162 Repositories
Python medical-diagnostics Libraries
MultiMix: Sparingly Supervised, Extreme Multitask Learning From Medical Images (ISBI 2021, MELBA 2021)
MultiMix This repository contains the implementation of MultiMix. Our publications for this project are listed below: "MultiMix: Sparingly Supervised,
Scripts used in the RayStation medical radiation dosimetry treatment planning system
Med Phys Scripts These are scripts that I, the medical physics assistant at Cookeville Regional Medical Center, wrote for use in our radiation therapy
The Research PACS on AWS solution facilitates researchers' access medical images stored in the clinical PACS in a secure and seamless manner
Research PACS on AWS Challenge to solve Solution presentation Deploy the solution Further reading Releases License Challenge to solve The rise of new
some classic model used to segment the medical images like CT、X-ray and so on
github_project This is a project for medical image segmentation. This project includes common medical image segmentation models such as U-net, FCN, De
An BlockChain Based solution for storing the medical records
Blockchain-based Medical Records 📄 Abstract Blockchain has the ability to keep an incorruptible, decentralized, and transparent log of all patient da
Official and maintained implementation of the paper "OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data" [BMVC 2021].
OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data Christoph Reich, Tim Prangemeier, Özdemir Cetin & Heinz Koeppl | Pr
Official and maintained implementation of the paper "OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data" [BMVC 2021].
OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data Christoph Reich, Tim Prangemeier, Özdemir Cetin & Heinz Koeppl | Pr
This is the 3D Implementation of 《Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation》
CoraNet This is the 3D Implementation of 《Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation》 Environment pytor
The PyTorch re-implement of a 3D CNN Tracker to extract coronary artery centerlines with state-of-the-art (SOTA) performance. (paper: 'Coronary artery centerline extraction in cardiac CT angiography using a CNN-based orientation classifier')
The PyTorch re-implement of a 3D CNN Tracker to extract coronary artery centerlines with state-of-the-art (SOTA) performance. (paper: 'Coronary artery centerline extraction in cardiac CT angiography using a CNN-based orientation classifier')
Copy Paste positive polyp using poisson image blending for medical image segmentation
Copy Paste positive polyp using poisson image blending for medical image segmentation According poisson image blending I've completely used it for bio
Public repo for the ICCV2021-CVAMD paper "Is it Time to Replace CNNs with Transformers for Medical Images?"
Is it Time to Replace CNNs with Transformers for Medical Images? Accepted at ICCV-2021: Workshop on Computer Vision for Automated Medical Diagnosis (C
Medical image analysis framework merging ANTsPy and deep learning
ANTsPyNet A collection of deep learning architectures and applications ported to the python language and tools for basic medical image processing. Bas
MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.
MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.
A collection of papers about Transformer in the field of medical image analysis.
A collection of papers about Transformer in the field of medical image analysis.
Breaking the Dilemma of Medical Image-to-image Translation
Breaking the Dilemma of Medical Image-to-image Translation Supervised Pix2Pix and unsupervised Cycle-consistency are two modes that dominate the field
Breaking the Dilemma of Medical Image-to-image Translation
Breaking the Dilemma of Medical Image-to-image Translation Supervised Pix2Pix and unsupervised Cycle-consistency are two modes that dominate the field
Useful materials and tutorials for 110-1 NTU DBME5028 (Application of Deep Learning in Medical Imaging)
Useful materials and tutorials for 110-1 NTU DBME5028 (Application of Deep Learning in Medical Imaging)
This is the remake of the program PYOBD. It works on Python3 and all new libraries. It was tested on Linux, Windows, and it should work on MAC too.
This is the remake of the program PYOBD. It works on Python3 and all new libraries. It was tested on Linux, Windows, and it should work on MAC too. You just need an ELM327 USB or bluetooth device and a PC(laptop preferably).
