Python Medical-imaging Resources

Disclaimer This code is provided for research and development use only. This code is not intended for use in clinical decision-making or for any other

Causality-inspired Single-source Domain Generalization for Medical Image Segmentation Arxiv preprint Repository under construction. Might still be bug

MedMCQA MedMCQA : A Large-scale Multi-Subject Multi-Choice Dataset for Medical domain Question Answering A large-scale, Multiple-Choice Question Answe

jie jie is a spatial genome aligner. This package parses true chromatin imaging signal from noise by aligning signals to a reference DNA polymer model

medical by LAION This repository will be a summary and outlook on all our open, medical, AI advancements. See the medical-general channel in the medic

Underwater Light Field Retention : Neural Rendering for Underwater Imaging (UWNR) (Accepted by CVPR Workshop2022 NTIRE) Authors: Tian Ye†, Sixiang Che

Project: Text Analysis - This project aims to conduct a text information retrieval and text mining on medical research publication regarding Covid19 -

On-the-Fly Adaptation Official Pytorch Code base for On-the-Fly Test-time Adaptation for Medical Image Segmentation Paper Introduction One major probl

Image-to-image regression with uncertainty quantification in PyTorch. Take any dataset and train a model to regress images to images with rigorous, distribution-free uncertainty quantification.

FAST is an open-source cross-platform framework with the main goal of making it easier to do high-performance processing and visualization of medical images on heterogeneous systems utilizing both multi-core CPUs and GPUs. To achieve this, FAST use modern C++, OpenCL and OpenGL.

Multi-atlas segmentation (MAS) is a promising framework for medical image segmentation. Generally, MAS methods register multiple atlases, i.e., medical images with corresponding labels, to a target image;

A small python package that allows the user to look up common medical abbreviations.

PyZebrascope - an open-source Python platform for brain-wide neural activity imaging in behaving zebrafish

DCSAU-Net: A Deeper and More Compact Split-Attention U-Net for Medical Image Segmentation By Qing Xu, Wenting Duan and Na He Requirements pytorch==1.1

Posterior temperature optimized Bayesian models for inverse problems in medical imaging Max-Heinrich Laves*, Malte Tölle*, Alexander Schlaefer, Sandy

SweiNet SweiNet is an uncertainty-quantifying shear wave speed (SWS) estimator for ultrasound shear wave elasticity (SWE) imaging. SweiNet takes as in

Deep High Dynamic Range Imaging Benchmark This repository is the pytorch impleme

Medical natural language parsing and utility library A natural language medical

1st place solution in CCF BDCI 2021 ULSEG challenge This is the source code of the 1st place solution for ultrasound image angioma segmentation task (

Medical-Insurance-Project-OOP Python Classes: Medical Insurance Project using Object Oriented Programming Concepts Classes are an incredibly useful pr

SegTransVAE: Hybrid CNN - Transformer with Regularization for medical image segmentation This repo is the official implementation for SegTransVAE. Seg

miseval: a metric library for Medical Image Segmentation EVALuation The open-source and free to use Python package miseval was developed to establish

coldcuts coldcuts is an R package that allows you to draw and plot automatically segmentations from 3D voxel arrays. The name is inspired by one of It

Ensemble Learning Priors Driven Deep Unfolding for Scalable Snapshot Compressive Imaging [PyTorch] Abstract Snapshot compressive imaging (SCI) can rec

An Analysis on Ensemble Learning optimized Medical Image Classification with Deep Convolutional Neural Networks Novel and high-performance medical ima

[Project] Equivariant Imaging: Learning Beyond the Range Space Project about the

Toward Model Interpretability in Medical NLP LING380: Topics in Computational Linguistics Final Project James Cross ([email protected]) and Daniel Kim

This repo supplements our Survey on Transformers in Medical Imaging Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat,

Introduction: X-Ray Report Generation This repository is for our EMNLP 2021 paper "Automated Generation of Accurate & Fluent Medical X-ray Reports". O

