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hms-dbmi / vizarr

A minimal Zarr image viewer based on Viv.
https://hms-dbmi.github.io/vizarr/?source=https://minio-dev.openmicroscopy.org/idr/v0.3/idr0062-blin-nuclearsegmentation/6001240.zarr
MIT License
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3D visualization of volumetric data (e.g. segmentations) #142

Closed aliaksei-chareshneu closed 2 years ago

aliaksei-chareshneu commented 2 years ago

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 commented 2 years ago

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:

aliaksei-chareshneu commented 2 years ago

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 commented 2 years ago

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.