ESQmodel: biologically informed evaluation of 2-D cell segmentation quality in multiplexed tissue images.

Eric Lee, Dongkyu Lee, Wayne Fan, Andrew Lytle, Yuxiang Fu, David W Scott, Christian Steidl, Samuel Aparicio, Andrew Roth, Bioinformatics (Oxford, England) 40, (2023)


Single cell segmentation is critical in the processing of spatial omics data to accurately perform cell type identification and analyze spatial expression patterns. Segmentation methods often rely on semi-supervised annotation or labeled training data which are highly dependent on user expertise. To ensure the quality of segmentation, current evaluation strategies quantify accuracy by assessing cellular masks or through iterative inspection by pathologists. While these strategies each address either the statistical or biological aspects of segmentation, there lacks a unified approach to evaluating segmentation accuracy.