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 analyzes tumor microenvironment morphology (A) Expert annotated tumors from immunofluorescent image, with anti-CD3 intensity in pink and DAPI intensity in green. IDC is outlined in yellow, carcinoma in situ is outlined in blue, benign hyperplasia is outlined in red, and unclassified tumor is in green. (B) Prominent multiscale domains identified by PHD-MS, selected from the most persistent domains. Regions are numbered to correspond with the labels in (A). (C) PHD-MS heterogeneity map highlights highly heterogeneous regions. The heterogeneity score approximates the number of persistent domains that contain each spot. (D) Mean normalized immune expression from a set of immune genes (PTPRC, CD4, CD8A, CD14, CD68, and IGHG3). (E) Normalized expression of key oncogenes APOE, PGK1, and MALAT1 in the lower IDC. From DGE analysis, APOE is overexpressed in region 7 relative to 8 and 9, PGK1 is overexpressed in 8, and MALAT1 is overexpressed in 9.
Article Snippet: Visium Invasive Ductal Carcinoma Stained With Fluorescent CD3 Antibody , Zhao et al. , https://www.10xgenomics.com/datasets/invasive-ductal-carcinoma-stained-with-fluorescent-cd-3-antibody-1-standard-1-2-0.
Techniques: In Situ, Expressing