Inference of Lineage-Resolved Cell Identities in Uncompressed C. elegans Embryos
Miles P Tran, Neil Peinado, Zhongying Zhao, Pavak K Shah · 2026
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Description
Miles Tran and co-authors present EmbAlign, software that names the cells of a worm embryo from a single snapshot. In Caenorhabditis elegans, every cell's lineage is known, but naming cells in a new embryo usually takes long live imaging and tracking. EmbAlign instead registers the snapshot in 3D against a spatiotemporal atlas of reference embryos. An iterative Sinkhorn alignment then settles each cell's identity, robust to the embryo's pose and natural shifts in cell position.
The method reached 96.9% accuracy up to the 190-cell stage. A built-in diagnostic layer scores how trustworthy each call is. The output turns raw spatial data into lineage-aware datasets, ready for studies of how embryos vary. A tool that reads the tree off one still image speeds every experiment that asks which cell did what.
Catalog record
| CREATOR | Miles P Tran, Neil Peinado, Zhongying Zhao, Pavak K Shah |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 19 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |