Open heeler opened 4 years ago
There have been some updates to this! :tada:
aicsimage
reader
class under a get_ome_metadata
or similarly named function so that we can extend this metadata handling to all readers if desiredOMEXML
object that can generate minimum OME XML given some parameters.@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.
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 inaicsimageio
and potentially make a PR bake to bioformats or wherever the original is with functions that can initialize theOMEXML
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.