Fig. 3: Application to mouse hypothalamic preoptic region dataset measured by MERFISH. | Nature Communications

Fig. 3: Application to mouse hypothalamic preoptic region dataset measured by MERFISH.

From: Spatial-ID: a cell typing method for spatially resolved transcriptomics via transfer learning and spatial embedding

Fig. 3

a The mouse hypothalamic preoptic region annotations in the Allen CCF v3 (http://atlas.brain-map.org/). b Visualization of the ground truth cell types using UMAP embedding. c Visualization of the Spatial-ID predictions using UMAP embedding. d 3D spatial organization of the ground truth cell types of a sample with naive behavior, and the predictions of Spatial-ID and the control methods. Scale unit (µm). e The comparison of cell type annotation accuracy; n = 3 independent samples; Center line, median; box limits, upper and lower quartiles; whiskers, 1.5× interquartile range. f The confusion matrixes show the fraction of cells from any ground truth cell type predicted by Spatial-ID and control methods. The vertical axis lists the ground truth cell types, and the horizonal axis lists the predicted cell types. Mature OD: Mature oligodendrocyte; Immature OD: Immature oligodendrocyte.

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