Showing 3D ISH data in a panel independent of the cells in UMAP (scRNAseq dataset)

[gauravgadhvi]

Hi team,

Thank you for providing a helpful forum for community discussions. I am trying to configure Vitessce to show some scRNAseq data as scatterPlots and other views such as cell sets, etc. I am able to successfully show these so far (link below)

http://vitessce.io/#?edit=false&url=https%3A%2F%2Frobbinsa.me%2Fcelldata%2Fwelchlab%2FpyTest%2FHY_Analysis2_NormData_zarrConfig_FINAL.json

Apart from this data, we have some ISH data from the same cells, voxelated into cubes and represented as 3D coordinates. Is there a way to add a view to show this as 3D points rendered in space or even as a GIF or image? We want this 3D data to be represented independent of the cells in the UMAP since the voxels don't have a direct mapping in the UMAP space. I basically have a file with X, Y and Z coordinates for around 100 observations. Wondering if anybody has tried displaying any 3D data which is not molecular segmentation data?

Thank you so much, any pointers or help are much appreciated!

[keller-mark]

Currently the spatial view only supports 3D rendering for images http://vitessce.io/#?dataset=blin-2019. We do not yet have support for point clouds or segmentations in rendered 3D. (We have experimented with these a little but nothing has made its way into the main branch for inclusion in a release.) I think for now I would suggest either viewing the ISH data as 2D slices, or rendering the 3D data into an OME-TIFF or OME-NGFF outside of Vitessce and loading as an image.