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 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.