bioformats2raw --file_type=zarr --dimension-order=XYZCT … will produce a multi-series zarr; each of those series is an ome-zarr. https://github.com/ome/ome-zarr-py has some methods for writing the multi-scale images, but it’s not yet a full API. I don’t imagine you would have issues adding to it, @sebi06.
Agreed! Thanks for the link. I was away last week and am still in the process of catching up. (This has not helped of course…)
If there’s anything we can do to help, let us know. Conda is usually the easiest way, but there are a number of wheels available for various platforms like https://github.com/ome/zeroc-ice-py-centos7/releases/download/0.2.1/zeroc_ice-3.6.5-cp36-cp36m-linux_x86_64.whl which speed things up tremendously. (Probably best to create a new thread if we want to go into that in more depth, though)
Nice! I’ll try to go through the code but I assume this is quite close to what https://github.com/ome/omero-cli-zarr/blob/73d0ea197139fd55960bc8c48f2e916dd70dfc6e/src/omero_zarr/raw_pixels.py is doing. There’s also work on downloading masks in https://github.com/ome/omero-cli-zarr/blob/73d0ea197139fd55960bc8c48f2e916dd70dfc6e/src/omero_zarr/masks.py that matches Multi-scale image labels v0.1 If there are you see things that need refactoring or integrating from one location to another, let us know.
The process is on plane 1300 now… I’m pretty sure that this will be an example where we should move to a different chunking. Very open to suggestions once it’s available for everyone to test it.