Visium CytAssist mouse brain
A 10x Visium CytAssist fresh-frozen mouse brain section: 4,881 spots on the CytAssist image, and the smallest of the demos.
Things to try
- Read the structure off the colors. The cellular neighborhoods come out as concentric bands across the section. Nothing told the clustering where the tissue's layers are; it recovered them from expression alone.
- Toggle the image. View → Show image, then back, to check the boundaries against the tissue itself.
- Switch to Leiden. Cells → Color by → leiden, and compare it against
cellular_neighborhood: one clusters spots by their own expression, the other by the mix of Leiden clusters in each spot's 20 nearest neighbors. - Open the Embeddings view. Both a UMAP and a PCA are stored; the Embedding dropdown switches between them, and the X/Y selectors pick which components to plot.
What is not in it
As with the other demos, the expression matrix was dropped when the checkpoint was downsampled for the web, so there is no color-by-gene. The obs columns, the embeddings and the image are all intact.