Metadata-Version: 2.4
Name: cellucid
Version: 0.9.2
Summary: Interactive Single-Cell Data Visualization
Author-email: Kemal Inecik <k.inecik@gmail.com>
Maintainer-email: Kemal Inecik <k.inecik@gmail.com>
License-Expression: BSD-3-Clause
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
Project-URL: Code of Conduct, https://github.com/theislab/cellucid-python/blob/main/CODE_OF_CONDUCT.md
Project-URL: Security Policy, https://github.com/theislab/cellucid-python/blob/main/SECURITY.md
Project-URL: Support, https://github.com/theislab/cellucid-python/blob/main/SUPPORT.md
Project-URL: Citation, https://github.com/theislab/cellucid-python/blob/main/CITATION.cff
Keywords: single-cell,visualization,umap,3d,webgl,scRNA-seq,bioinformatics,anndata,jupyter
Classifier: Development Status :: 4 - Beta
Classifier: Programming Language :: Python :: 3
Classifier: Programming Language :: Python :: 3 :: Only
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Classifier: Programming Language :: Python :: 3.13
Classifier: Programming Language :: Python :: 3.14
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: <3.15,>=3.11
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy<3,>=1.26
Requires-Dist: pandas!=2.1.2,<3,>=2.1.0
Requires-Dist: scipy!=1.17.0,<2,>=1.12
Requires-Dist: tqdm>=4.45
Requires-Dist: anndata<0.13,>=0.12.19
Requires-Dist: zarr<4,>=3.1.4
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Dynamic: license-file

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

[![PyPI version](https://img.shields.io/pypi/v/cellucid.svg)](https://pypi.org/project/cellucid/)
[![Python versions](https://img.shields.io/badge/python-3.11%20%7C%203.12%20%7C%203.13%20%7C%203.14-blue.svg)](https://cellucid.readthedocs.io/en/latest/user_guide/python_package/installation.html)
[![Documentation Status](https://readthedocs.org/projects/cellucid/badge/?version=latest)](https://cellucid.readthedocs.io/en/latest/)
[![License: BSD-3-Clause](https://img.shields.io/badge/license-BSD--3--Clause-blue.svg)](https://opensource.org/licenses/BSD-3-Clause)

# 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](https://cellucid.readthedocs.io/en/latest/user_guide/python_package/installation.html)
to choose PyPI or GitHub based on current registry availability. To install the
active source directly from the official GitHub repository:

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

From PyPI:

```bash
pip install cellucid
```

The [PyPI package page](https://pypi.org/project/cellucid/) 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](https://www.cellucid.com)
2. Load a prepared folder, one `.h5ad`, or one `.zarr.zip` archive

Or visualize an AnnData from Python/Jupyter:

```python
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](https://cellucid.readthedocs.io/en/latest/user_guide/python_package/index.html)
- [Complete Cellucid documentation](https://cellucid.readthedocs.io/en/latest/)
- [Live web application](https://www.cellucid.com) and
  [web viewer source](https://github.com/theislab/cellucid)
- [R package](https://github.com/theislab/cellucid-r)
- [Official public demo datasets](https://github.com/theislab/cellucid-datasets)
- [Three custom dataset repository examples](https://github.com/theislab/cellucid-demo-custom-datasets)
- [Community annotation repository](https://github.com/theislab/cellucid-annotation)
  and [annotation guide](https://cellucid.readthedocs.io/en/latest/user_guide/web_app/j_community_annotation/index.html)
- [Python package issues](https://github.com/theislab/cellucid-python/issues)

## Community

- [Contributing](https://github.com/theislab/cellucid-python/blob/main/CONTRIBUTING.md)
- [Code of Conduct](https://github.com/theislab/cellucid-python/blob/main/CODE_OF_CONDUCT.md)
- [Security](https://github.com/theislab/cellucid-python/blob/main/SECURITY.md)
- [Support](https://github.com/theislab/cellucid-python/blob/main/SUPPORT.md)
- [Citation](https://github.com/theislab/cellucid-python/blob/main/CITATION.cff)

## License

BSD-3-Clause
