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Kitware / UPennContrast

UPenn ?
https://upenn-contrast.netlify.com/
Apache License 2.0
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OME-zarr support #523

Open arjunrajlab opened 1 year ago

arjunrajlab commented 1 year ago

After talking with the BioImage Archive people, I think implementing OME-zarr support (remote and local) would be a HUGE driver for adoption. Here's some samples I got from them:

  1. The first one, S-BIAD319 hasn’t been converted to OME-zarr however we can use the tif image uris to test your software to view the tifs directly using the uris. The submission webpage is here: https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD319

The image uris can be viewed by right clicking each image on the page, e.g.

https://www.ebi.ac.uk/biostudies/files/S-BIAD319/A1-TNNT2_ISL1_WT1/60x_tiffs/20210703_FISHwellA1_60xtest001/20210703_FISHwellA1_60xtest001_DAPI.tif

  1. The second dataset, S-BIAD696 has been converted to OME-zarr so can be used to test the OME-zarr viewing once it’s been implemented. You can also use it to test the OME-zarr conversion as we have both the original images and the OME-zarr images. The original submission was done using zipped folders instead of individual images so you’d need to download the folders and unzip them to get the individual tif files (one of the other reasons we convert everything to ome-zarr; to overcome the need to download images or folders).

The original submission webpage is here (where you can download the folders and use them to test ome-zarr conversion): https://www.ebi.ac.uk/biostudies/BioImages/studies/S-BIAD696

The page where you can view the OME-zarr images of S-BIAD696: https://uk1s3.embassy.ebi.ac.uk/bia-integrator-data/pages/S-BIAD696.html

I think it would be great to be able to support both a URL and file source. @bruyeret, would be cool to think about the UI for just giving a URL instead of a file.

manthey commented 1 year ago

This is a superset of https://github.com/girder/large_image/issues/1008.

bruyeret commented 1 year ago

I will have to copy / paste the component from "girder web components" into Nimbus Image

I was thinking about something like this (from online-convert.com): image image

arjunrajlab commented 1 year ago

I think something like that looks good! I think we can also coordinate with Faiza as she comes up with a way to refactor the data ingestion interface.