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. 2024 Jan 5;15:207. doi: 10.1038/s41467-023-44367-9

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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. 4 — A–H Application of MENDER on a mouse brain atlas using MERSCOPE. A The dataset contains 9 slices from 3 different brain positions. For each slice, we show the MENDER result (top). We also highlight one slice for each position to compare with the Allen brain reference (bottom). Specific brain domains are shown, including Pontine Gray (B), Isocortex Layers (C), Corpus Callosum (D), Hippocampal region (E), Thalamus (F), and Caudoputamen (G). H The UMAP embedding on the top of MENDER cellular context representation. I Summary of benchmark datasets for unsupervised spatial domain identification. J Running time comparison of different spatial methods across the 4 datasets. Error bars are based on mean and 95% confidence interval. Source data are provided as a Source Data file.