Repository Index

Multi-platform, free open source software for visualization and image computing.

• medical-imaging
• vtk
• itk
• python

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

Vision-Language Pathology Foundation Model - Nature Medicine

• bioimage-analysis
• bioimage-informatics
• conch
• foundation-model

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

Automated 3D cell detection in very large images

• microscopy
• cell-detection
• deep-learning
• image-analysis

A Python interface to access neuroanatomical atlases

• neuroscience
• python
• microscopy
• registration

AI-based pathology predicts origins for cancers of unknown primary - Nature

• histology
• pathology
• wsi-images
• histopathology

Automated 3D brain registration with support for multiple species and atlases.

• registration
• atlases
• brain
• neuroscience