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PHD-MS identifies stable brain structures in a <t>Visium</t> <t>mouse</t> brain (A) An annotated coronal section from Allen Brain Atlas as the ground truth. (B) NeST coexpression hotspots of the Visium mouse brain data. NeST identifies 5 relevant layers of structure, color coded by layer (bottom), matched to the annotated regions of Allen Atlas (right). (C) Nested PHD-MS domains with layer labels, color coded with matched regions in Allen Atlas. Top layer represents the domain at its broadest scale, including low-coreness spots. Middle layer includes medium-coreness spots, and core layer forms the domain’s stable core.
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PHD-MS identifies stable brain structures in a <t>Visium</t> <t>mouse</t> brain (A) An annotated coronal section from Allen Brain Atlas as the ground truth. (B) NeST coexpression hotspots of the Visium mouse brain data. NeST identifies 5 relevant layers of structure, color coded by layer (bottom), matched to the annotated regions of Allen Atlas (right). (C) Nested PHD-MS domains with layer labels, color coded with matched regions in Allen Atlas. Top layer represents the domain at its broadest scale, including low-coreness spots. Middle layer includes medium-coreness spots, and core layer forms the domain’s stable core.
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PHD-MS identifies stable brain structures in a <t>Visium</t> <t>mouse</t> brain (A) An annotated coronal section from Allen Brain Atlas as the ground truth. (B) NeST coexpression hotspots of the Visium mouse brain data. NeST identifies 5 relevant layers of structure, color coded by layer (bottom), matched to the annotated regions of Allen Atlas (right). (C) Nested PHD-MS domains with layer labels, color coded with matched regions in Allen Atlas. Top layer represents the domain at its broadest scale, including low-coreness spots. Middle layer includes medium-coreness spots, and core layer forms the domain’s stable core.
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PHD-MS identifies stable brain structures in a Visium mouse brain (A) An annotated coronal section from Allen Brain Atlas as the ground truth. (B) NeST coexpression hotspots of the Visium mouse brain data. NeST identifies 5 relevant layers of structure, color coded by layer (bottom), matched to the annotated regions of Allen Atlas (right). (C) Nested PHD-MS domains with layer labels, color coded with matched regions in Allen Atlas. Top layer represents the domain at its broadest scale, including low-coreness spots. Middle layer includes medium-coreness spots, and core layer forms the domain’s stable core.

Journal: Cell Reports Methods

Article Title: Multiscale domain identification for spatial transcriptomics via persistent homology

doi: 10.1016/j.crmeth.2026.101376

Figure Lengend Snippet: PHD-MS identifies stable brain structures in a Visium mouse brain (A) An annotated coronal section from Allen Brain Atlas as the ground truth. (B) NeST coexpression hotspots of the Visium mouse brain data. NeST identifies 5 relevant layers of structure, color coded by layer (bottom), matched to the annotated regions of Allen Atlas (right). (C) Nested PHD-MS domains with layer labels, color coded with matched regions in Allen Atlas. Top layer represents the domain at its broadest scale, including low-coreness spots. Middle layer includes medium-coreness spots, and core layer forms the domain’s stable core.

Article Snippet: Visium mouse brain section (coronal) , 10x Genomics , https://squidpy.readthedocs.io/en/stable/api/squidpy.datasets.visium_hne_adata.html#squidpy.datasets.visium_hne_adata.

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