Napari_spatialdata colouring cell_labels and plotting specific transcripts

Help spatialdata
1

Hi there, I am wanting to create a similar plot to the one below with my Xenium sample. There are cell type labels in the Anndata.obs, but I can only plot them on the cell_circles and not the cell_labels. I also want to be able to plot transcripts for specific genes, but it seems like I can only plot all or none of the transcripts.

The plot below was done by someone else using Napari, but not from spatialdata, and has cells coloured by a metadata column and is plotting the transcripts for just one gene. Is there a way to do this napari_spatialdata? Thanks.

cosmx_napari
cosmx_napari1920×1225 313 KB

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Hi @lhock17, plotting the table annotation on the labels instead of the circles can be done both in napari-spatialdata and spatialdata-plot by setting a new target for the table. This is shown in this new tutorial here: Technology focus: Xenium — spatialdata.

Plotting only a particular cell-type is currently only possible for spaitaldata-plot (please see the last plot in the notebook above). We want to eventually enable the functionality also in napari-spatialdata.