An open-source platform for structured annotation and computational workflows in digital pathology research

The rapid evolution of digital pathology has enabled large-scale data acquisition, driving sophisticated clinical research and advancing the development of AI-driven tools. These innovations have also revolutionised histopathological slide review, especially the annotation step (i.e. the process of marking specific areas of interest on glass-mounted tissue samples to add relevant clinical information) by digitising the process, enhancing precision and efficiency, and facilitating collaboration. However, currently available open-source annotation tools typically employ single-label approaches that provide a flat representation of whole-slide images (WSI), limiting their ability to capture the complexity of the diagnosis-significant elements in a detailed and structured way. Furthermore, the difficulty of strictly following precise review protocols and lack of provenance tracking during annotation processes can result in high variability and limit reproducibility and reusability of the collected data. In this work we present the CRS4 Digital Pathology Platform (CDPP), an open-source system for research studies that manages WSI collections and focuses on high-quality, structured annotations, gathered according to well-defined protocols. Its main features include: (1) structured, multi-label morphological and clinical image annotation; (2) support for controlled but customisable annotation protocols; (3) dedicated annotation tools to facilitate enhanced accuracy, efficiency and consistency in the annotation process; and (4) workflow-based computational analysis with integrated provenance tracking. We show how the platform has successfully supported three different studies, demonstrating the CDPP’s ability to assist pathologists in the generation of high-quality annotated datasets, also suitable for reuse, in the context of digital pathology research.