oncologylab/histopia

What it solves

Histopia addresses the complexity of analyzing serial-section histology and proteomic images. It provides tools to align multiple tissue sections, segment morphology across those sections, and reconstruct the tissue in 3D to understand spatial topology and omics profiling.

How it works

The software implements several specialized workflows:

• Registration: Aligns tissue sections using group-aware masks and hybrid affine alignment to ensure correct orientation and order.
• Semantic Atlas: Uses UNI2-h morphology regions to create a global map of tissue structures, including automatic evaluation of K-values and cross-section topology.
• Semantic Topology: Creates 3D reconstructions of tissue envelopes and semantic surfaces based on registered masks and physical z-spacing.
• Stain Profiling: Calculates relative optical density for various stains (like H-DAB and Sirius Red) with background correction.
• Visualization: Provides interactive 3D views of histology and stain stacks with quantitative quality control and ROI probes.
• QuPath Integration: Offers an extension to launch registration and semantic jobs directly from QuPath, using GeoJSON regions and native WSI coordinates.

Who it’s for

It is designed for computational researchers working with serial-section histology, proteomic image analysis, and 3D tissue reconstruction.

Highlights

• Interactive 3D Reconstruction: Visualizes histology, semantic, and stain stacks in 3D.
• Hardware Acceleration: Supports CPU, CUDA, and MPS for feature extraction.
• Review-Gated Workflow: Includes explicit review gates and integrity audits to ensure results are approved before publishing.
• QuPath Extension: Seamlessly integrates with the QuPath image analysis software.