An interactive explorer for single-cell lineage tracing.

CELLxLINEAGE is a fork of CELLxGENE extended to support TreeData objects and lineage tree visualization alongside the standard UMAP embedding.

Installation

You need to have Python 3.10 or newer installed on your system. If you don't have Python installed, we recommend installing Mambaforge.

Install the latest release of cellxlineage from PyPI:

pip install cellxlineage

Usage

# Launch with a TreeData file
cellxlineage launch data.h5td

CELLxGENE documentation

CELLxLINEAGE inherits all standard CELLxGENE Annotate features. For documentation on exploration, filtering, differential expression, and annotations, see the CELLxGENE Annotate documentation.

Hosting

CELLxLINEAGE can be hosted for a small group (≈10 concurrent users) to explore one shared dataset. Add --ephemeral-annotations:

cellxlineage launch data.h5td --host 0.0.0.0 --port 5005 --ephemeral-annotations

In this mode:

  • No "user generated data directory" prompt. Custom annotations and gene sets are kept in memory, per browser session, and never written to disk.
  • Annotations reset on reload and are isolated between users — reloading the page or a new visitor starts from a clean slate. Differential expression is already per-session and resets the same way.

Notes:

  • Run as a single process — the in-memory annotations and lineage caches live in that process, so multiple workers would not share them. The built-in threaded server is fine for a small trusted group; to harden it, put it behind a reverse proxy (e.g. nginx) and, if you want a production WSGI server, run gunicorn with --workers 1 --threads N.
  • Do not pass --backed in this mode (rejected at startup): concurrent reads on a single shared file handle are unsafe. The default in-memory data load is what you want.
  • A heavy differential-expression or ancestral-linkage request briefly occupies the process; at this scale that is acceptable.

Contact

For questions and bug reports please use the issue tracker.

License

MIT — see LICENSE. Portions copyright Chan Zuckerberg Initiative; lineage extensions copyright William Colgan.

Project links

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Credits

Author: William Colgan

GitHub Statistics

Data verified by PyPI on Jul 29, 2026
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License

MIT License (MIT)

Requires

Python >=3.10

Provides Extra

prepare annotate

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