Figure 2.

Comparative performance of SpaCAE to existing spatial and non-spatial methods on spatial domain identification. (A) DLPFC layers were annotated by Maynard et al. The ground truth of spots was mapped on their spatial position in slide 151675 (n = 3592 spots), which was separated into six cortical layers (L1–L6) and WM. Layers with annotations are provided on the remaining slides (Supplementary Figure 4). (B) Boxplots of the performance of SpaCAE and other algorithms for all 12 DLPFCs. The y-axis shows the ARI, which was used to compare the similarity of the predicted spatial layers and the manually annotated layers for each algorithm. (C) ARI boxplots of whether deep spatial contrast is used, whether spatial data augmentation is used and whether replace GCN/GDN with linear layer in SpaCAE are shown. (D) Identification of spatial domains by SpaCAE and existing state-of-the-art algorithms (GraphST, STAGATE, DeepST, BayesSpace, SpaGCN), VAE and GAE for slide 151675.