oncologylab/histopia

What it solves

Histopia is a toolkit for analyzing histology images, specifically focusing on the spatial organization of tissues. It addresses the problem of aligning multiple serial sections of tissue, quantifying stains, and reconstructing the 3D spatial topology of tissues from 2D images.

How it works

The project provides a set of modular workflows for different analysis tasks. It uses registration tools for tissue masking and serial-section alignment, specialized tools for chromogenic stain quantification and cell segmentation, and protein-expression models for protein prediction. It also generates histology embeddings to create semantic atlases of tissue regions.

Who it’s for

Researchers in pathology and oncology who need to process histology slides and perform spatial omics profiling and inter-section alignment.

Highlights

• Serial-Section Alignment: Tools for aligning multiple tissue sections to create a coherent spatial view.
• Protein Prediction: Models for predicting protein expression from histology images.
• Protein Visualization: Ability to create per-cell protein atlases.
• Semantic Atlas: Generation of histology embeddings to identify tissue regions.
• Cell Segmentation: Tools for defining cell boundaries and merging segmentation results.