Python Medical-physics Resources

Deep Latent Force Models This repository contains a PyTorch implementation of the deep latent force model (DLFM), presented in the paper, Compositiona

VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen

Mask_Detection_System A system used to detect whether a person is wearing a medical mask or not. To open the program, please follow these steps: Make

A simple script written using symbolic python that takes as input a desired metric and automatically calculates and outputs the Christoffel Pseudo-Tensor, Riemann Curvature Tensor, Ricci Tensor, Scalar Curvature and the Kretschmann Scalar

VGPL-Visual-Prior PyTorch implementation for the visual prior component (i.e. perception module) of the Visually Grounded Physics Learner (VGPL). Give

R interface to fastai The fastai package provides R wrappers to fastai. The fastai library simplifies training fast and accurate neural nets using mod

FAIMED 3D use fastai to quickly train fully three-dimensional models on radiological data Classification from faimed3d.all import * Load data in vari

fmi Adding additional functionality to fastai's medical imaging module To learn more about medical imaging using Fastai you can view my blog Install g

pyradiomics v3.0.1 Build Status Linux macOS Windows Radiomics feature extraction in Python This is an open-source python package for the extraction of

FInite volume Neural Network (FINN) This repository contains the PyTorch code for models, training, and testing, and Python code for data generation t

DiLBERT Repo for the paper "DiLBERT: Cheap Embeddings for Disease Related Medical NLP" Pretrained Model The pretrained model presented in the paper is

TransMorph: Transformer for Medical Image Registration keywords: Vision Transformer, Swin Transformer, convolutional neural networks, image registrati

pybullet-planning (previously ss-pybullet) A repository of PyBullet utility functions for robotic motion planning, manipulation planning, and task and

GGB Color Space This package is implementation of GGB color space from Development of a Robust Algorithm for Detection of Nuclei and Classification of

CFPNet-M: A Light-Weight Encoder-Decoder Based Network for Multimodal Biomedical Image Real-Time Segmentation This repository contains the implementat

Medical Open Network for AI MONAI is a PyTorch-based, open-source framework for deep learning in healthcare imaging, part of PyTorch Ecosystem. Its am

Front-end View Backend View Table of Contents Description Prerequisites Running Basic Information Measurements User Interface Feedback and usage Descr

AI-powered literature discovery and review engine for medical/scientific papers paperai is an AI-powered literature discovery and review engine for me

Effect of Deep Transfer and Multi task Learning on Sperm Abnormality Detection Introduction This repository includes codes and models of "Effect of De

Ohm-s-Law-Visualizer It's an application to calculate I from v and r using Ohm's Law. It can also plot a graph between V vs I. Story I'm doing my Unde

UTNet (Accepted at MICCAI 2021) Official implementation of UTNet: A Hybrid Transformer Architecture for Medical Image Segmentation Introduction Transf

CaloGAN Simulating 3D High Energy Particle Showers in Multi-Layer Electromagnetic Calorimeters with Generative Adversarial Networks. This repository c

Location-Aware Generative Adversarial Networks (LAGAN) for Physics Synthesis This repository contains all the code used in L. de Oliveira (@lukedeo),

UNet++: A Nested U-Net Architecture for Medical Image Segmentation UNet++ is a new general purpose image segmentation architecture for more accurate i

Medical Image Segmentation with Guided Attention This repository contains the code of our paper: "'Multi-scale self-guided attention for medical image

Implementation for paper LadderNet: Multi-path networks based on U-Net for medical image segmentation This implementation is based on orobix implement

Attention Gated Networks (Image Classification & Segmentation) Pytorch implementation of attention gates used in U-Net and VGG-16 models. The framewor

Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras This tutorial shows how to use Keras library to build deep ne

3D-printable hexagonal mirror array capable of reflecting sunlight into arbitrary patterns

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

PINO Physics-informed Neural Operator for Learning Partial Differential Equation Abstract: Machine learning methods have recently shown promise in sol

