Extended Data Fig. 3: Comparison of methods on mouse cortex dataset from STARmap, related to Fig. 3.

(a) tSNE visualization of latent representations by different methods with pseudo-colors labeling cortex depth along x-coordinate (on right side). (b) Comparison of cell clusters on (top) numbers of identified clusters with or without significant spatial co-localization properties and (bottom) feature quality evaluation by cluster compactness in latent space using Silhouette coefficient. (c) Stability analysis of identified clusters to the choice of hyperparameter n_neighbor in PhenoGraph. Red circles: major differences in subpopulations compared with the result using default parameters (left panel) annotated with affected cortex layers. (d) Spatial mapping and annotations of clusters with significant spatial co-localization patterns. Significantly co-localized clusters are identified using spatial co-localization score with permutation test. Clusters are assigned to one layer with respect to the anatomic annotations by original paper (Methods). (e) tSNE visualization of MUSE clusters in MUSE latent space. All clusters were classified into ‘Refined’, ‘Reproduced’ or ‘Discovered’ types based on comparison with clusters identified from transcript-alone or morphological-alone analysis (corresponding to Fig. 3a). (f) 3D mapping of three types of MUSE clusters in the latent space of morphological features (top layer of each 3D plot), MUSE latent features (middle layer) or transcriptional features (bottom layer). Lines connect the same cells across the three spaces.