AbstractIntegration and mining of bioimaging data remains a challenge and lags behind the rapidly expanding digital pathology field. We introduce Hourglass, an open‐access analytical framework that streamlines biology‐driven visualization, interrogation, and statistical assessment of multiparametric datasets. Cognizant of tissue and clinical heterogeneity, Hourglass systematically organizes observations across spatial and global levels and within patient subgroups. Applied to an extensive bioimaging dataset, Hourglass promptly consolidated a breadth of known interleukin‐6 (IL‐6) functions via its downstream effector STAT3 and uncovered a so‐far unknown sexual dimorphism in the IL‐6/STAT3‐linked intratumoral T‐cell response in human pancreatic cancer. As an R package and cross‐platform application, Hourglass facilitates knowledge extraction from multi‐layered bioimaging datasets for users with or without computational proficiency and provides unique and widely accessible analytical means to harness insights hidden within heterogeneous tissues at the sample and patient level. © 2023 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of The Pathological Society of Great Britain and Ireland.