Metadata-Version: 2.4
Name: cellucid
Version: 0.0.9
Summary: Interactive Single-Cell Data Visualization
Author-email: Kemal Inecik <k.inecik@gmail.com>
Maintainer-email: Kemal Inecik <k.inecik@gmail.com>
License: BSD 3-Clause License
        
        Copyright (c) 2025, Kemal Inecik
        
        Redistribution and use in source and binary forms, with or without
        modification, are permitted provided that the following conditions are met:
        
        1. Redistributions of source code must retain the above copyright notice, this
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Project-URL: Homepage, https://github.com/theislab/cellucid-python
Project-URL: Repository, https://github.com/theislab/cellucid-python
Project-URL: Documentation, https://cellucid.readthedocs.io
Project-URL: Issues, https://github.com/theislab/cellucid-python/issues
Project-URL: Changelog, https://github.com/theislab/cellucid-python/blob/main/CHANGELOG.md
Project-URL: Contributing, https://github.com/theislab/cellucid-python/blob/main/CONTRIBUTING.md
Keywords: single-cell,visualization,umap,3d,webgl,scRNA-seq,bioinformatics,anndata,jupyter
Classifier: Development Status :: 3 - Alpha
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Operating System :: OS Independent
Classifier: Intended Audience :: Science/Research
Classifier: Topic :: Scientific/Engineering :: Visualization
Classifier: Topic :: Scientific/Engineering :: Bio-Informatics
Classifier: Typing :: Typed
Classifier: Framework :: Jupyter
Requires-Python: >=3.10
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy>=1.21
Requires-Dist: pandas>=1.4
Requires-Dist: scipy>=1.7
Requires-Dist: tqdm>=4.45
Requires-Dist: anndata>=0.8
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Requires-Dist: jupyter-server-proxy>=4.1
Provides-Extra: dev
Requires-Dist: pytest>=7.0; extra == "dev"
Requires-Dist: pytest-cov>=4.0; extra == "dev"
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Dynamic: license-file

![Cellucid](https://raw.githubusercontent.com/theislab/cellucid-python/main/cellucid-logo.svg)

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# 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

```bash
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:

```python
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
