3D visualization of volumetric data (e.g. segmentations)

[aliaksei-chareshneu]

Dear all,

Could you tell me if vizarr currently supports 3D visualization of volumetric data in zarr format, specifically segmentation data, e.g. from microscopy or cell tomography?

Best regards,
Aliaksei

[manzt]

Hello, thanks for taking interest in vizarr! Unfortunately vizarr does not currently support 3D visualization of volumetric data. Some more in-depth discussion can be found in:

• Wrong chunk loaded at low-resolutions #60 (comment)

[aliaksei-chareshneu]

Hello, thank you for the response! If I may ask, why you decided to not support 3D visualisation, given that Viv do support it via raycasting?

[manzt]

Thanks for the question. 3D visualization is a newer feature that we've released in Viv that isn't supported for multiscale volumes or volumes where the data are "chunked" with a chunksize > 1 along the z dimension. Therefore only a subset of Zarr-based volumes are supported by Viv, whereas all OME-TIFF volumes are supported (since for OME-TIFF, chunksize == 1 for all non-XY axes and the format is not suitable for multiscale 3D).

We plan to add support for 3D in Vizarr when we can handle a larger subset of Zarr-based volumes in Viv, as well as when the OME-NGFF metadata for spatial transformations is better defined.