Fig. 3: Performance evaluation of scNiche on spatial transcriptomics datasets.

a The mouse V1 neocortex STARmap data from one slice, each cell is colored by the cell type labels (left) and the niche labels (right). b The cell niches identified by each method on the mouse V1 neocortex STARmap data. c Performance comparison of scNiche with other methods using the adjusted Rand index (ARI) (top) and the macro-F1 score (bottom) metrics on mouse V1 neocortex STARmap dataset. The ARI and macro-F1 score metrics relative to the niche annotation are calculated based on the result of each method. d, The mouse frontal cortex and striatum MERFISH data from one representative slice, each cell is colored by the cell type labels (top) and the niche labels (bottom). e The cell niches identified by each method on the mouse frontal cortex and striatum MERFISH data. f Performance comparison of scNiche with other methods across 31 slices using the adjusted Rand index (ARI) (left) and the macro-F1 score (right) metrics on mouse frontal cortex and striatum MERFISH dataset. The ARI and macro-F1 score metrics relative to the niche annotation are calculated based on the result of each method. Data are presented as boxplots (minima, 25th percentile, median, 75th percentile, and maxima). n = 31 slices for each method. Source data are provided as a Source Data file.