STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping
Kalen Clifton, Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K. Aimiuwu, Justus M. Kebschull, Michael I. Miller, Daniel Tward, Jean Fan · 2023
Read STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping by Kalen Clifton, Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K. Aimiuwu, Justus M. Kebschull, Michael I. Miller, Daniel Tward, Jean Fan (2023) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-10709594.txt.
Description
Kalen Clifton and eight colleagues present STalign, open-source software that lines up spatial transcriptomics data sets so gene activity maps from different tissue slices can be compared. The method measures gene expression in place. But slices warp, tear, and only partly overlap, defeating simple alignment.
STalign uses smooth, invertible deformation mapping to handle partial matches and local distortion. Across methods it achieved a far better match of gene expression and cell types than older landmark methods. Applied to mouse brain data, it lifted region labels from the Allen Brain Atlas onto new samples. It also exposed differences in makeup across structures. The toolkit is released in public, with tutorials for the spatial biology community.
Catalog record
| CREATOR | Kalen Clifton, Manjari Anant, Gohta Aihara, Lyla Atta, Osagie K. Aimiuwu, Justus M. Kebschull, Michael I. Miller, Daniel Tward, Jean Fan |
|---|---|
| YEAR | 2023 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 86 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |