Fig. 3: SpatialTopic identifies tertiary lymphoid structures from a whole-slide melanoma tissue sample. | Nature Communications

Fig. 3: SpatialTopic identifies tertiary lymphoid structures from a whole-slide melanoma tissue sample.

From: Scalable topic modelling decodes spatial tissue architecture for large-scale multiplexed imaging analysis

Fig. 3: SpatialTopic identifies tertiary lymphoid structures from a whole-slide melanoma tissue sample.The alternative text for this image may have been generated using AI.

A Pseudocolor plot showing spatial topic assignments from SpatialTopic, identifying five topics across the whole-slide melanoma tissue sample: topic 1 (tumor region), topic 2 (CD4 T cell region), topic 3 (stroma), topic 4 (immune-enriched stroma-tumor boundary), and topic 5 (putative tertiary lymphoid structures). Three regions of interest (ROIs) are highlighted. This panel is a pseudocolor representation of the same tissue shown in (C). B Hematoxylin and Eosin (H&E)-stained images of the whole-slide tissue and three ROIs49. B corresponds to an adjacent section of the tissue shown in (A, C). C Merged multiplexed immunofluorescence images of the same tissue section as in (A), showing PanCK/SOX10 (red), CD3 (blue), and CD20 (green) across the full slide and selected ROIs. D Heatmap shows per-topic cell type composition for the five topics identified by SpatialTopic. Topic 5 (tertiary lymphoid structures) mainly consists of B cells and CD4 T cells, with a small proportion of CD8 T cells and regulatory T (Treg) cells. Source data are provided as a Source Data file.

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