Skip to main content

Bring your single-cell data to life

Project description


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

Quick Start

Install the package:

pip install cirrocumulus

Launch cirrocumulus via the command line:

cirro launch <path_to_dataset>
  • Launch accepts more than one dataset to enable quick dataset switching or to combine modalities (e.g gene fusions and expression) stored in separate files.

Example Data


Complete documentation available at

Project details

Release history Release notifications | RSS feed

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

cirrocumulus-1.1.56.tar.gz (6.1 MB view hashes)

Uploaded source

Built Distribution

cirrocumulus-1.1.56-py3-none-any.whl (3.0 MB view hashes)

Uploaded py3

Supported by

AWS AWS Cloud computing and Security Sponsor Datadog Datadog Monitoring Fastly Fastly CDN Google Google Download Analytics Microsoft Microsoft PSF Sponsor Pingdom Pingdom Monitoring Sentry Sentry Error logging StatusPage StatusPage Status page