Software Development for Clinical Use in Pathology

Peter Gershkovich, MD. MHA
Yale University School of Medicine | June 2025

Introduction

  • Why pathology residents should care about software: LIS limitations, workflow inefficiencies, unmet needs.
  • Custom software can improve diagnostics, communication, and safety.
  • Real-world impact: frozen section alerts, digital image management, urgent case triage.

Why Build Custom Software?

  • Tailored to your lab's needs and workflow — especially important for subspecialty services.
  • Enables integration with external systems (EHRs, image viewers, AI pipelines).
  • Supports innovation and regulatory adaptation (e.g., NGS reporting, frozen sections).
  • From Gershkovich & Sinard: Functionality gaps arise when needed tech exists but isn't in your LIS.

Challenges to Be Aware Of

  • Development effort requires domain understanding.
  • Validation and long-term support must be considered.
  • Institutional inertia: "we're not in the software business" is often a myth.
  • From Sinard & Gershkovich: Even one or two developers with domain knowledge can be effective.

Software Lifecycle & DevSecOps in Pathology

  • 1. Requirement Gathering – Start with specific use cases from the clinical workflow.
  • 2. Functional Specification – What should the system do? Create screen diagrams, button behaviors, exceptions.
  • 3. Technical Specification – Database, architecture, and performance planning.
  • 4. Implementation and Testing – Use version control, containers (Docker), staging environments.
  • 5. Security and Compliance – HIPAA, access logs, secure APIs.
  • 6. Deployment & Feedback Loop – Track usage and iterate.

DevSecOps Philosophy

  • Secure-by-design.
  • Rapid, adaptive iterations.
  • Infrastructure-as-code and automation.
  • Key point: LIS vendors often cannot move fast enough due to outdated architecture.

Image Analysis & AI

  • QPath – Use Groovy scripts to quantify cell populations, analyze TILs, or export tiles for deep learning.
  • ImageJ/Fiji – Open-source, powerful for smaller ROI and pixel-level analysis.
  • HistomicsTK – Feature extraction and visualization for whole slide images.

Digital Pathology Infrastructure

  • Digital Slide Archive (DSA) – WSI management with REST APIs.
  • OpenSeadragon – Lightweight JS-based WSI viewer you can embed in web tools.
  • Open Source Repositories – GitHub, SourceForge, MONAI.

Clinical Applications

  • Alerting systems for STAT/RUSH cases.
  • Specimen tracking and intraoperative diagnosis tools.
  • NGS variant interpretation modules.

Spotting Gaps in Workflow

  • What is frustrating in your daily workflow? What leads to delays, errors, or repetitive effort?
  • From lecture material: If your LIS doesn't notify you of STAT slides without a resident, that's a gap.

Solutions

  • 7 Options: Ignore, patch manually, switch LIS, request vendor fix, outsource, build yourself, or integrate OSS.
  • Residents can help design or prototype solutions with Jupyter Notebooks, low-code tools.
  • Learn to write or read functional specs to guide developers.

Conclusion and Call to Action

  • Pathology informatics is a core discipline – not optional.
  • Custom software development is powerful, cost-effective, and sustainable.
  • You can participate by reporting gaps, helping design use cases, or even coding solutions.
  • Every meaningful tool starts with someone who understood the problem deeply.

Q&A and Demo Time

  • Live demo of QPath on an H&E slide.
  • Jupyter notebook using DSA API to pull case info.
  • Discussion: What bugs you the most in your LIS today — and what would you build to fix it?

Workflow Augmentation Example

Enter text below and press Enter or click Submit. The server will process your input.

Note: Special characters $ and # will trigger an error.