Fig. 3

MATISSE improves identification of specific cell subsets in colorectal tissue. a Forty-five regions of interest (ROIs) in 10 different tissue sections were imaged and segmented using IMC or MATISSE pipelines, and 10% of all identified single cells were included in a t-SNE. Twenty-six phenoclusters [16] were identified and displayed with a color-code. N = 29242 cells for IMC, 38430 cells for MATISSE. b Numbers of cells contained per cluster were calculated and displayed for both IMC and MATISSE methods. N = 45 images. N = 291919 cells for IMC, 384804 cells for MATISSE. c Heatmap display of the mean signal intensity per cell in each cluster. The ratio of number of cells identified by both segmentation methods (IMC / MATISSE) per cluster is displayed on the right. N = 45 images. d, e Spatial location of single cells in the tissue was visualized and color-coded by phenocluster. Displayed are overview images of an entire ROI (left) and a zoom of a specific region (right), shown are all phenoclusters (d), top 6 differential phenoclusters with higher cell numbers in MATISSE (e). Scale bar 25 μm