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. 2024 Dec 5;25:308. doi: 10.1186/s13059-024-03435-z

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© The Author(s) 2024

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — Phenotyping of cells following assignment with InSituType. A and C show UMAPs of T cells and MNPs, respectively, calculated with all cells in all FOV. Refined phenotypes from calculating new PCA/UMAP, clustering the subset with Louvain, and identifying markers with “FindAllMarkers” can be seen in B and D. Final cell assignments of all cells, including tumor cells, are shown in E. Abbreviations: FOV, fields of view; MNPs, mononucleic phagocytes; PCA, principal component analysis; UMAP, uniform manifold approximation and projection