RATCHET: RAdiological Text Captioning for Human Examined Thoraxes RATCHET is a Medical Transformer for Chest X-ray Diagnosis and Reporting. Based on t

Accelerated Multi-Modal MR Imaging with Transformers Dependencies numpy==1.18.5 scikit_image==0.16.2 torchvision==0.8.1 torch==1.7.0 runstats==1.8.0 p

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

MT-UNet Update 2022/01/05 By another round of training based on previous weights, our model also achieved a better performance on ACDC (91.61% DSC). W

LeViT_UNet For medical image segmentation Our model is based on LeViT (https://github.com/facebookresearch/LeViT). You'd better gitclone its codes. Th

TransFuse This repo holds the code of TransFuse: Fusing Transformers and CNNs for Medical Image Segmentation Requirements Pytorch=1.6.0, 1.9.0 (=1.

Introduction This repository contains the modified caffe library and network architectures for our paper "Automated Melanoma Recognition in Dermoscopy

Cascaded-FCN This repository contains the pre-trained models for a Cascaded-FCN in caffe and tensorflow that segments the liver and its lesions out of

Shield: This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Deep Learning to Improve Breast

Medical Data for Machine Learning This is a curated list of medical data for machine learning. This list is provided for informational purposes only,

HistoSeg : Quick attention with multi-loss function for multi-structure segmentation in digital histology images Histological Image Segmentation This

SI_EXPLAINER_tg_bot This bot is an assistant for medical professionals in interpreting the results of patient clustering. ABOUT This chatbot was devel

MedViLL This repository provides the code for MedViLL(Medical Vision Language Learner). Our proposed architecture MedViLL is a single BERT-based model

NLP PubMed Medical Research Paper Abstract (Randomized Controlled Trial) A natural language processing model for sequential sentence classification in

Pneumonia Detection from X-Rays Project Overview In this project, you will apply the skills that you have acquired in this 2D medical imaging course t

Patient Selection for Diabetes Drug Testing Project Overview EHR data is becoming a key source of real-world evidence (RWE) for the pharmaceutical ind

Quantifying Hippocampus Volume for Alzheimer's Progression Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder that result

Cross-level Contrastive Learning and Consistency Constraint for Semi-supervised Medical Image Introduction This repository contains the PyTorch implem

MOOSE (Multi-organ objective segmentation) a data-centric AI solution that generates multilabel organ segmentations to facilitate systemic TB whole-person research.The pipeline is based on nn-UNet and has the capability to segment 120 unique tissue classes from a whole-body 18F-FDG PET/CT image.

Machine Learning use case in the field of Healthcare. In this project MONAI and pytorch frameworks are used for 3D Liver segmentation.

Introduction This is an implementation of our paper Supervised 3D Pre-training on Large-scale 2D Natural Image Datasets for 3D Medical Image Analysis.

Repository for papers: Benchmark: Effect of Prior-based Losses on Segmentation Performance: A Benchmark Midl: A Surprisingly Effective Perimeter-based

CrowdCurio Time Series Annotator Library The CrowdCurio Time Series Annotation Library implements classification tasks for time series. Features Suppo

Medical Appointments No-shows Why do 20% of patients miss their scheduled appointments? A person makes a doctor appointment, receives all the instruct

Chinese Medical Entity Recognition Based on BERT+Bi-LSTM+CRF Step 1 I share the dataset on my google drive, please download the whole 'CCKS_2019_Task1

ehtim (eht-imaging) Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This ve

Auto Vaidya An open source solution for creating end-end web app for employing the power of deep learning in various clinical scenarios like implant d

Medical-Insurance-Cost-Prediction-using-Machine-learning - Here in this project, I will use regression analysis to predict medical insurance cost for people in different regions, and based on several aspects like : Smoking, Number of children, BMI...etc.

pysero pysero enables serological measurements with multiplexed and standard ELISA assays. The project automates estimation of antibody titers from da

Contrastive learning of global and local features for medical image segmentation with limited annotations The code is for the article "Contrastive lea

tedana: TE Dependent ANAlysis TE-dependent analysis (tedana) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI)

