Used BioNGFF Viewer instead of Vizarr

[zonia3000]

Checklist before merging

• I added an appropriate entry to CHANGELOG.md

---

Note: the .gitmodules file of the BioNGFF Viewer needs to be changed to reference our Vizarr fork.
It has been done calling the following commands before the git submodule ones:

sed -i 's|hms-dbmi|fractal-analytics-platform|g' .gitmodules
printf "\tbranch = workaround-labels-bug\n" >> .gitmodules

Moreover, I renamed vizarr into viewer, to use a more generic term. So:

• VIZARR_STATIC_FILES_PATH -> VIEWER_STATIC_FILES_PATH
• /vizarr -> /viewer

[Netomek]

Why exactly did you decide to change the viewer from vizarr to BioNGFF? I saw problems with labels using vizarr but is there any other reason?

[jluethi]

@Netomek Given the question marks about ViZarr maintenance & the ambition of BioNGFF to become (in name or just in functionality) a maintained ViZarr 2.0 implementation (as presented at the OME-NGFF community call, see https://docs.google.com/presentation/d/1azX0kenr0TlkD9J2IHtrvzKv2xjbB3sCZDkN2N_0-Hk/edit), we want to see whether we could replace our ViZarr integration with BioNGFF and what kind of issues we'd hit. Unsurprisingly, we've hit a first batch of minor issues that we've now reported upstream to BioNGFF.

We're also really interested in their implementation of table loading form AnnData & coloring labels by table features.

There is no final decision made yet on our end about whether this will work, whether this will be an option per deployment (e.g. decide which viewer you want to deploy) or eventually a new default. Hopefully, we can learn more about what's feasible by engaging in this process and see how the different repos progress.

@Netomek out of curiosity, what's your background or connection to this? Do you have experience working with either and recommendations you'd share? Your Github profile doesn't give enough context to know where the question is coming from :)

[Netomek]

@jluethi I am a junior contractor working with companies and I was told to check and possibly develop a OmeZarr viewer. Currently I am checking for possible viewers and I am aware of the few. Have you heard of Aviator? It has some interesting functions like split screen or minimap indicating the position on the image. It might be valuable to incorporate those functions to other viewers.

[jluethi]

Hey @Netomek
Nice to hear & good luck! From my experience with this so far, I'd recommend checking out BioNGFF and getting in touch with the developers there to see if things align, especially if 2D & 2.5D renderings are key. It's an effort with a clear strategy & long-term funding to maintain the viewer. Also, keep an eye out for potential web viewer work by @thewtex towards the end of the year (known for the ITK web viewer: https://kitware.github.io/itk-vtk-viewer/docs/viewer.html). That's currently my best guess for where 3D web viewing of OME-Zarrs may go.

Your choice will obviously depend on the actual requirements.

I've heard of Avivator (https://avivator.gehlenborglab.org/ which I assume you referred to above). It's also built on top of Viv, like ViZarr and includes OME-TIFF support & some 3D rendering. We haven't used it on our end so far though, so no experience we can share.

For broader OME-Zarr viewer discussions, I'd recommend posting on the image.sc forum