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. 2022 Aug 4;23:168. doi: 10.1186/s13059-022-02734-7

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© The Author(s) 2022

Open AccessThis 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/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 6 — Detecting spatial domains in the MERFISH dataset. A An anatomic reference atlas obtained from the Allen Mouse Brain Atlas displays the spatial domains of the mouse hypothalamus region. B Annotated spatial domain labels for the tissue section Bregma-0.14 based on spatial gene expression patterns and the Allen Mouse Brain Atlas. C Barplots of ARI show the accuracy of different methods for spatial domain detection on the tissue section Bregma-0.14. The compared methods include BASS, HMRF, BayesSpace, and SpaGCN. For HMRF, the range of ARI based on a pre-defined list of βs is shown with an error bar. D The identified spatial domains on the tissue section Bregma-0.14 are shown for BASS, HMRF, BayesSpace, and SpaGCN. E The identified spatial domains on five tissue sections (Bregma-0.04, Bregma-0.09, Bregma-0.14, Bregma-0.19, and Bregma-0.24) were obtained with the multi-sample analysis of BASS. V3: the third ventricle; BST: bed nuclei of the strata terminalis; fx: columns of the fornix; MPA: medial preoptic area; MPN: medial preoptic nucleus; PV: periventricular hypothalamic nucleus; PVH: paraventricular hypothalamic nucleus; and PVT: paraventricular nucleus of the thalamus