Repository Index

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• segmentation

This repository includes the official project of TransUNet, presented in our paper: TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation.

Tool for robust segmentation of >100 important anatomical structures in CT and MR images

Unsupervised Learning for Image Registration

• image-registration
• image-alignment
• machine-learning
• deep-learning

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

• medical-imaging
• vtk
• itk
• python

Semi Supervised Learning for Medical Image Segmentation, a collection of literature reviews and code implementations.

• semi-supervised-learning

[IEEE TMI Best Paper Award] Official Implementation for UNet++

• medical-imaging
• segmentation
• unet
• biomedical-imaging

Medical imaging processing for AI applications.

• pytorch
• medical-image-computing
• deep-learning
• data-augmentation

Pytorch 3D U-Net Convolution Neural Network (CNN) designed for medical image segmentation

Use of Attention Gates in a Convolutional Neural Network / Medical Image Classification and Segmentation

• convolutional-neural-networks
• attention-model
• image-classification
• image-segmentation

A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation

• segmentation
• deep-learning
• pytorch
• medical-imaging

TorchXRayVision: A library of chest X-ray datasets and models. Classifiers, segmentation, and autoencoders.

• medical-imaging
• medical-ai
• deep-learning
• machine-learning

3D medical imaging reconstruction software

• dicom
• dicom-viewer
• magnetic-resonance-imaging
• medical-image-processing

Pathology Foundation Model - Nature Medicine

• foundation
• foundation-model
• histopathology
• mahmoodlab

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

Clinical Histopathology Imaging Evaluation Foundation Model

Prov-GigaPath: A whole-slide foundation model for digital pathology from real-world data

Vision-Language Pathology Foundation Model - Nature Medicine

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

U-Net Brain Tumor Segmentation

• tensorflow
• tensorlayer
• unet
• medical-imaging

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

Tools for computational pathology

• machine-learning
• digital-pathology
• computational-pathology
• biomedical-image-processing

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

Neural networks toolbox focused on medical image analysis

• python
• keras
• convolutional-neural-networks
• brain

Library for multiscale visualization of high-resolution multiplexed bioimaging data on the web. Directly renders Zarr and OME-TIFF.

• hubmap
• imaging
• openmicroscopy
• ome-tiff