Python Medical-imaging-datasets Resources

The Breathing K-Means Algorithm (with examples) The Breathing K-Means is an approximation algorithm for the k-means problem that (on average) is bette

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')

Copy Paste positive polyp using poisson image blending for medical image segmentation According poisson image blending I've completely used it for bio

img2texture Command line utility for converting images to seamless tiles. The resulting tiles can be used as textures in games, compositing and 3D mod

Glue Glue is a python project to link visualizations of scientific datasets across many files. Click on the image for a quick demo: Features Interacti

Tensor2Tensor Tensor2Tensor, or T2T for short, is a library of deep learning models and datasets designed to make deep learning more accessible and ac

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

Masader The first online catalogue for Arabic NLP datasets. This catalogue contains 200 datasets with more than 25 metadata annotations for each datas

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.

A collection of papers about Transformer in the field of medical image analysis.

Overview The Open Graph Benchmark (OGB) is a collection of benchmark datasets, data loaders, and evaluators for graph machine learning. Datasets cover

ConditionalQA Datasets accompanying the paper ConditionalQA: A Complex Reading Comprehension Dataset with Conditional Answers. Disclaimer This dataset

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

The Python Package for DataHerb A DataHerb Core Service to Create and Load Datasets.

HyperSpy is an open source Python library for the interactive analysis of multidimensional datasets that can be described as multidimensional arrays o

MIMIC-III Benchmarks Python suite to construct benchmark machine learning datasets from the MIMIC-III clinical database. Currently, the benchmark data

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

Examples for Hub - Dataset Format for AI A repository showcasing examples of using Hub Uploading Dataset Places365 Colab Tutorials Notebook Link Getti

torchxrayvision A library for chest X-ray datasets and models. Including pre-trained models. ( 🎬 promo video about the project) Motivation: While the

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

multitask-learning-transformers A simple recipe for training and inferencing Transformer architecture for Multi-Task Learning on custom datasets. You

C++ Implementation of PyTorch Tutorials for Everyone OS (Compiler)\LibTorch 1.9.0 macOS (clang 10.0, 11.0, 12.0) Linux (gcc 8, 9, 10, 11) Windows (msv

AlignShift NEW: Code for our new MICCAI'21 paper "Asymmetric 3D Context Fusion for Universal Lesion Detection" will also be pushed to this repository

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

Reddit-Image-Scraper Reddit Reddit is an American Social news aggregation, web content rating, and discussion website. Reddit has been devided by topi

Scientific Computational Imaging COde (SCICO) SCICO is a Python package for solving the inverse problems that arise in scientific imaging applications

Dense Deep Unfolding Network with 3D-CNN Prior for Snapshot Compressive Imaging, ICCV2021 [PyTorch Code]

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

chazutsu photo from Kaikado, traditional Japanese chazutsu maker chazutsu is the dataset downloader for NLP. import chazutsu r = chazutsu.data

Pillow Python Imaging Library (Fork) Pillow is the friendly PIL fork by Alex Clark and Contributors. PIL is the Python Imaging Library by Fredrik Lund

TorchGeo is a PyTorch domain library, similar to torchvision, that provides datasets, transforms, samplers, and pre-trained models specific to geospatial data.

S3-plugin is a high performance PyTorch dataset library to efficiently access datasets stored in S3 buckets.

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

Roboflow makes managing, preprocessing, augmenting, and versioning datasets for computer vision seamless. This is the official Roboflow python package that interfaces with the Roboflow API.

bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo

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

BanglaBERT This repository contains the official release of the model "BanglaBERT" and associated downstream finetuning code and datasets introduced i

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

normalizer This python module is an easy-to-use port of the text normalization used in the paper "Not low-resource anymore: Aligner ensembling, batch

EasyDatas An easy way to build PyTorch datasets. Modularly build datasets and automatically cache processed results Installation pip install git+https

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.

[Japanese/English] GrabCut-Annotation-Tool GrabCut-Annotation-Tool.mp4 OpenCVのGrabCut()を利用したアノテーションツールです。 セマンティックセグメンテーション向けのデータセット作成にご使用いただけます。 ※Grab

About This repository provides data and code for the paper: Scalable Data Annotation Pipeline for High-Quality Large Speech Datasets Development (subm

Thermostat is a large collection of NLP model explanations and accompanying analysis tools. Combines explainability methods from the captum library wi

Codebase for training transformers on systematic generalization datasets. The official repository for our EMNLP 2021 paper The Devil is in the Detail:

GraphGT: Machine Learning Datasets for Graph Generation and Transformation Dataset Website | Paper Installation Using pip To install the core environm

This is a playground for pytorch beginners, which contains predefined models on popular dataset. Currently we support mnist, svhn cifar10, cifar100 st

PyTorch Image Classifier Updates As for many users request, I released a new version of standared pytorch immage classification example at here: http:

Simple tool/toolkit for evaluating NLG (Natural Language Generation) offering various automated metrics. Jury offers a smooth and easy-to-use interface. It uses datasets for underlying metric computation, and hence adding custom metric is easy as adopting datasets.Metric.

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

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

An Effective Loss Function for Generating 3D Models from Single 2D Image without Rendering Papers with code | Paper Nikola Zubić Pietro Lio University

Meeting Summarization Dataset Meeting plays an essential part in our daily life, which allows us to share information and collaborate with others. Wit

ml4h is a toolkit for machine learning on clinical data of all kinds including genetics, labs, imaging, clinical notes, and more

Common Sense Beyond English: Evaluating and Improving Multilingual LMs for Commonsense Reasoning This is the Github repository of our paper, "Common S

Deep Automatic Natural Image Matting [IJCAI-21] This is the official repository of the paper Deep Automatic Natural Image Matting. Introduction | Netw

Deep Optics for Single-shot High-dynamic-range Imaging Code associated with the paper "Deep Optics for Single-shot High-dynamic-range Imaging" CVPR, 2

A curated list of amazingly awesome Cybersecurity datasets

PyTorch Remote Sensing (torchrs) (WIP) PyTorch implementation of popular datasets and models in remote sensing tasks (Change Detection, Image Super Re

Deduplicating Training Data Makes Language Models Better This repository contains code to deduplicate language model datasets as descrbed in the paper

NCRF Prerequisites Data Whole slide images Annotations Patch images Model Training Testing Tissue mask Probability map Tumor localization FROC evaluat

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening Introduction This is an implementation of the model used for breast

UNet for segmenting salt deposits from seismic images with PyTorch. General We, tugstugi and xuyuan, have participated in the Kaggle competition TGS S

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.

Rapid Neural Architecture Search by Learning to Generate Graphs from Datasets This is the official PyTorch implementation for the paper Rapid Neural A

Project page for the paper Semi-Supervised Raw-to-Raw Mapping 2021.

RSG: A Simple but Effective Module for Learning Imbalanced Datasets (CVPR 2021) A Pytorch implementation of our CVPR 2021 paper "RSG: A Simple but Eff

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

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

What is nnDetection? Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of hi

Meerkat makes it easier for ML practitioners to interact with high-dimensional, multi-modal data. It provides simple abstractions for data inspection, model evaluation and model training supported by efficient and robust IO under the hood.

NoW Evaluation This is the official repository for evaluation on the NoW Benchmark Dataset. The goal of the NoW benchmark is to introduce a standard e

Unified Multimodal Transformer (UMT) for Multimodal Named Entity Recognition (MNER) Two MNER Datasets and Codes for our ACL'2020 paper: Improving Mult

UmlsBERT: Clinical Domain Knowledge Augmentation of Contextual Embeddings Using the Unified Medical Language System Metathesaurus General info This is

PTR Code and datasets for our paper "PTR: Prompt Tuning with Rules for Text Classification" If you use the code, please cite the following paper: @art

Deep Active Learning for Biased Datasets via Fisher Kernel Self-Supervision https://arxiv.org/abs/2003.00393 Abstract Active learning (AL) aims to min

Ozeu Ozeu is the toolkit to autolabal dataset for instance segmentation. You can generate datasets labaled with segmentation mask and bounding box fro

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 Introduction This repository contains the code of the IJCAI'2021 paper 'Medical Im

This repository contains 20 annotated datasets of Automatic Keyphrase Extraction made available by the research community. Following are the datasets and the original papers that proposed them. If you know more datasets, and want to contribute, please, notify me.

TSForecasting This repository contains the implementations related to the experiments of a set of publicly available datasets that are used in the tim

Covid-QA Fine tuned models for question answering on Covid-19 data. Hosted Inference This model has been contributed to huggingface.Click here to see

PosteriorStacker Combines Bayesian analyses from many datasets. Introduction Method Tutorial Output plot and files Introduction Fitting a model to a d

BOOKSUM: A Collection of Datasets for Long-form Narrative Summarization Authors: Wojciech Kryściński, Nazneen Rajani, Divyansh Agarwal, Caiming Xiong,

tfds-korean A collection of Korean Text Datasets ready to use using Tensorflow-Datasets. TensorFlow-Datasets를 이용한 한국어/한글 데이터셋 모음입니다. Dataset Catalog |

Public Datasets Pipelines Cloud-native, data pipeline architecture for onboarding datasets to the Google Cloud Public Datasets Program. Overview Requi

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.

ViT-V-Net: Vision Transformer for Volumetric Medical Image Registration keywords: vision transformer, convolutional neural networks, image registratio

A curated list of awesome anomaly detection works in medical imaging, inspired by the other awesome-* initiatives.

Awesome Video Datasets