QuTILs: Open-Source Image-Based Infiltrating Immune Cell Detection for Research Application.

Stromal tumor infiltrating lymphocytes (sTILs), quantified via hematoxylin and eosin (H&E) tumor slides, are associated with improved response to chemotherapy and better overall survival (OS) in triple-negative breast cancer (TNBC). Digitization of H&E slides offers the opportunity for image-based computational approaches to enumerate sTILs. We describe QuTILs, a research-based TIL enumeration approach using a multilayer perceptron-based framework trained on open-source H&E images using the QuPath software and executed on a standard computer. QuTILs was applied to H&E images from two phase III TNBC clinical trials, CALGB 40502 and 40603 (total n = 462 patients). In Cox proportional hazards models, QuTILs showed significant univariate association in CALGB 40502, with higher TIL% associated with reduced hazard (HR: 0.75, 95% CI: 0.63-0.91), which remained significant in multivariable models and validation CALGB 40603 TNBC clinical trial. In summary, QuTILs provides a computationally efficient, open-source workflow for sTIL identification from digital H&E images for research application.