Fig. 3

Prediction of expression levels of unmeasured genes for MERFISH. a Predicted expression patterns (top) and corresponding ISH images (bottom) of seven spatially unmeasured genes. b Known patterns in MERFISH. The first row displays the expression levels averaged by measured genes, while the second row shows the expression levels averaged by unmeasured genes. The number of genes within each pattern is indicated. Representative unmeasured genes for each pattern and their corresponding ISH images are presented in the third row. Each pattern co-localizes with distinct cell types (bottom). c Multimodality structure of likelihood scores. Unmeasured genes are categorized into three groups by two dashed lines. The x-axis point marked as s (blue point) represents the likelihood score at the low peak between two high peaks. The two dashed lines are located at s ± 0.05. d Discovery of three novel expression patterns in MERFISH. The first row illustrates the expression levels of three novel patterns, along with the number of genes composing each pattern. The second row showcases representative genes and their corresponding ISH images. These novel patterns exhibit co-localization with various non-neuronal cell types (bottom). e Functional enrichment analysis. The top six biological process-related functional enrichment results are displayed for the three novel patterns