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. 2024 Oct 30;30(11):3236–3249. doi: 10.1038/s41591-024-03215-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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Extended Data Fig. 9 — a) Spatial scatter plot overlaid onto H&E images depicting the expression levels of CD163 in macrophages for all biopsies, based on cell-segmented MERFISH data. b) UMAPs of all observations confidently annotated as macrophages across biopsies based on their unaligned or harmony sample-integrated expression profiles, colored by sample/patient or Leiden clusters (resolution: 0.6). c) Clustered heatmap depicting the pairwise Pearson correlation of scaled Leiden cluster-wise expression profiles across methods. Method and cluster ID (as in panel b) are indicated. d) Boxplots depicting the expression of macrophage marker and function genes in the method-specific macrophage clusters grouped in cross-method cluster 1 (N = 15) and 2 (N = 20) according to panel c). Genes are ordered by the median difference between cross-method cluster 1 and 2. N = method-specific clusters.