QuPath: Open Source Bioimage Analysis and Quantitative Pathology
Peter Bankhead (University of Edinburgh)
To accelerate biomedical research, biomarker discovery, and the translation of artificial intelligence into clinical practice by enhancing the QuPath open source platform and by integrating it with other CZI-funded software.
QuPath is an open source software for bioimage analysis. It provides a freely-available, cross-platform, user-friendly, extensible platform that enables biologists, pathologists, image analysts and machine learning experts to work together to maximize the insights we can extract from biological and medical images, including large and complex whole slide images not supported by other open software. Written from scratch with Java and JavaFX, QuPath is fully scriptable and integrates with other popular open tools, including ImageJ and OpenCV. By combining built-in novel algorithms for common tasks (e.g. cell segmentation) with interactive machine learning and powerful visualization tools, QuPath offers a unique and intuitive platform to rapidly develop and deploy customized and sophisticated image analysis workflows for a wide range of tasks.