JaMIE: a Japanese Medical Information Extraction toolkit Joint Japanese Medical Problem, Modality and Relation Recognition The Train/Test phrases requ

Recurrent Mask Refinement for Few-Shot Medical Image Segmentation Steps Install any missing packages using pip or conda Preprocess each dataset using

meddlr Getting Started Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems. Installation To av

DiffuseAnimals: Reaction-Diffusion Models for the Generation of Biological Patterns Introduction Reaction-diffusion equations can be utilized in order

WORD: Revisiting Organs Segmentation in the Whole Abdominal Region. This repository provides the codebase and dataset for our work WORD: Revisiting Or

Code for sound field predictions in domains with impedance boundaries. Used for generating results from the paper

Test symmetries with sklearn decision tree models Setup Begin from an environment with a recent version of python 3. source setup.sh Leave the enviro

DistMIS Distributing Deep Learning Hyperparameter Tuning for 3D Medical Image Segmentation. DistriMIS Distributing Deep Learning Hyperparameter Tuning

MedAI: Transparency in Medical Image Segmentation What is this repo This repo contains the code and experiments that are implemented to contribute in

bayesmedaug: Bayesian Optimization Library for Medical Image Segmentation. bayesmedaug optimizes your data augmentation hyperparameters for medical im

How to Leverage Multimodal EHR Data for Better Medical Predictions? This repository contains the code of the paper: How to Leverage Multimodal EHR Dat

VRDP (NeurIPS 2021) Dynamic Visual Reasoning by Learning Differentiable Physics Models from Video and Language Mingyu Ding, Zhenfang Chen, Tao Du, Pin

Pytorch Classification A general, feasible and extensible framework for 2D image classification. Features Easy to configure (model, hyperparameters) T

MedMNIST Project (Website) | Dataset (Zenodo) | Paper (arXiv) | MedMNIST v1 (ISBI'21) Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bili

MultiMix This repository contains the implementation of MultiMix. Our publications for this project are listed below: "MultiMix: Sparingly Supervised,

Med Phys Scripts These are scripts that I, the medical physics assistant at Cookeville Regional Medical Center, wrote for use in our radiation therapy

Research PACS on AWS Challenge to solve Solution presentation Deploy the solution Further reading Releases License Challenge to solve The rise of new

ElectriPy ⚡ Visualize the electric field of a point charges network. 🔌 Installation Install ElectriPy package: $ pip install electripy You are all d

DQC: Differentiable Quantum Chemistry Differentiable quantum chemistry package. Currently only support differentiable density functional theory (DFT)

Physion: Evaluating Physical Prediction from Vision in Humans and Machines This repo contains code and data to reproduce the results in our paper, Phy

github_project This is a project for medical image segmentation. This project includes common medical image segmentation models such as U-net, FCN, De

Blockchain-based Medical Records 📄 Abstract Blockchain has the ability to keep an incorruptible, decentralized, and transparent log of all patient da

OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data Christoph Reich, Tim Prangemeier, Özdemir Cetin & Heinz Koeppl | Pr

solar-system-pygame Controls UP/DOWN for Emulation Speed Control ESC for Pause/Unpause q to Quit c or ESC again to Continue LEFT CLICK to Add an orbit

OSS-Net: Memory Efficient High Resolution Semantic Segmentation of 3D Medical Data Christoph Reich, Tim Prangemeier, Özdemir Cetin & Heinz Koeppl | Pr

dm_control: DeepMind Infrastructure for Physics-Based Simulation. DeepMind's software stack for physics-based simulation and Reinforcement Learning en

CoraNet This is the 3D Implementation of 《Inconsistency-aware Uncertainty Estimation for Semi-supervised Medical Image Segmentation》 Environment pytor

Multi-Objective Loss Balancing for Physics-Informed Deep Learning Code for ReLoBRaLo. Abstract Physics Informed Neural Networks (PINN) are algorithms

