Fig. 2: Application to mouse primary motor cortex dataset measured by MERFISH.

a The MOP region annotations in the Allen CCF v3 (http://atlas.brain-map.org/). b The ground truth cell types using UMAP embedding. c The Spatial-ID prediction using UMAP embedding. d Spatial organization of the ground truth cell types in a coronal slice (slice153). Bar scale 400 μm. e Spatial organization of the Spatial-ID prediction in d. Bar scale 400 μm. f The comparison of cell type annotation accuracy; n = 12 independent samples; center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range. Notably, the mean accuracy of Cell-ID is 17.08%, that is far below those shown and is therefore not shown. g The confusion matrix of Spatial-ID prediction. The vertical axis and the horizonal axis list the ground truth cell types and the prediction of Spatial-ID, respectively. h The ground truth of L5 ET, L5/6 NP, L6 CT, and L6b neurons, and the prediction of Spatial-ID and the control methods. Bar scale 400 μm. i The neighborhood complexity of a given cell is defined as the number of different cell types presented within a neighborhood of 100 μm in radius. The neighborhood purity of a given cell is defined as the fraction of the most abundant cell type to all cells in the neighborhood of 100 μm in radius. j Simulations of different gene dropout rates. From left to right, the comparison of cell type annotation accuracy at different gene dropout rates, spatial organization of the Spatial-ID prediction at the dropout rate of 0.5, the comparison of cell type annotation accuracy at the dropout rate of 0.5 (n = 12 independent samples; Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range), the confusion matrix of Spatial-ID prediction at the dropout rate of 0.5. Bar scale 400 μm. k New cell type discovery. From left to right, ground truth of L4/5 IT and L6 IT Car3 neurons, a pipeline of new cell type discovery, unassigned cells after thresholding, clusters derived from clustering for unassigned cells, and the finally found new cell types (i.e., L4/5 IT and L6 IT Car3). Bar scale 400um.