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Add OME-Zarr HCS plate support #984
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I am working/finishing on an example notebook which just writes the necessary MoBIE views for a ome-zarr plate. |
Great! |
As I am trying out stuff with S3 and OME-zarr at the moment, may I ask if there was any progress regarding opening an OME-zarr plate from S3? |
@JensWendt thank you for your interest. No progress yet. Issue is that currently I am using this code to find the paths to the sites:
The code is here. This is fine on a file system but too slow on S3. On S3 one would need to replace this code by fetching this information by parsing the top level
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Here is one HCS example data set on S3: https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/5966.zarr |
I am working on it #1064 |
Couple of hours of work, seems to be working for: https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.1/plates/5966.zarr |
Hello @tischi , |
@JensWendt I would be great if you could test it and report bugs and feature requests here. It is available right now on MoBIE-beta. |
Heyo,
and in the Log:
the
the same as other I have no clue what the issue is. Any ideas? |
Same with another plate that I took of the official NGFF example page. |
This should be fixed now in the latest MoBIE-beta (see #1065 for more details). |
Works like a charm!! Many thanks. |
Nice! Please consider citing the publication: https://www.nature.com/articles/s41592-023-01776-4 |
@JensWendt this is now also available on the normal MoBIE update site. So no need to do the complicated MoBIE-beta stuff. Important: uncheck the MoBIE-beta update site when you activate the normal one; otherwise there will be conflicts! |
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