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 corresponding Zarr multiscales group:
  • either the absolute path to the multiscales group if the Zarr is on the filesystem e.g. /data/CMU-1.ome.zarr/0
  • or the URI to the multiscales group if the Zarr is on Amazon S3 defined as s3://s3.<region>.amazonaws.com/<bucket>/<key> e.g. s3://s3.us-east-1.amazonaws.com/gs-public-zarr-archive/CMU-1.ome.zarr/0

The Zarr multiscales group 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

For Zarr data hosted on AWS S3, requests must supply credentials. OMERO Zarr Pixel Buffer looks for credentials in this order:

1. the credentials profiles file, typically located at ~/.aws/credentials` and shared by the AWS CLI
2. instance profile credentials for EC2 instances configured 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.