Image Metadata Handling

[heeler]

Use Case

Better handling and standardization of metadata from multiple formats. Instead of having many different metadata formats it would be great to have a single object to handle them all.

Solution

It would be great to reuse the OMEXML object already found in aicsimageio and potentially make a PR bake to bioformats or wherever the original is with functions that can initialize the OMEXML object with CZI, LEICA, Slidebook, etc metadata. OMEXML.read_czi for example.

Would be nice

If we baked in the support that Gohlke's CziFile has for metadata / using it as a functionality template for desirable metadata reading.

Alternatives

Stakeholders

The entire institute but more specifically key groups to keep in contact with:
Nathalie, Aditya, Dan, Jackson, 4DN, OME, and someone on software.

Major Components

[ ] Produce minimum mapping from CZI to 4DN OMEXML
[ ] Rework or add to OMEXML object to include functions to transform CZI metadata

Dependencies

[ ] (optional) PR back into bioformats with updates to OMEXML

Other Notes

Other ideas welcome. This is a rough start.

[evamaxfield]

There have been some updates to this! 🎉

• Minimum mapping from CZI to 4DN OMEXML is done
• The planned implementation of the conversion tool will be on each aicsimage reader class under a get_ome_metadata or similarly named function so that we can extend this metadata handling to all readers if desired
• We may need to fork: https://github.com/ome/ome-model/ so that we can maintain a pure Python OMEXML object that can generate minimum OME XML given some parameters.

[evamaxfield]

@toloudis and I have an idea for how to maintain a better OMEXML object (and potentially a CZIXML object) using a library to convert xsd -> Python. Work to come on that front.

After testing it out we noticed that the 4DN spec doesn't have a Pixels element which is labeled as "to be removed in future OME specifications" but we are unsure as to if current viewers will be able to read the 4DN spec naturally without that element. @heeler something to be aware of.