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Masks with Z or T null should apply across all Z or T indices

Open will-moore opened this issue 4 years ago • 1 comments

See https://github.com/ome/omero-cli-zarr/pull/82#issuecomment-940179664

Currently, if all masks have no Z or T index, the omero zarr masks Image:ID exports a label data block with size-Z or size-T = 1. However, this relies on all other clients to interpret this in the same way that OMERO does (to display that label image across all Z/T indices). Instead, it it better to export a better representation of how we want the data to appear. If a Mask should apply across all Z or T planes, then we should export a Label that spans all those Z/T planes.

cc @pwalczysko

will-moore avatar Oct 12 '21 09:10 will-moore

A couple of additional notes from the discussion of this morning:

  1. the OME model unambiguously specifies empty values of TheZ and/or TheT means the shape should apply to all Z-sections and/or time points

https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Shape_TheZ https://www.openmicroscopy.org/Schemas/Documentation/Generated/OME-2016-06/ome_xsd.html#Shape_TheT

  1. I am unaware of any provision in the Zarr specification or the NGFF spec to handle these types of scenarios and re-use existing chunks for other indices

sbesson avatar Oct 12 '21 09:10 sbesson