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Fig. 1 | BMC Biology

Fig. 1

From: Automated identification of the mouse brain’s spatial compartments from in situ sequencing data

Fig. 1

Graph-based ISS signal decoding and spatial mapping. a Cut-out composite images from four sequencing cycles (1–4) with four fluorescent channels (magenta, cyan, orange, and green representing the letters A, C, T, and G) are shown in the left panel. Each detected signal is marked with a white cross, labeled D1-D14, and represented as a node in the graphical model (with the same color and label). The graphical representation of the fluorescent signals results in two independent connected components, represented by two graphs A and B. Edges between nodes represent distance between signals, where bold lines represent direct connections (distance < dth), and dash-dotted lines represent forced connections (distance < dmax). Solving the graph gives three black paths: {D1,D5,D8,D12}, {D3,D6,D10,D13}, {D4,D7,D11,D14}, corresponding to three decoded sequences: TAGT, GCAC and GCAG. b Overview of a full coronal section of a mouse brain with zoomed-in regions showing detected barcodes and corresponding genes. Scale bar, 1000 μm. Analyzed samples are available for interactive viewing at [17], and video tutorial on how to visualize spatial gene expression data is available at [18]

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