# Pathology Viewer

> A web app for interacting with digital pathology slides

- HTML version: https://robbiepalmer.me/projects/pathology-viewer
- Status: completed
- Started: 2021-11-01
- Product: https://sonraianalytics.com/biomarker-platform-features/imaging-ai/
- Technologies: Python, Leaflet, Plotly, OpenSlide, Shapely, GeoPandas

# Vision

The goal of this project was to evolve Sonrai's bioinformatics platform from a tabular-data-focused tool into a truly multi-modal and [multi-omic](/blog/2022-02-28-enabling-multi-omic-data-management) system. The platform needed to move beyond simple datasets to handle the complexity of biological imagery.

# Problem Statement

"Whole Slide Images" (WSI) in digital pathology represent a massive engineering challenge:

* **Geospatial Complexity**: Similar to maps, these are multi-resolution, pyramidal images that are gigabytes in size.
* **Fragmentation**: Unlike radiology (which has the DICOM standard), digital pathology is fragmented. Every scanner manufacturer (Leica, Aperio, Philips, etc.) uses their own proprietary format.
* **Data integration**: We needed to treat these images not just as pictures, but as data sources for geospatial aggregations and feature extraction.

# User Stories

* **As a pathologist**, I want to view and interact with slides from any scanner vendor without worrying about file formats.
* **As a researcher**, I need to draw precise regions of interest (polygons, points) and overlay analysis results directly onto the tissue image.
* **As a platform user**, I want an app that seamlessly exchanges data in pipelines with other bioinformatics tools in the ecosystem.

# Platform Capabilities

* **Multi-Format Support**: proprietary format ingestion for major vendors (Leica, Aperio, Philips).
* **Responsive High-Resolution Viewer**: Efficient handling of multi-gigabyte files using tiling and pyramidal resolution strategies.
* **Interactive Annotations**: Support for drawing and editing regions of interest (polygons, points) overlaid on the slide.
* **Geospatial Analysis**: Performing aggregations and feature extraction on image data, treating biological structures with the same logic as geospatial features.
* **Pipeline Integration**: Full compatibility with Sonrai's no-code GUI ecosystem for multi-omic workflows.

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