Alternative file formats

[iandobbie]

Cockoit only currently deals with .dv files, pretty obscure. We should consider alternative file formats, the most promising I think is the ngff which has a python library implementation and will store the relevant metadata.

This should be linked up with the expansion of metadata in non-experiment image files, like snaps or mosaic images. This is an ongoing effort see issues #676 and #391.

[juliomateoslangerak]

A recent post of Josh Moore in image.sc on the status of NGFF
https://forum.image.sc/t/ngff-updates-oct-2023/86957

[iandobbie]

So I have implemented a function to save snaps from the camera views as a zarr file. So far contains no metadata as I couldn't work out how we were meant to add it. However it does save the data into a zarr file which can then be loaded in napari via the open folder menu item.

Code is in my zarr-snap-save branch at the moment. I will research the metadata to see how to get that stored with the file.

[juliomateoslangerak]

The OME metadata is stored as a ome.xml file in the group level
https://ngff.openmicroscopy.org/latest/#bf2raw-details
There is a library to easily produce these ome xml files that might be worth considering… I’ll look for it.

[iandobbie]

I asked on image.sc (thread at https://forum.image.sc/t/microscopy-metadata-in-zarr-files/87399) and was pointed at:

ome/ngff#104 and https://github.com/tlambert03/ome-types

I plan to explore the python libraray and try to get as much metadata as we can into the ome-xml format for storage into the zarr.