137 Repositories
Python whole-slide-imaging Libraries
ML-based medical imaging using Azure
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
A spatial genome aligner for analyzing multiplexed DNA-FISH imaging data.
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
This is the official implementation code repository of Underwater Light Field Retention : Neural Rendering for Underwater Imaging (Accepted by CVPR Workshop2022 NTIRE)
Underwater Light Field Retention : Neural Rendering for Underwater Imaging (UWNR) (Accepted by CVPR Workshop2022 NTIRE) Authors: Tian Ye†, Sixiang Che
Code base for "On-the-Fly Test-time Adaptation for Medical Image Segmentation"
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
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.
A framework for GPU based high-performance medical image processing and visualization
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.
PyZebrascope - an open-source Python platform for brain-wide neural activity imaging in behaving zebrafish
PyZebrascope - an open-source Python platform for brain-wide neural activity imaging in behaving zebrafish
Posterior temperature optimized Bayesian models for inverse problems in medical imaging
Posterior temperature optimized Bayesian models for inverse problems in medical imaging Max-Heinrich Laves*, Malte Tölle*, Alexander Schlaefer, Sandy
SweiNet is an uncertainty-quantifying shear wave speed (SWS) estimator for ultrasound shear wave elasticity (SWE) imaging.
SweiNet SweiNet is an uncertainty-quantifying shear wave speed (SWS) estimator for ultrasound shear wave elasticity (SWE) imaging. SweiNet takes as in
Pytorch implementation of various High Dynamic Range (HDR) Imaging algorithms
Deep High Dynamic Range Imaging Benchmark This repository is the pytorch impleme
Generate meme GIFs in which an image you choose can be viewed by the user only after they wait a whole hour.
Generate meme GIFs in which an image you choose can be viewed by the user only after they wait a whole hour.
This is the source code of the 1st place solution for segmentation task (with Dice 90.32%) in 2021 CCF BDCI challenge.
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 (
coldcuts is an R package to automatically generate and plot segmentation drawings in R
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]
Ensemble Learning Priors Driven Deep Unfolding for Scalable Snapshot Compressive Imaging [PyTorch] Abstract Snapshot compressive imaging (SCI) can rec
Equivariant Imaging: Learning Beyond the Range Space
[Project] Equivariant Imaging: Learning Beyond the Range Space Project about the
Awesome Transformers in Medical Imaging
This repo supplements our Survey on Transformers in Medical Imaging Fahad Shamshad, Salman Khan, Syed Waqas Zamir, Muhammad Haris Khan, Munawar Hayat,
Multimodal Co-Attention Transformer (MCAT) for Survival Prediction in Gigapixel Whole Slide Images
Multimodal Co-Attention Transformer (MCAT) for Survival Prediction in Gigapixel Whole Slide Images [ICCV 2021] © Mahmood Lab - This code is made avail
Accelerated Multi-Modal MR Imaging with Transformers
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
TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification
TransMIL: Transformer based Correlated Multiple Instance Learning for Whole Slide Image Classification [NeurIPS 2021] Abstract Multiple instance learn
Mixed Transformer UNet for Medical Image Segmentation
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
Pre-trained models for a Cascaded-FCN in caffe and tensorflow that segments
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
Deep Learning to Improve Breast Cancer Detection on Screening Mammography
Shield: This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License. Deep Learning to Improve Breast
MAg: a simple learning-based patient-level aggregation method for detecting microsatellite instability from whole-slide images
MAg Paper Abstract File structure Dataset prepare Data description How to use MAg? Why not try the MAg_lib! Trained models Experiment and results Some
The final project of "Applying AI to 2D Medical Imaging Data" of "AI for Healthcare" nanodegree - Udacity.
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
The final project of "Applying AI to 3D Medical Imaging Data" from "AI for Healthcare" nanodegree - Udacity.
Quantifying Hippocampus Volume for Alzheimer's Progression Background Alzheimer's disease (AD) is a progressive neurodegenerative disorder that result
MOOSE (Multi-organ objective segmentation) a data-centric AI solution that generates multilabel organ segmentations to facilitate systemic TB whole-person research
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.
Liver segmentation using MONAI and pytorch
Machine Learning use case in the field of Healthcare. In this project MONAI and pytorch frameworks are used for 3D Liver segmentation.
Time series annotation library.
CrowdCurio Time Series Annotator Library The CrowdCurio Time Series Annotation Library implements classification tasks for time series. Features Suppo
Imaging, analysis, and simulation software for radio interferometry
ehtim (eht-imaging) Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This ve
PyPresent - create slide presentations from notes
PyPresent Create slide presentations from notes Add some formatting to text file
An open-source project for applying deep learning to medical scenarios
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
serological measurements from multiplexed ELISA assays
pysero pysero enables serological measurements with multiplexed and standard ELISA assays. The project automates estimation of antibody titers from da
TE-dependent analysis (tedana) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI) data
tedana: TE Dependent ANAlysis TE-dependent analysis (tedana) is a Python library for denoising multi-echo functional magnetic resonance imaging (fMRI)
BisQue is a web-based platform designed to provide researchers with organizational and quantitative analysis tools for 5D image data. Users can extend BisQue by implementing containerized ML workflows.
Overview BisQue is a web-based platform specifically designed to provide researchers with organizational and quantitative analysis tools for up to 5D
An End-to-End Machine Learning Library to Optimize AUC (AUROC, AUPRC).
