Submit images to the BIA

[kostrykin]

There is a tool for submission of images to the BIA: https://github.com/Euro-BioImaging/Galaxy-OME-Zarr/blob/multiple-tools/DataIO/ascp2BIA.xml

This tool should be used to deposit some images to the BIA, preferably as OME-Zarr. There is a tool for conversion of regular images to OME-Zarr: https://usegalaxy.eu/root?tool_id=toolshed.g2.bx.psu.edu/repos/imgteam/bioformats2raw/bf2raw/0.7.0+galaxy3

For example, this can be segmentation results obtained using Cellpose (see #15).

This tool should be covered by a tutorial. This doesn't necessarily have to be a dedicated tutorial specifically for that tool, it's sufficient to be included as a step in some other tutorial.

It should also be mentioned in the tutorial that it is good practice to deposit images to the BIA as OME-Zarr:

1. When publishing data to BIA, metadata is required (license, authors, description, etc.). Users are encouraged to add as much information/metadata as needed to reproduce their research findings.
2. OME-Zarr is a format with ample metadata; data can be shared on an S3-compatible bucket without requiring every user to download it locally. Additionally, data can be chunked, which can significantly increase performance when accessing it.

Maybe the tool can also be used in a workflow.

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Caution

This issue is currently blocked. Seemingly, the above mentioned tool for submission of images to the BIA wasn't deployed to the toolshed yet: Euro-BioImaging/Galaxy-OME-Zarr#2