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Fix formatting of hyperlink
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jburel committed Jan 24, 2025
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Expand Up @@ -52,9 +52,9 @@ The new default behaviour of the `omezarr.include_labels` option introduced in v

**Note:** If you had imported data with labels into OMERO using version v0.3 or earlier then you will need to ensure that the `omezarr.include_labels` option is set to true. You can do this by adding a `bfoptions` file to the fileset. This will require running psql commands to update the database to include the new `bfoptions` file. If you need help with this scenario then please contact us on [image.sc](https://forum.image.sc/).

In version v0.5.0 a new option `omezarr.alt_store` was added. This allows for the source of an alternative file store to be configured. Setting the option means the pixel data to be read from a different source than originally used when initialising the reader. The initial implementation was intended for use with the [IDR] (https://idr.openmicroscopy.org/), allowing IDR to read data directly from an S3 location. The current implementation only allows for S3 access when using a public https endpoint with unauthenticated access using anonymous credentials. A more complete, general purpose implementation will follow in a future release.
In version v0.5.0 a new option `omezarr.alt_store` was added. This allows for the source of an alternative file store to be configured. Setting the option means the pixel data to be read from a different source than originally used when initialising the reader. The initial implementation was intended for use with the [IDR](https://idr.openmicroscopy.org/), allowing IDR to read data directly from an S3 location. The current implementation only allows for S3 access when using a public https endpoint with unauthenticated access using anonymous credentials. A more complete, general purpose implementation will follow in a future release.

An example of how this could be used would be to download locally a public dataset such as [6001240.zarr] (https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr). Setting the option as below, either via the API or using a `bfoptions` file, will allow you to call setID on the local file but have the pixel data read from the public S3 endpoint.
An example of how this could be used would be to download locally a public dataset such as [6001240.zarr](https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr). Setting the option as below, either via the API or using a `bfoptions` file, will allow you to call setID on the local file but have the pixel data read from the public S3 endpoint.

```
omezarr.alt_store = https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr
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