Fig. 3: FISHnCHIPs profiling of 18 gene modules in the mouse cortex.

a Gene-gene correlation heatmap (of the pairwise Pearson’s correlation (r) coefficients) grouped into 18 clusters of gene modules (colored boxes, M1-M18). Each module (14 genes on average) was imaged sequentially under an automated fluidics-coupled fluorescence microscope system. Example FISHnCHIPs images of a mouse brain tissue slice stained for gene module 1, 2, 3, and 18. Scale bar, 50 μm. b Single cells were segmented using DAPI stain and the cell masks were applied to define 6180 cells after quality control. Heatmap of the mean fluorescence intensity per cell for each imaged module. The cell-by-module intensity matrix was clustered using the Louvain algorithm, resulting in eight cell clusters. c–j Spatial maps of the detected cells, colored by their cell types: Glutamatergic neurons (gray), GABAergic neurons (purple), astrocytes (blue), oligodendrocytes (red), endothelial cells (cyan), microglial cells (orange), peri-vascular cells (green), and vascular leptomeningeal cells (yellow). Scale bar, 500 μm. k Scatter plot of cell type frequency detected by MERFISH versus FISHnCHIPs fitted with a linear regression model: \(y=-0.025+x,{R}^{2}=0.96\), where \(x,y\) is the cell type frequency in FISHnCHIPs and in MERFISH, respectively. The gray band surrounding the regression line represents the 95% confidence interval for the linear regression model. Insert is a pie chart showing the proportion of each FISHnCHIPs cluster. Source data are provided as a Source Data file.