Display network diagrams in TissUUmaps 3.1¶

Use squidpy to download an example of AnnData object with image and markers:

In [6]:
import squidpy as sq
import numpy as np

adata = sq.datasets.visium_hne_adata_crop()

## Compute spatial neighbors graph:
sq.gr.spatial_neighbors(adata, delaunay=True, coord_type="generic")

Save AnnData to disk:

In [7]:
adata_path = "test_visium.h5ad"
adata.write(adata_path)

Load the AnnData object into TissUUmaps:

In [8]:
import tissuumaps.jupyter as tj
viewer = tj.opentmap(adata_path)

Loading url:  http://localhost:5100/test_visium.h5ad?path=Users\chrav452\Documents\GitHub\TissUUmaps\flask\examples