Medical-Image-Triage-and-Classification-System-Based-on-COVID-19-CT-and-X-ray-Sc

Overview BisQue is a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for up to 5D

UMLS-Graph Build a medical knowledge graph based on Unified Language Medical System (UMLS) Requisite Install MySQL Server 5.6 and import UMLS data int

FFA-IR The official start-up code for paper "FFA-IR: Towards an Explainable and Reliable Medical Report Generation Benchmark." The framework is inheri

Logo by Zhuoning Yuan LibAUC: A Machine Learning Library for AUC Optimization Website | Updates | Installation | Tutorial | Research | Github LibAUC a

Keyhole Imaging Code & Dataset Code associated with the paper "Keyhole Imaging: Non-Line-of-Sight Imaging and Tracking of Moving Objects Along a Singl

MISSFormer Code for paper "MISSFormer: An Effective Medical Image Segmentation Transformer". Please read our preprint at the following link: paper_add

CPPE - 5 CPPE - 5 (Medical Personal Protective Equipment) is a new challenging dataset with the goal to allow the study of subordinate categorization

WORD: Revisiting Organs Segmentation in the Whole Abdominal Region (Paper and DataSet). [New] Note that all the emails about the download permission o

NHDRRNet-PyTorch This is the PyTorch implementation of Deep HDR Imaging via A Non-Local Network (TIP 2020). 0. Differences between Original Paper and

MT-UNet Update 2021/11/19 Thank you for your interest in our work. We have uploaded the code of our MTUNet to help peers conduct further research on i

Hypernet-Ensemble Learning of Segmentation Probability for Medical Image Segmentation with Ambiguous Labels The implementation of Hypernet-Ensemble Le

Read and write TIFF files Tifffile is a Python library to store numpy arrays in TIFF (Tagged Image File Format) files, and read image and metadata fro

AHDRNet-PyTorch This is the PyTorch implementation of Attention-guided Network for Ghost-free High Dynamic Range Imaging (CVPR 2019). The official cod

Larch: Data Analysis Tools for X-ray Spectroscopy and More Documentation: http://xraypy.github.io/xraylarch Code: http://github.com/xraypy/xraylarch L

Robust Place Recognition using an Imaging Lidar A place recognition package using high-resolution imaging lidar. For best performance, a lidar equippe

Simulation of moving particles under microscopic imaging Install scipy numpy scikit-image tiffile Run python simulation.py Read result https://imagej

Simple pipeline for experimenting with radiomics features Installation git clone https://github.com/piotrekwoznicki/ClassyRadiomics.git cd classrad pi

U-Net Brain Tumor Segmentation 🚀 ：Feb 2019 the data processing implementation in this repo is not the fastest way (code need update, contribution is

Grouped SSD (GSSD) for liver lesion detection from multi-phase CT Note: the MICCAI 2018 paper only covers the multi-phase lesion detection part of thi

Imaging Transcriptomics Imaging transcriptomics is a methodology that allows to identify patterns of correlation between gene expression and some prop

Self-Supervised Generative Style Transfer for One-Shot Medical Image Segmentation This repository contains the Pytorch implementation of the proposed

farabio is a minimal PyTorch toolkit for out-of-the-box deep learning support in biomedical imaging. For further information, see Wikis and Docs.

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

ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics This is the code implementation of the paper "ContIG: Self-s

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

Data Consistency for Magnetic Resonance Imaging Data Consistency (DC) is crucial for generalization in multi-modal MRI data and robustness in detectin

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

Few-shot Deep HDR Deghosting This repository contains code and pretrained models for our paper: Self-Gated Memory Recurrent Network for Efficient Scal

CodedCam Coded Illumination for Improved Lensless Imaging Paper | Supplementary results | Data and Code are available. Coded illumination for improved

The repository contains the implementations for Hyperspectral Image Classification -- Traditional to Deep Models: A Survey for Future Prospects. Model

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

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

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

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