A pytorch-based deep learning framework for multi-modal 2D/3D medical image segmentation
A 3D multi-modal medical image segmentation library in PyTorch We strongly believe in open and reproducible deep learning research. Our goal is to imp
[IROS'21] SurRoL: An Open-source Reinforcement Learning Centered and dVRK Compatible Platform for Surgical Robot Learning
SurRoL IROS 2021 SurRoL: An Open-source Reinforcement Learning Centered and dVRK Compatible Platform for Surgical Robot Learning Features dVRK compati
PyTorch Implementation of Small Lesion Segmentation in Brain MRIs with Subpixel Embedding (ORAL, MICCAIW 2021)
Small Lesion Segmentation in Brain MRIs with Subpixel Embedding PyTorch implementation of Small Lesion Segmentation in Brain MRIs with Subpixel Embedd
Semi Supervised Learning for Medical Image Segmentation, a collection of literature reviews and code implementations.
Semi-supervised-learning-for-medical-image-segmentation. Recently, semi-supervised image segmentation has become a hot topic in medical image computin
An implementation of the research paper "Retina Blood Vessel Segmentation Using A U-Net Based Convolutional Neural Network"
Retina Blood Vessels Segmentation This is an implementation of the research paper "Retina Blood Vessel Segmentation Using A U-Net Based Convolutional
A PyTorch implementation for V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation
A PyTorch implementation of V-Net Vnet is a PyTorch implementation of the paper V-Net: Fully Convolutional Neural Networks for Volumetric Medical Imag
Segmentation for medical image.
EfficientSegmentation Introduction EfficientSegmentation is an open source, PyTorch-based segmentation framework for 3D medical image. Features A whol
[MedIA2021]MIDeepSeg: Minimally Interactive Segmentation of Unseen Objects from Medical Images Using Deep Learning
MIDeepSeg: Minimally Interactive Segmentation of Unseen Objects from Medical Images Using Deep Learning [MedIA or Arxiv] and [Demo] This repository pr
gcp-doctor - Diagnostics for Google Cloud Platform
gcp-doctor is a command-line diagnostics tool for GCP customers. It finds and helps to fix common issues in Google Cloud Platform projects. It is used to test projects against a wide range of best-practices and frequent mistakes, based on the troubleshooting experience of the Google Cloud Support team.
This is an example of object detection on Micro bacterium tuberculosis using Mask-RCNN
Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN
This is an example of object detection on Micro bacterium tuberculosis using Mask-RCNN
Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN
A scalable implementation of WobblyStitcher for 3D microscopy images
WobblyStitcher Introduction A scalable implementation of WobblyStitcher Dependencies $ python -m pip install numpy scikit-image Visualization ImageJ
TorchIO is a Medical image preprocessing and augmentation toolkit for deep learning. Part of the PyTorch Ecosystem.
Medical image preprocessing and augmentation toolkit for deep learning. Part of the PyTorch Ecosystem.
Jittor Medical Segmentation Lib -- The assignment of Pattern Recognition course (2021 Spring) in Tsinghua University
THU模式识别2021春 -- Jittor 医学图像分割 模型列表 本仓库收录了课程作业中同学们采用jittor框架实现的如下模型: UNet SegNet DeepLab V2 DANet EANet HarDNet及其改动HarDNet_alter PSPNet OCNet OCRNet DL
Context Axial Reverse Attention Network for Small Medical Objects Segmentation
CaraNet: Context Axial Reverse Attention Network for Small Medical Objects Segmentation This repository contains the implementation of a novel attenti
Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening
Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening Introduction This is an implementation of the model used for breast
The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.
Official PyTorch implementation of UACANet: Uncertainty Aware Context Attention for Polyp Segmentation
UACANet: Uncertainty Aware Context Attention for Polyp Segmentation Official pytorch implementation of UACANet: Uncertainty Aware Context Attention fo
MONAI Label is a server-client system that facilitates interactive medical image annotation by using AI.
MONAI Label is a server-client system that facilitates interactive medical image annotation by using AI. It is an open-source and easy-to-install ecosystem that can run locally on a machine with one or two GPUs. Both server and client work on the same/different machine. However, initial support for multiple users is restricted. It shares the same principles with MONAI.
PyMedPhys is an open-source Medical Physics python library
PyMedPhys is an open-source Medical Physics python library built by an open community that values and prioritises code sharing, review, improvement, and learning from each other. I
The codes for the work "Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation"
Swin-Unet The codes for the work "Swin-Unet: Unet-like Pure Transformer for Medical Image Segmentation"(https://arxiv.org/abs/2105.05537). A validatio
nnDetection is a self-configuring framework for 3D (volumetric) medical object detection which can be applied to new data sets without manual intervention. It includes guides for 12 data sets that were used to develop and evaluate the performance of the proposed method.
