BDV-OMERO connector for opening OMERO multiresolution images in BigDataViewer

Dear community,

I’m happy to present a proof-of-concept BDV-OMERO connector for the viewing of OMERO images in BigDataViewer.

This is still very experimental, but it already shows what we are aiming to do and how things should work.

In short, this connector:

  • handles multiresolution 5D images
  • provides lazy loading of raw data (using Omero RawPixelsStore(s))

and could easily be adapted to support the display of multiple images positioned in 3d space using bigdataviewer-playground. Together with @NicoKiaru we plan to make an imageloader compatible with the Fiji “Big plugins” (BigStitcher, BigWarp, Labkit,…).

We’re interested to know what other options are available in the community that have equivalent functionalities (already existing or planned, e.g lazy loading from napari). To our knowledge, this combination of features is not available yet in Fiji (Scifio has no support for multiresolution and OMERO doesn’t provide a direct way to access raw pixel data via its web API) yet.

We are aware that this will be available in the future thanks to the Zarr service. But since it’s already possible to stream raw data via RawPixelsStores, we were wondering if there is a good reason for not using it ? Is there a big performance difference to expect between RawPixelStore and zarr ?

Link to the Github repo:

We’re happy to get your feedback on this connector!

Cheers,

Claire
@NicoKiaru @oburri @romainGuiet @seitz

Ping @will-moore @joshmoore @OMETeam @ctrueden @petebankhead

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Hi Claire Very nice! A quick response from my side:

There should be little difference between RawPixelstore and omero-ms-zarr: they are both using the same underlying code. One is using Ice for remote access; the other HTTP. Both are returning byte streams. Probably the more important and longer-term question is what API will be more generally implementable, and I think for that there’s an argument for Zarr. But if you are familiar with the OMERO API (as you clearly are), then there’s no reason not to start as you have.

~Josh

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