Pycea brings single-cell lineage tracing into the scverse ecosystem with TreeData
anshulkundaje · x · 2026-11-02
Researchers led by William Colgan at the Whitehead Institute, with Jonathan Weissman, Nir Yosef and MIT collaborators, released Pycea, a Python toolkit for single-cell lineage tracing analysis and visualization, described in a new bioRxiv preprint.
- Core contribution is TreeData, an AnnData extension that stores lineage trees alongside gene expression and spatial measurements, compatible with Scanpy and other scverse tools.
- Unifies two lineage data sources: molecular recording and live-cell tracking.
- Supports the full workflow: lineage tree reconstruction, UMAP/clustering, lineage visualization, and downstream lineage-aware analysis, integrating cassiopeia and cell×lineage.
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