What is nnDetection? Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of hi
UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus
UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus General info This is
Clairvoyance: a Unified, End-to-End AutoML Pipeline for Medical Time Series
Clairvoyance: A Pipeline Toolkit for Medical Time Series Authors: van der Schaar Lab This repository contains implementations of Clairvoyance: A Pipel
Medical Image Segmentation using Squeeze-and-Expansion Transformers
Medical Image Segmentation using Squeeze-and-Expansion Transformers Introduction This repository contains the code of the IJCAI'2021 paper 'Medical Im
PRAnCER is a web platform that enables the rapid annotation of medical terms within clinical notes.
PRAnCER (Platform enabling Rapid Annotation for Clinical Entity Recognition) is a web platform that enables the rapid annotation of medical terms within clinical notes. A user can highlight spans of text and quickly map them to concepts in large vocabularies within a single, intuitive platform.
Vision Transformer for 3D medical image registration (Pytorch).
ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio
Awesome anomaly detection in medical images
A curated list of awesome anomaly detection works in medical imaging, inspired by the other awesome-* initiatives.
Code for "Graph-Evolving Meta-Learning for Low-Resource Medical Dialogue Generation". [AAAI 2021]
Graph Evolving Meta-Learning for Low-resource Medical Dialogue Generation Code to be further cleaned... This repo contains the code of the following p
PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos
PyKale is a PyTorch library for multimodal learning and transfer learning as well as deep learning and dimensionality reduction on graphs, images, texts, and videos. By adopting a unified pipeline-based API design, PyKale enforces standardization and minimalism, via reusing existing resources, reducing repetitions and redundancy, and recycling learning models across areas.
ivadomed is an integrated framework for medical image analysis with deep learning.
Repository on the collaborative IVADO medical imaging project between the Mila and NeuroPoly labs.
Weakly supervised medical named entity classification
Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers
A medical imaging framework for Pytorch
Welcome to MedicalTorch MedicalTorch is an open-source framework for PyTorch, implementing an extensive set of loaders, pre-processors and datasets fo
Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT
CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT CheXbert is an accurate, automated dee
A collection of loss functions for medical image segmentation
A collection of loss functions for medical image segmentation
Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images
SASSnet Code for paper: Shape-aware Semi-supervised 3D Semantic Segmentation for Medical Images(MICCAI 2020) Our code is origin from UA-MT You can fin
The code release of paper 'Domain Generalization for Medical Imaging Classification with Linear-Dependency Regularization' NIPS 2020.
Domain Generalization for Medical Imaging Classification with Linear Dependency Regularization The code release of paper 'Domain Generalization for Me
[CVPR'21] FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space
FedDG: Federated Domain Generalization on Medical Image Segmentation via Episodic Learning in Continuous Frequency Space by Quande Liu, Cheng Chen, Ji
CoTr: Efficiently Bridging CNN and Transformer for 3D Medical Image Segmentation
CoTr: Efficient 3D Medical Image Segmentation by bridging CNN and Transformer This is the official pytorch implementation of the CoTr: Paper: CoTr: Ef
3D medical imaging reconstruction software
InVesalius InVesalius generates 3D medical imaging reconstructions based on a sequence of 2D DICOM files acquired with CT or MRI equipments. InVesaliu
Pytorch Code for "Medical Transformer: Gated Axial-Attention for Medical Image Segmentation"
Medical-Transformer Pytorch Code for the paper "Medical Transformer: Gated Axial-Attention for Medical Image Segmentation" About this repo: This repo
This repo holds code for TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation
TransUNet This repo holds code for TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation Usage
This repository is an unoffical PyTorch implementation of Medical segmentation in 3D and 2D.
Pytorch Medical Segmentation Read Chinese Introduction:Here! Recent Updates 2021.1.8 The train and test codes are released. 2021.2.6 A bug in dice was
Official PyTorch implementation for paper Context Matters: Graph-based Self-supervised Representation Learning for Medical Images
Context Matters: Graph-based Self-supervised Representation Learning for Medical Images Official PyTorch implementation for paper Context Matters: Gra