Binary-SPA: a reference-free method for cell annotation in high-resolution spatial transcriptomics
Honghao Bi, Wenjie Cai, Pan Wang, Kehan Ren, Inci Aydemir, Ermin Li, Johanna Melo-Cardenas, Matthew J Schipma, Ching Man Wai, Peng Ji · 2026
Read Binary-SPA: a reference-free method for cell annotation in high-resolution spatial transcriptomics by Honghao Bi, Wenjie Cai, Pan Wang, Kehan Ren, Inci Aydemir, Ermin Li, Johanna Melo-Cardenas, Matthew J Schipma, Ching Man Wai, Peng Ji (2026) 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/PMC13478750.txt.
Description
Bi and co-workers in the United States built in 2026 a computer method that names cell types in spatial gene maps with no outside guide set. Spatial methods read gene use cell by cell, but keep each cell's spot in the tissue. Naming the cells is the hard step: guide based tools fail when no matched guide set exists. Their tool, Binary-SPA, works in two rounds. Round one tags the sure cells with known marker genes, and round two spreads the tags to the rest.
Across many tissue types and rigs, the tool beat plain marker tools. It also matched or beat guide based tools, with no guide set at all. Tough samples like bone marrow cores came out well. A side check with protein stains backed the names the tool gave. The authors pitch it for lab and clinic samples where guides are thin.
Catalog record
| CREATOR | Honghao Bi, Wenjie Cai, Pan Wang, Kehan Ren, Inci Aydemir, Ermin Li, Johanna Melo-Cardenas, Matthew J Schipma, Ching Man Wai, Peng Ji |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 63 KB |
| LICENSE | https://creativecommons.org/licenses/by/4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |