Automated Tissue Microarray Analysis

Separate projects were created within QuPath for each biomarker, and the slide images imported to the corresponding projects. QuPath’s automated TMA dearrayer was applied in batch over all slides within each project to identify tissue cores. The resulting TMA grid was manually verified and amended where necessary, e.g. to adjust the locations of cores that were outside their expected position, or to remove cores where prominent artefacts were visible. Patient identifiers were then imported into QuPath for each core to assist alignment with survival data later. Additionally, stain vector (i.e. color) and background estimates were applied for each IHC analysis project to improve stain separation within QuPath using color deconvolution^{17 (link)}. This was achieved by selecting a representative area containing an area of background along with examples of strong hematoxylin and DAB staining, and applying QuPath’s Estimate stain vectors command to identify stain vectors within this region. The resulting vectors were then used for all images in the project.