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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.
Tools for computational pathology
CellViT: Vision Transformers for Precise Cell Segmentation and Classification
Automated 3D cell detection in very large images
Deep and Machine Learning for Microscopy
PyTorch Connectomics: segmentation toolbox for EM connectomics
Axon/Myelin segmentation using Deep Learning
Nellie: Automated organelle segmentation, tracking, and hierarchical feature extraction in 2D/3D live-cell microscopy
A foundation model-driven whole slide image-scale cell phenotyping method with QuPath integration Resources
Accurate segmentation of bacterial microscope images using deep learning synthetically generated image data.
Panoptic segmentation algorithms for 2D and 3D electron microscopy images