cellucid 0.0.9

Interactive Single-Cell Data Visualization

Cellucid

See every cell. Query any gene. Fly through millions. 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 adaptive detail for millions of cells
• 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

pip install cellucid

Quickstart

Try the web app (no setup):

1. Open https://cellucid.com
2. Load a pre-exported folder, .h5ad, or .zarr

Or visualize an AnnData from Python/Jupyter:

from cellucid import show_anndata

show_anndata(adata)  # or: show_anndata("dataset.h5ad")

Links

• Web app: https://cellucid.com
• Documentation: https://cellucid.readthedocs.io
• Community annotation voting: https://cellucid.readthedocs.io/en/latest/user_guide/web_app/j_community_annotation/index.html
• Source: https://github.com/theislab/cellucid-python
• Web viewer: https://github.com/theislab/cellucid
• Annotation template: https://github.com/theislab/cellucid-annotation
• Issues: https://github.com/theislab/cellucid-python/issues

License

BSD-3-Clause