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.
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# Launch with a TreeData file
cellxlineage launch data.h5tdCELLxLINEAGE inherits all standard CELLxGENE Annotate features. For documentation on exploration, filtering, differential expression, and annotations, see the CELLxGENE Annotate documentation.
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-annotationsIn 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
--backedin 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.
For questions and bug reports please use the issue tracker.
MIT — see LICENSE. Portions copyright Chan Zuckerberg Initiative; lineage extensions copyright William Colgan.