I realize that it’s been quite some time since there’s been an #ome-ngff status update. (Perhaps the lightweight updates in NGFF 2020 Newsfeed - #14 by joshmoore were a good idea…) I’ve captured most of the highlights of 2021 to date below, though I’ve likely left something out. If anyone has anything to add or ask, please feel free.
Of course, the largest portion of sweat and tears over the last 5 months went into the biorxiv preprint. (tweet in case you missed it.) We’ve just begun revisions, so if you have thoughts, now and here are as good a time & place for feedback as ever.
One of the rabbit holes we went down in trying to get the preprint completed was “nested chunks” for Zarr. The details aren’t too terribly important, but basically it took about 2 months to specify whether all Zarr implementations used a “/” or a “.” in files name in order to speed up access for large volumes. In the end, it led to v0.2 of OME-NGFF which is now released at http://ngff.openmicroscopy.org/0.2 .
Ongoing now and ready for feedback () is the specification of axes information led by @constantinpape in https://github.com/ome/ngff/pull/46. This should hopefully make #ome-ngff compatible with xarray, “N-D labeled arrays and datasets in Python”, and begin further N-dimensionalification steps.
There are a couple of other specification issues which are being moved forward right now, for example, around Polygons and Meshes thanks to @glyg, @Anatole_Chessel, et al. Anyone who is working on a spec and needs help/support/feedback, please speak up.
In other news (again, in case you missed it) NetCDF 4.8.0 (written in C) has added support for Zarr as a backend alongside HDF5 (tweet). This will hopefully guarantee significant support for the format moving forward.
Finally, it’s pass time for another community call. The last one was on Feb. 23rd. However, with the upcoming OME community meeting I don’t foresee myself organizing a full day of calls within the next 3 weeks. It might be that something more focused on ongoing specs would still be useful. If someone would like to take the lead on that, I’ll happily attend. Otherwise, I’d propose we try to chat early summer. Thoughts & suggestions welcome (as always).