Extended Data Fig. 10: Clustering results for large-scale mouse brain spatial transcriptomics (10x Visium) and metabolomics (MALDI-MSI) dataset described in Extended Data Fig. 9.
From: Resolving tissue complexity by multimodal spatial omics modeling with MISO
Results were obtained using RNA, metabolomics, and image features as input, but RNA was only accounted for in the interaction terms due to its low quality. For all applicable results, other than the MUSE results obtained when taking metabolomics and image data as input, metabolomics data were normalized by total intensity and log transformed. MUSE was not able to evaluate the combination of metabolomics and image data when the metabolomics data were log normalized, so this step was not utilized to obtain the corresponding results. The dataset used to generate the results in (a-e) contains 74,851 pseudo-spots of size 32×32 pixels. The dataset used to generate the results in (f) contains 299,350 pseudo-spots of size 16×16 pixels. Due to memory requirements, MISO was the only method that could evaluate the dataset with pseudo-spots of size 16×16 pixels. a, Clustering results from MISO, MUSE, and SpatialGlue when taking RNA and histology image data as input. b, Clustering results from MISO, MUSE, and SpatialGlue when taking RNA and metabomics data as input. c, Clustering results from MISO, MUSE, and SpatialGlue when taking metabolomics and histology image data as input. d, Clustering results from MISO when taking RNA, histology image, and metabolomics data as input. e, RNA, image, and metabolomics ICC distributions across all clusters and features for each method when taking each possible combination of modalities as input (n = 1500 ICC values for each group). For each method, the mean ICC for each modality is printed on the corresponding box plot for its top-performing combination of modalities. Test statistics and p-values were obtained using one-sided t-tests when comparing each method’s top-performing results for a given modality. f, Clustering results from MISO when taking RNA, histology image, and metabolomics data from the dataset with pseudo-spots of size 16×16 pixels as input. Test statistics and p-values were obtained using one-sided t-tests when comparing each method’s top-performing results for a given modality. Box plots: center line, median; box limits, upper and lower quartiles; whiskers, 1.5x interquartile range; points, outliers.
