Closing the gap in the clinical adoption of computational pathology: a standardized, open-source framework to integrate deep-learning models into the laboratory information system.

Abstract

Background: Digital pathology (DP) has revolutionized cancer diagnostics and enabled the development of deep-learning (DL) models aimed at supporting pathologists in their daily work and improving patient care. However, the clinical adoption of such models remains challenging. Here, we describe a proof-of-concept framework that, leveraging Health Level 7 (HL7) standard and open-source DP resources, allows a seamless integration of both publicly available and custom developed DL models in the clinical workflow.

Methods: Development and testing of the framework were carried out in a fully digitized Italian pathology department. A Python-based server-client architecture was implemented to interconnect through HL7 messaging the anatomic pathology laboratory information system (AP-LIS) with an external artificial intelligence-based decision support system (AI-DSS) containing 16 pre-trained DL models. Open-source toolboxes for DL model deployment were used to run DL model inference, and QuPath was used to provide an intuitive visualization of model predictions as colored heatmaps.

Results: A default deployment mode runs continuously in the background as each new slide is digitized, choosing the correct DL model(s) on the basis of the tissue type and staining. In addition, pathologists can initiate the analysis on-demand by selecting a specific DL model from the virtual slide tray. In both cases, the AP-LIS transmits an HL7 message to the AI-DSS, which processes the message, runs DL model inference, and creates the appropriate visualization style for the employed classification model. The AI-DSS transmits model inference results to the AP-LIS, where pathologists can visualize the output in QuPath and/or directly as slide description in the virtual slide tray.

Conclusions: Taken together, the developed integration framework through the use of the HL7 standard and freely available DP resources offers a standardized, portable, and open-source solution that lays the groundwork for the future widespread adoption of DL models in pathology diagnostics.