Cirrocumulus

Cirrocumulus is an interactive visualization tool for large-scale single-cell genomics data, with the following features:

• Visualize datasets in h5ad, 10x h5, Xenium, loom, Seurat, TileDB, or zarr formats
• View MERFISH or other spatial transcriptomics data overlaid on an image
• Easily deploy on a laptop, on-premise server, cloud VM, or Google App Engine
• Share the current visualization state in a URL
• Share datasets securely with collaborators
• Create dotplots, heatmaps, and violin plots to explore relationships between categorical variables and expression
• Generate composition plots to inspect cluster makeup
• Explore complete differential expression results generated by Scanpy or Pegasus/Cumulus
• Interactively create and share “AND” or “OR” filters
• Collaboratively annotate cell types in real time, optionally using a controlled vocabulary (example ontology)
• Quickly load multiple features from predefined lists (see example)
• Explore multiple features and embeddings simultaneously
• Fast interactive exploration of 2 and 3-d embeddings of millions of cells, including zoom, pan, rotate (3-d), and lasso tools
• Save publication quality images
• Highly customizable - for example, set the color map, point size, or whether to use fog for 3-d embeddings to fade distant points