Fig. 2: BIAS for integrative image analysis and automated LMD single-cell isolation.
From: Deep Visual Proteomics defines single-cell identity and heterogeneity
a, AI-driven nucleus and cytoplasm segmentation of normal-appearing and cancer cells and tissue using BIAS. b, We benchmarked the accuracy of its segmentation approach using the F1 metric and compared results to three additional methods—M1 is unet4nuclei6, M2 is CellProfiler8 and M3 is Cellpose7—while OUR refers to nucleAIzer3. Bars show mean F1 scores with s.e.m.; n = 10 independent images for melanoma tissue and (U2OS) cells, and n = 20 for salivary gland tissue. Visual representation of the segmentation results: green areas correspond to true positive, blue to false positive and red to false negative. c, BIAS serves as the interface between the scanning and an LMD microscope, allowing high-accuracy transfers of cell contours between the microscopes. Illustration of cutting offset with respect to the object of interest and optimal path finding. d, Practical illustration of the functions in the upper panel. e, Immunofluorescence staining of the human fallopian tube epithelium with FOXJ1 and EpCAM antibodies, detecting ciliated and epithelial cells, respectively. Left panel: Ciliated (FOXJ1-positive) and secretory (FOXJ1-negative) cells. Right panel: Cell classification based on FOXJ1 intensity. Class 1 (FOXJ1-positive) and class 2 (FOXJ1-negative); magnification factor = ×387. f, PCA of FOXJ1-positive and FOXJ1-negative cell proteomes. g, Heat map of known protein markers for secretory and ciliated cells. Protein levels are z-scored. Asterisks represent imputed data. The marker list was derived from the Human Protein Atlas20 project and based on literature mining. h, Volcano plot of the pairwise proteomic comparison between FOXJ1-positive and FOXJ1-negative cells. Cell-type-specific marker proteins are highlighted in green and turquoise, and black represents potential novel marker proteins. Significant enriched cell-type-specific proteins are displayed above the black lines (two-sided t-test, FDR < 0.05, s0 = 0.1, n = 4 biological replicates).
