Repository Index

Code for the Nature Scientific Reports paper "Pathologist-level classification of histologic patterns on resected lung adenocarcinoma slides with deep neural networks." A sliding window framework for classification of high resolution whole-slide images, often microscopy or histopathology images.

• histopathology-images
• microscopy
• sliding-windows
• medical-image-analysis

Pathology Language and Image Pre-Training (PLIP) is the first vision and language foundation model for Pathology AI (Nature Medicine). PLIP is a large-scale pre-trained model that can be used to extract visual and language features from pathology images and text description. The model is a fine-tuned version of the original CLIP model.

• artificial-intelligence
• clip
• pathology
• vision-and-language

Autonomous multi-agent framework to optimize scientific software

• acceleration
• agentic-ai
• ai-agents
• bioinformatics

MCP server for spatial transcriptomics analysis through natural language interfaces.

• bioinformatics
• cell-communication
• deconvolution
• machine-learning

Fast, deterministic cell-type deconvolution for million-bin spatial transcriptomics

• bioinformatics
• cell-type-deconvolution
• computational-biology
• deconvolution