Cellucid

See every cell. Query any gene. Explore in 2D and 3D. Interactive, GPU-accelerated single-cell visualization in the browser.

Cellucid is a browser-first viewer for exploring large single-cell datasets in real time: fly through 2D/3D embeddings (UMAP/t-SNE/PCA), color by genes or metadata, filter and compare populations, and share reproducible views with collaborators.

Highlights

• GPU-accelerated WebGL rendering with level-of-detail culling; a built-in synthetic benchmark measures what your own GPU sustains
• AnnData-first workflow for the Scanpy ecosystem (.h5ad and Zarr supported)
• Shareable exports you can host locally, on GitHub, or behind a server
• Genes + metadata overlays optimized for interactive querying
• Connectivity + dynamics: KNN edges and animated vector fields (RNA velocity / drift)
• Collaboration: community annotation voting with optional GitHub sync
• Publication export: SVG (vector) and high-DPI PNG figures
• Works everywhere: web app, local/remote server, and Jupyter notebooks

Install

Cellucid requires Python 3.11, 3.12, 3.13, or 3.14. Use the dedicated Installation guide to choose PyPI or GitHub based on current registry availability. To install the active source directly from the official GitHub repository:

pip install "cellucid @ git+https://github.com/theislab/cellucid-python"

From PyPI:

pip install cellucid

The PyPI package page is authoritative for registry availability. Until it lists the active version, pip install cellucid resolves only to the versions PyPI already holds, and those are earlier generations whose API differs from the one this README and the documentation describe.

Quickstart

Try the web app (no setup):

1. Open cellucid.com
2. Load a prepared folder, one .h5ad, or one .zarr.zip archive

Or visualize an AnnData from Python/Jupyter:

from cellucid import show_anndata

show_anndata(
    adata,
    dataset_name="My dataset",
    dataset_id="my-dataset",
)

An adata straight out of Scanpy works as written.

Documentation and ecosystem

• Python package guide
• Complete Cellucid documentation
• Live web application and web viewer source
• R package
• Official public demo datasets
• Three custom dataset repository examples
• Community annotation repository and annotation guide
• Python package issues

Citation

Placeholder citation. The Cellucid preprint is in preparation for bioRxiv and has no DOI yet; the reference below is a placeholder and will be replaced when the preprint is published.

If you use Cellucid, please cite:

Inecik, K. PLACEHOLDER: Cellucid preprint, title to be announced (forthcoming on bioRxiv). bioRxiv (in preparation).

BibTeX and other formats: Citing Cellucid.

Community

• Contributing
• Code of Conduct
• Security
• Support
• Citation

License

BSD-3-Clause