Visium CytAssist human colon

A 10x Visium CytAssist FFPE human colon section: 6,356 spots on the CytAssist image, colored by the cellular neighborhood each spot falls in.

Visium CytAssist human colonOpen in a new tab

Things to try

• Compare the neighborhoods against the tissue. View → Show image toggles the CytAssist image underneath, so you can see which neighborhood boundaries fall on something visible in the stain and which do not.
• Switch to Leiden. Cells → Color by → leiden is the clustering the neighborhoods were built from — each spot's 20 nearest neighbors, grouped by their mix of Leiden labels — so the two colorings say different things about the same spots.
• Use the legend as a filter. Click a category to isolate it and dim the rest.
• Grow the spots. Cells → Point size, with the Hexagon glyph — Visium spots sit on a honeycomb array, so at the right size they tile the section rather than dotting it.
• Open the Embeddings view. It opens on the UMAP colored by region, which has a single value here and so comes out one color — switch Color by to leiden or cellular_neighborhood to see the structure.

What is not in it

The expression matrix was dropped when the checkpoint was downsampled for the web, so there is no color-by-gene; the 17,012 genes are listed in var and nothing else. The per-spot QC columns (total_counts, n_genes_by_counts, the pct_counts_in_top_* series) survived and are colorable.