Repository Index

Simultaneous Nuclear Instance Segmentation and Classification in H&E Histology Images.

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

A tool for semi-automatic cell type classification

• python
• single-cell
• machine-learning
• scrna-seq

MOGONET (Multi-Omics Graph cOnvolutional NETworks) is a novel multi-omics data integrative analysis framework for classification tasks in biomedical applications.

code to run sei and obtain sei and sequence class predictions

Toolbox for the analysis of smFISH images.

• pattern-classification
• rna-localization
• segmentation
• smfish

A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources

• bioimage-analysis
• cell-classification
• computer-vision
• digital-pathology