Leveraging Open-Source Solutions to Build a Low-Cost Digital Pathology Pipeline for Translational Research.

Area of Science:

• Pathology
• Medical Informatics
• Biotechnology

Background:

• Digital Pathology (DP) offers significant potential but faces cost and implementation barriers for smaller labs.
• Existing DP solutions often require substantial investment in instrumentation and infrastructure.
• Translational research demands efficient and accessible methods for pathology data analysis.

Purpose of the Study:

• To develop an affordable, end-to-end digital pathology pipeline for translational research.
• To assess the feasibility of using low-cost, open-source components for a functional DP system.
• To evaluate the user experience and image quality for remote, asynchronous pathology slide review.

Main Methods:

• Assembled a DP pipeline using repurposed microscopy components and a low-cost Canon CMOS camera.
• Utilized OMERO v.5.6.4 open-source image management system on Ubuntu 22.04 for Whole Slide Image (WSI) hosting.
• Conducted remote, asynchronous WSI evaluation by pathologists across different locations using a 23-question survey.

Main Results:

• The custom, low-cost WSI pipeline was rated as robust and user-friendly by pathologists.
• The system demonstrated feasibility for small-scale, asynchronous translational pathology research.
• The setup is not suitable for large-scale commercial clinical applications but offers educational value.

Conclusions:

• A low-cost, end-to-end digital pathology pipeline can be successfully established for asynchronous translational research in academic settings.
• Repurposing existing equipment and utilizing open-source software significantly reduces implementation costs.
• This approach provides valuable training for pathology residents in DP workflows.