Colab from this branch)

%%time 
name = 'bia-integrator-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0'
data = load_binary_from_s3(name)

Error:

ClientResponseError                       Traceback (most recent call last)

<timed exec> in <module>

[/tmp/ipykernel_900/441810667.py](https://localhost:8080/#) in load_binary_from_s3(name, resolution)
      3 def load_binary_from_s3(name, resolution='0'):
      4     root = '%s/%s/' % (name, resolution)
----> 5     return da.from_zarr(ENPOINT_URL + root)

11 frames

[/usr/local/lib/python3.12/dist-packages/aiohttp/client_reqrep.py](https://localhost:8080/#) in raise_for_status(self)
    634                 self.release()
    635 
--> 636             raise ClientResponseError(
    637                 self.request_info,
    638                 self.history,

ClientResponseError: 403, message='Forbidden', url='https://livingobjects.ebi.ac.uk/bia-integrator-data/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c/804b2976-1111-4099-8bfc-21d1d1d2163c.zarr/0/0/.zarray'

[pwalczysko]

Notebook:
Cellpose_parallel.ipynb

Cell (markdown)

Lazy Loading of data

To find the name, go to [https://livingobjects.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html](https://www.google.com/url?q=https%3A%2F%2Flivingobjects.ebi.ac.uk%2Fbia-integrator-data%2Fpages%2FS-BIAD338%2F804b2976-1111-4099-8bfc-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](https://www.google.com/url?q=https%3A%2F%2Flivingobjects.ebi.ac.uk).

The workflow as described ^^^ does not wfm. Going to the url suggested is just erroring.

<Error>
<Code>AccessDenied</Code>
<Message>Access Denied.</Message>
<Key>
pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html
</Key>
<BucketName>bia-integrator-data</BucketName>
<Resource>
/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html
</Resource>
<RequestId>18A2854C4737377E</RequestId>
<HostId>54b010ed-8961-4fc6-b7b1-76200f2e5c61</HostId>

[pwalczysko]

Please address the 2 comments above.

@wil-moore Is it maybe that the livingobjects bucket will become accessible later ?

[pwalczysko]

This one does not work either. Access denied.
Click on https://livingobjects.ebi.ac.uk/.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html and observe

<Error>
<Code>AccessDenied</Code>
<Message>Access Denied.</Message>
<Key>
bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html
</Key>
<BucketName>.ebi.ac.uk</BucketName>
<Resource>
/.ebi.ac.uk/bia-integrator-data/pages/S-BIAD338/804b2976-1111-4099-8bfc-21d1d1d2163c.html
</Resource>
<RequestId>18A285AB176674EE</RequestId>
<HostId>54b010ed-8961-4fc6-b7b1-76200f2e5c61</HostId>
</Error>

[will-moore]

bia-integrator-data not migrated yet. BIA are doing that (hopefully).
Also duplicate .ebi.ac.uk/.ebi.ac.uk in url

[pwalczysko]

Changes in Reading_zarr_images.ipynb are working fine. Note that Reading_zarr_images.ipynb does not use bia-integrator-data

[pwalczysko]

In summary:

1. bia-integration-data usage needs clarification
2. typo in url - just accept Update endpoint #4 (comment) please

[pwalczysko]

In summary:

1. `bia-integration-data` usage needs clarification

2. typo in url - just accept [Update endpoint #4 (comment)](https://github.com/ome/EMBL-EBI-imaging-course-03-2026/pull/4#discussion_r3027448561) please

The Ad 1. above is fixed in #5

[pwalczysko]

Note the follow-up PR of #5