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OME-Zarr Validator

Validate local and remote OME-Zarrs using the OME-Zarr validator.

Validate local data

Terminal

Activate the conda environment ngff_workshop:

conda activate ngff_workshop

Browse into the example data directory 

cd /path/to/example_omezarrs

Validate one of the example OME-Zarrs:

ome_zarr view /path/to/example_omezarrs/6001240.zarr

The validator will open in a web browser and demonstrate various metadata fields of the OME-Zarr dataset.

  • Find out the metadata fields such as axes, units and scales.
  • Check the array and chunk shapes and bytes per resolution level.
  • Visualize a single chunk.

Python

Make sure the environment ngff_workshop is active and you are in the example_omezarrs folder.

Then access Python:

python

Do the relevant imports and validate the dataset: 

from ome_zarr import utils
utils.view(input_path = "./6001240.zarr")

Validate remote data

Now the aim is to validate the remotely stored version of the same dataset.

Enter the following into your browser: 

https://ome.github.io/ome-ngff-validator/?source=

Then paste the following dataset url after the 'equal' sign: 

https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr

Thus construct the following link:

https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0062A/6001240.zarr

Note that with the remote url it is possible to copy the link from your browser and share it with your colleagues.