MuJoCo Physics MuJoCo stands for Multi-Joint dynamics with Contact. It is a general purpose physics engine that aims to facilitate research and develo

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 According poisson image blending I've completely used it for bio

Links to works on deep learning algorithms for physics problems, TUM-I15 and beyond

Is it Time to Replace CNNs with Transformers for Medical Images? Accepted at ICCV-2021: Workshop on Computer Vision for Automated Medical Diagnosis (C

ANTsPyNet A collection of deep learning architectures and applications ported to the python language and tools for basic medical image processing. Bas

pySPEDAS pySPEDAS is an implementation of the SPEDAS framework for Python. The Space Physics Environment Data Analysis Software (SPEDAS) framework is

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.

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 Supervised Pix2Pix and unsupervised Cycle-consistency are two modes that dominate the field

Python-Orbit-Sim A 2D physics sim for orbits. Made using pygame and tkinter. High degree of intractability, allowing you to create celestial bodies of

Useful materials and tutorials for 110-1 NTU DBME5028 (Application of Deep Learning in Medical Imaging)

PhyCRNet Physics-informed convolutional-recurrent neural networks for solving spatiotemporal PDEs Paper link: [ArXiv] By: Pu Ren, Chengping Rao, Yang

PiSL A python implementation of Physics-informed Spline Learning for nonlinear dynamics discovery. Sun, F., Liu, Y. and Sun, H., 2021. Physics-informe

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

SurRoL IROS 2021 SurRoL: An Open-source Reinforcement Learning Centered and dVRK Compatible Platform for Surgical Robot Learning Features dVRK compati

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. Recently, semi-supervised image segmentation has become a hot topic in medical image computin

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 of V-Net Vnet is a PyTorch implementation of the paper V-Net: Fully Convolutional Neural Networks for Volumetric Medical Imag

💻 Physics2Calculator A simple and powerful calculator for Physics 2 🔌 Predefined constants pi = 3.14159... k = 8988000000 (coulomb constant) e0 = 8.

EfficientSegmentation Introduction EfficientSegmentation is an open source, PyTorch-based segmentation framework for 3D medical image. Features A whol

MIDeepSeg: Minimally Interactive Segmentation of Unseen Objects from Medical Images Using Deep Learning [MedIA or Arxiv] and [Demo] This repository pr

PINNpapers Contributed by IDRL lab. Introduction Physics-Informed Neural Network (PINN) has achieved great success in scientific computing since 2017.

Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN

Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN

Zero-Shot Domain Adaptation with a Physics Prior [arXiv] [sup. material] - ICCV 2021 Oral paper, by Attila Lengyel, Sourav Garg, Michael Milford and J

WobblyStitcher Introduction A scalable implementation of WobblyStitcher Dependencies $ python -m pip install numpy scikit-image Visualization ImageJ

Medical image preprocessing and augmentation toolkit for deep learning. Part of the PyTorch Ecosystem.

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

zoofs is a Python library for performing feature selection using a variety of nature-inspired wrapper algorithms. The algorithms range from swarm-intelligence to physics-based to Evolutionary. It's easy to use , flexible and powerful tool to reduce your feature size.

CaraNet: Context Axial Reverse Attention Network for Small Medical Objects Segmentation This repository contains the implementation of a novel attenti

Interaction-Network-Pytorch Pytorch Implementraion of Interaction Networks for Learning about Objects, Relations and Physics. Interaction Network is a

Visual-Interaction-Networks An implementation of Deepmind visual interaction networks in Pytorch. Introduction For the purpose of understanding the ch

IDRLnet IDRLnet is a machine learning library on top of PyTorch. Use IDRLnet if you need a machine learning library that solves both forward and inver

Brax is a differentiable physics engine that simulates environments made up of rigid bodies, joints, and actuators. It's also a suite of learning algorithms to train agents to operate in these environments (PPO, SAC, evolutionary strategy, and direct trajectory optimization are implemented).

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.

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. 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.