Bioformats2raw & omero CLI Zarr (Linux-CentOS)

Is there a guide for how to get large files onto OMERO? I have figured out how to convert files with bioformats2raw, but I don’t quite understand where to go from here and how to use the ome-cli-zarr plugin

Hi @willama33

There is a blog post about the conversion process https://www.glencoesoftware.com/blog/2019/12/09/converting-whole-slide-images-to-OME-TIFF.html
and also a useful notebook (prepared for our community meeting in May) explaining the various conversion steps
https://mybinder.org/v2/gh/joshmoore/ome-guide-zarr/master?filepath=notebooks%2Fconversion.ipynb.

To import the data into OMERO, the files will need to be either TIFF or OME-TIFF.

I hope it helps

Cheers

Jean-marie

Hi @willama33,

jumping in a bit late, but it’d be good to know what you’d like to do with the Zarr. Currently the ome-zarr format supported by the plugin is not an official format and so is not supported by OMERO. If you are trying to do something large in production, then the best path is to stick with the complete conversion to OME-TIFF using bioformats2raw and raw2ometiff. If you are looking to do something more exploratory, we’ll be happy to help.

~Josh