PAST facilitates multislice joint embedding and automatic domain annotation. UMAP visualization of spots based on the joint embeddings of all the 12 DLPFC slices colored by (A) slices and (B) spatial domains. (C) Performance of supervised annotation evaluated by accuracy (Acc), Cohen's kappa value (κ), mean F1 score (mF1), and weighted F1 score (wF1), where Slice 151,673 was taken as the training set and other 11 slices were taken as test sets. The center line, box limits, and whiskers in the boxplots are the median, upper and lower quartiles, and 1.5× interquartile range, respectively. (D) The manual annotation of BCS1, in which the IDC_3 tumor region was black circled. UMAP visualization of the joint embeddings of spots in BCS1/2 sections colored by (E) sections and (F) spatial domains. (G) The supervised annotation results on BCS2 by different methods. The black circle denotes the supervised annotated IDC_3 and Tumor_edge_3, whereas the blue and orange circles denote the supervised annotated DCIS/LCIS_1 and DCIS/LCIS_2, respectively. (H) The annotation results of Tumor_edge_3 and DCIS/LCIS_2 by PAST-TL and PAST-3DStack and the spatial expression patterns of BCS1-marker genes on BCS2.
