Question: Should label-index mapping metadata be stored in the BIDS *.tsv file or OME-Zarr zarr.json file?

[kabilar]

Hi BIDS team,

We have annotated/segmented images and are trying to determine the best location to store the label-index mapping metadata.

In the BIDS specification, a sidecar <matches>.tsv file or top-level dseg.tsv file can specify how the integer values of the segmentations map to custom labels.

In the OME-Zarr version 0.5 specification the labels metadata in the zarr.json file can be used to store metadata associated with the label in the properties key. In the example provided in the link, there are the class and cell type keys.

For BIDS datasets that contain OME-Zarr labeled images, is there a preference on whether the label-index mapping metadata should be stored in the BIDS *.tsv file or OME-Zarr zarr.json file?

Thank you.

cc @jingjingwu1225 @balbasty @satra

[Remi-Gau]

for me the dseg are more for MRI based segmentations and have not been extended to other modalities like mricroscopy

Though the first line in this page may suggest you could be tempted to have them cover microscopy.

This section pertains to imaging data, which characteristically have spatial extent and resolution.