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OMERO Zarr Pixel Buffer

Requirements

  • OMERO 5.6+
  • Java 11+

Artifacts

The latest artifacts built and deployed by GitHub actions can be found on the Glencoe Software artifactory

Usage

The OMERO Zarr Pixel Buffer follows the principles of a classical OMERO.server service extension.

After putting the omero-zarr-pixel-buffer.jar under lib/server, the server must be restarted. To use the ZarrPixelBuffer, an Image or Mask object must be populated with an ExternalInfo object with the following properties:

  • entityType must be set to com.glencoesoftware.ngff:multiscales
  • entityId must be set to 3
  • lsid must be set to the location of the Zarr data:
    • the absolute path to the dataset if available via the filesystem
    • an URI defined as s3://s3.<region>.amazonaws.com/<bucket>/<path/to/dataset.zarr> for datasets stored on Amazon S3

The Zarr dataset must be conformant with the default layout generated by bioformats2raw i.e.:

  • the version of the NGFF specification must be 0.4
  • the image and the Zarr multiscales group must have 5 declared dimensions
  • the chunks must be stored in the (t, c, z, y, x) order
  • the resolution level must be downsampled along the (y, x) axis

Permissions for accessing Zarr dataset hosted on S3 buckets can be managed:

  • either via named profiles stored under a local credentials file as for the AWS CLI
  • or via EC2 instance profile condifigured with a policy allowing to assume an IAM role

Development

Clone the repository:

git clone https://github.com/glencoesoftware/omero-zarr-pixel-buffer

Run the Gradle build including the tests

./gradlew build

License

The converter is distributed under the terms of the GPL license. Please see LICENSE.txt for further details.