README updates (requirements, installation & usage) #35
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- Add libblosc as a requirement of the extension - Separate the installation from the usage as top-level section - Describe the deployment via modifying an existing server or rebuilding - Expand the requirements of the Zarr data that can be read - Describe the two types of Zarr paths that can be used (filesystem and S3) - Describe the profile and anonymous query parameters
melissalinkert
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Sep 16, 2025
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Minor suggestions aside, looks good to me.
Co-authored-by: Melissa Linkert <[email protected]>
melissalinkert
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will-moore
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README.md
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| as `s3://<endpoint>/<bucket>/<prefix>` where `<endpoint>` is the S3 | ||
| endpoint - see https://docs.aws.amazon.com/general/latest/gr/s3.html#s3_region | ||
| for the list of the regional AWS S3 endpoints, <bucket> is the bucket name | ||
| and `<prefix>` is the prefix to the Zarr multiscales group e.g. |
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Maybe mention that this can now be done on the command-line:
$ omero obj ext-info-set Image:1 3 com.glencoesoftware.ngff:multiscales s3://<endpoint>/<bucket>/<prefix>
since ome/omero-py#453
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Similarly to other cross-references in the README, is there a dedicated page either in the OMERO reference documentation or an OMERO guide that would describe the command and its prerequisites and could be linked here?
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No, I don't think so. It's quite recent and has a limited audience so far.
But this is a good place to start!
kkoz
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Sep 17, 2025
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Looks good - just a couple notes
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| - or the URI specifying the location of the multiscales group if the Zarr is | ||
| stored on AWS S3 or S3 compatible storage. The location must be specified | ||
| as `s3://<endpoint>/<bucket>/<prefix>` where `<endpoint>` is the S3 | ||
| endpoint - see https://docs.aws.amazon.com/general/latest/gr/s3.html#s3_region |
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Two notes here:
- If the expectation is that users will be manually setting the
lsid, I think we should mention that at least for S3 URIs we need them to be URL encoded. - We might want to make it clear that the URI will probably end with the series as we do in the local filesystem example. People might expect the URI for their Zarr image would end in
.zarr.
kkoz
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Sep 18, 2025
chris-allan
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Sep 18, 2025
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Fixes #29 and documents the new features introduced in #27 and #28, currently released as
0.6.0-rc1/cc @dominikl @jburel