OME-Zarr and newer docs?

[lubianat]

Hi,

I am exploring the documentation at https://ome-model.readthedocs.io/en/stable/ome-xml/index.html, and it redirects me here.

I might be missing something (perhaps @joshmoore may help there?) as I try to understand the relation between https://ome-model.readthedocs.io/en/latest/index.html and https://ngff.openmicroscopy.org.

E.g., the OME Model docs say OME-XML as a file format is superseded by OME-TIFF, which is the preferred container format for image data making use of the OME Data Model. I would expect some mention of OME-Zarr there at least.

Is it safe to assume it is outdated? Maybe a link to the OME-Zarr docs with a small comment could already help a bit there.

[joshmoore]

Very safe to assume it's outdated :)

Some background: The Pixels element in OME-XML can contain one of three types:

• BinData: the original element of base64 encoded data. This was the "OME-XML as a file format" which has been superseded.
• TiffData: a block which explains how a given element in the XML maps to an offset within the TIFF
• MetataOnly: such an OME-XML file has no direct link to the data it contains. However, this is used in OME-Zarr to embed OME metadata within the Zarr hierarchy. See https://ngff.openmicroscopy.org/0.5/index.html#bf2raw

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

[joshmoore]

cc: @gouttegd (along with #1 in terms of taking over the maintenance of this repos)