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. 2022 Apr 1;13:1739. doi: 10.1038/s41467-022-29439-6

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© The Author(s) 2022

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 license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license 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 license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 7 — a Visualization of the 3D hippocampal volume stacked by seven aligned consecutive sections profiled by Slide-seq. b The 3D SNN is a combination of the 2D SNN within each section and the spatial network between consecutive sections. c Cluster assignments generated by STAGATE-2D with the 2D SNN. d The UMAP plots generated by STAGATE-2D embeddings. The spots are colored by the identified spatial domains (left) and the section IDs (right) respectively. e Cluster assignments generated by STAGATE-3D with the 3D SNN. f The UMAP plots generated by STAGATE-3D embeddings. The spots are colored by the identified spatial domains (left) and the section IDs (right) respectively.