OME-Zarr HCS specification (Dec. 2020)01 Dec 2020
As discussed in our previous post, we have now extended our NGFF specification to support high-content screening.
The official specification has been migrated to its own repository and the current version 0.1 including support for multiscale images, labels and HCS is published at https://ngff.openmicroscopy.org/0.1/.
All the open-source projects reading or writing the specification in various languages are listed in an implementations section.
Like previously, we have converted representative plates from Image Data Resource (IDR) for various HCS acquisition modalities into OME-Zarr. Samples are publicly available and hosted on S3 storage in the Embassy Cloud at the European Bioinformatics Institute (EBI).
Below is an example of a visual representation of an OME-Zarr plate using the vizarr viewer.
The table below list all plates converted into version 0.1 of the OME-Zarr spec. This list is also available in JSON format.
|Plate||Study||Wells||Fields of view (acquisitions)||Image dimensions (XYZCT)||Viewer||S3-endpoint|
|idr0001||96||6 ( 6)||1376x1040x16x2x1||view||copy|
|idr0002||96||1 ( 1)||1344x1024x1x2x329||view||copy|
|idr0004||69||1 ( 1)||672x510x10x2x1||view||copy|
|idr0033||384||9 ( 1)||1080x1080x1x5x1||view||copy|
|idr0094||96||9 ( 1)||1080x1080x1x1x1||view||copy|