How to cite¶
If you use SP Classify in your work, please cite both the software and the CellTune paper it
derives from, plus any method papers for the specific features you used. This page mirrors the
in-app Extensions ▸ SP Classify ▸ How to Cite… dialog and the machine-readable
CITATION.cff.
Software¶
Mckay, M. SP Classify: an active-learning cell classifier extension for QuPath. Zenodo. https://doi.org/10.5281/zenodo.21782421
The Zenodo DOI above is a concept DOI that always resolves to the latest release.
Always cite¶
The human-in-the-loop workflow this extension derives from:
CellTune (Keren Lab). Nature Methods (2026). https://doi.org/10.1038/s41592-026-03162-2
Cite if you used the corresponding feature¶
| Feature | Citation |
|---|---|
| Cellular Neighborhoods | Schürch CM, Bhate SS, Barlow GL, et al. Cell 182(5):1341–1359 (2020). doi:10.1016/j.cell.2020.07.005 |
| Leiden clustering | Traag VA, Waltman L, van Eck NJ. Sci Rep 9:5233 (2019). doi:10.1038/s41598-019-41695-z |
| Clustering (scanpy recipe) | Wolf FA, Angerer P, Theis FJ. Genome Biol 19:15 (2018). doi:10.1186/s13059-017-1382-0 |
| Cohort / all-cells Leiden (HNSW) | Malkov YA, Yashunin DA. IEEE TPAMI 42(4):824–836 (2020). doi:10.1109/TPAMI.2018.2889473 |
| arcsinh cofactor (0.05) for MIBI | Hartmann FJ, Mrdjen D, McCaffrey E, et al. Nat Biotechnol 39:186–197 (2021). doi:10.1038/s41587-020-0651-8 |
| Batch Normalisation (UniFORM) | Wang K, Ait-Ahmad K, Kupp S, et al. bioRxiv 2024.12.06.626879 (2024); Cell Reports Methods (2025). doi:10.1101/2024.12.06.626879 |