Journal: Genome Biology

Article Title: STHD: probabilistic cell typing of single spots in whole transcriptome spatial data with high definition

doi: 10.1186/s13059-025-03608-4

Figure Lengend Snippet: Spot-level predictions and benchmarking of a zoomed patch in a colon cancer VisiumHD sample. a Example of STHD results of a patch from the human colon cancer VisiumHD sample, revealing tumor-like epithelial cells and intercryptic immune population, visualized using the interactive STHDviewer. b Cell type posterior probabilities at spot level for the same patch, visualized using Squidpy. Top row, three epithelial cell types; Bottom row, two immune cell types. c A spatial plot of unsupervised Leiden clustering on spot gene expression. d Spatial plots of unsupervised Leiden clustering of gene expression aggregated by bins in size of 4 × 4 spots. Left, clustering bins within patch, right, global cluster group of bins. e Cell type proportion decomposed by RCTD on bins of size of 4 × 4 spots, demonstrating two tumor epithelial classes, enterocytes, and stem-like cells. f The H&E histopathology image in full resolution of the same crop. g Comparison to other cell typing and clustering methods adaptive to high-resolution spots. h The STHD predicted labels at spot-level and STHD-guided binning in bins of 4 × 4 spots and 8 × 8 spots, visualized using Squidpy using the same colon cancer cell type colormap. i Benchmarking with simulated high-resolution spatial data. Left, ground truth cell type labels; middle, STHD predicted cell type labels; right, receiver operating characteristic curve (ROC) curve for all cell types. j Benchmarking against other methods for spot annotation in repeated spatial transcriptomics simulations. k Expression dot plots for marker genes of normal epithelial cells, at spot level or STHD-guided bin level. Left to right: normal epithelial cell types in reference human colon cancer sample, normal epithelial cell types based on STHD predicted spots, normal epithelial cell types from STHD-guided bins of size 4 × 4 spots, normal epithelial cell types in STHD-guided bins of size 8 × 8 spots. The same cell type-specific gene markers from the original colon cancer study were used. ROC, Receiver operating characteristic. AUC, area under the curve

Article Snippet: Spatial transcriptomics (ST) technologies have enabled gene expression profiling in the native spatial context of tissues.

Techniques: Gene Expression, Histopathology, Comparison, Expressing, Marker