OME-Zarr HCS specification (Dec. 2020)

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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

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
IDR thumbnail for image:1229801 idr0001 96 6 ( 6) 1376x1040x16x2x1 view
IDR thumbnail for image:179693 idr0002 96 1 ( 1) 1344x1024x1x2x329 view
IDR thumbnail for image:692149 idr0004 69 1 ( 1) 672x510x10x2x1 view
IDR thumbnail for image:3230447 idr0033 384 9 ( 1) 1080x1080x1x5x1 view
IDR thumbnail for image:10567921 idr0094 96 9 ( 1) 1080x1080x1x1x1 view

December 1, 2020

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