Logo by Zhuoning Yuan LibAUC: A Machine Learning Library for AUC Optimization Website | Updates | Installation | Tutorial | Research | Github LibAUC a
Makes patches from huge resolution .svs slide files using openslide
openslide_patcher Makes patches from huge resolution .svs slide files using openslide Example collage I made from outputs:
Keyhole Imaging: Non-Line-of-Sight Imaging and Tracking of Moving Objects Along a Single Optical Path
Keyhole Imaging Code & Dataset Code associated with the paper "Keyhole Imaging: Non-Line-of-Sight Imaging and Tracking of Moving Objects Along a Singl
The ldap2json script allows you to extract the whole LDAP content of a Windows domain into a JSON file.
ldap2json The ldap2json script allows you to extract the whole LDAP content of a Windows domain into a JSON file. Features Authenticate with password
A way to integrate Latex, VSCode, and Inkscape in macOS. Adopted the whole workflow from Gilles Castel.
VSCode-LaTeX-Inkscape A way to integrate LaTeX, VSCode, and Inkscape in macOS Abstract I use LaTeX heavily in past two years for both academic work an
Real-Time and Accurate Full-Body Multi-Person Pose Estimation&Tracking System
News! Aug 2020: v0.4.0 version of AlphaPose is released! Stronger tracking! Include whole body(face,hand,foot) keypoints! Colab now available. Dec 201
The code written during my Bachelor Thesis "Classification of Human Whole-Body Motion using Hidden Markov Models".
This code was written during the course of my Bachelor thesis Classification of Human Whole-Body Motion using Hidden Markov Models. Some things might
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region (Paper and DataSet). [New] Note that all the emails about the download permission o
PyTorch implementation of Deep HDR Imaging via A Non-Local Network (TIP 2020).
NHDRRNet-PyTorch This is the PyTorch implementation of Deep HDR Imaging via A Non-Local Network (TIP 2020). 0. Differences between Original Paper and
Mixed Transformer UNet for Medical Image Segmentation
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
Whole-day timezone comparison
Timezone Converter Compare a full day of your local timezone with foreign ones $ timezone-converter tijuana --zone $ timezone-converter tijuana new_yo
Read and write TIFF files
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
Unofficial PyTorch Implementation of AHDRNet (CVPR 2019)
AHDRNet-PyTorch This is the PyTorch implementation of Attention-guided Network for Ghost-free High Dynamic Range Imaging (CVPR 2019). The official cod
Larch: Applications and Python Library for Data Analysis of X-ray Absorption Spectroscopy (XAS, XANES, XAFS, EXAFS), X-ray Fluorescence (XRF) Spectroscopy and Imaging
Larch: Data Analysis Tools for X-ray Spectroscopy and More Documentation: http://xraypy.github.io/xraylarch Code: http://github.com/xraypy/xraylarch L
ICRA 2021 - Robust Place Recognition using an Imaging Lidar
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
Simulation of moving particles under microscopic imaging Install scipy numpy scikit-image tiffile Run python simulation.py Read result https://imagej
U-Net Brain Tumor Segmentation
U-Net Brain Tumor Segmentation 🚀 :Feb 2019 the data processing implementation in this repo is not the fastest way (code need update, contribution is
A package, and script, to perform imaging transcriptomics on a neuroimaging scan.
Imaging Transcriptomics Imaging transcriptomics is a methodology that allows to identify patterns of correlation between gene expression and some prop
PyTorch toolkit for biomedical imaging
farabio is a minimal PyTorch toolkit for out-of-the-box deep learning support in biomedical imaging. For further information, see Wikis and Docs.
This is the old code for bitcoin risk metric, the whole purpose form it is to help you DCA your investment according to bitcoin risk.
About The Project This is the old code for bitcoin risk metric, the whole purpose form it is to help you DCA your investment according to bitcoin risk
Pre-Training with Whole Word Masking for Chinese BERT
Pre-Training with Whole Word Masking for Chinese BERT
Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation
VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen
Official implementation of the method ContIG, for self-supervised learning from medical imaging with genomics
ContIG: Self-supervised Multimodal Contrastive Learning for Medical Imaging with Genetics This is the code implementation of the paper "ContIG: Self-s
Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018
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 for Magnetic Resonance Imaging Data Consistency (DC) is crucial for generalization in multi-modal MRI data and robustness in detectin
This repository is for the preprint "A generative nonparametric Bayesian model for whole genomes"
BEAR Overview This repository contains code associated with the preprint A generative nonparametric Bayesian model for whole genomes (2021), which pro
Code for A Volumetric Transformer for Accurate 3D Tumor Segmentation
VT-UNet This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmentaion results of VT-UNet. Environmen
[IEEE Transactions on Computational Imaging] Self-Gated Memory Recurrent Network for Efficient Scalable HDR Deghosting
Few-shot Deep HDR Deghosting This repository contains code and pretrained models for our paper: Self-Gated Memory Recurrent Network for Efficient Scal
Coded illumination for improved lensless imaging
CodedCam Coded Illumination for Improved Lensless Imaging Paper | Supplementary results | Data and Code are available. Coded illumination for improved
Pytorch and Keras Implementations of Hyperspectral Image Classification -- Traditional to Deep Models: A Survey for Future Prospects.
The repository contains the implementations for Hyperspectral Image Classification -- Traditional to Deep Models: A Survey for Future Prospects. Model
The source code and slide for my talk about the subject: unittesing in python
PyTest Talk This talk give you some ideals about the purpose of unittest? how to write good unittest? how to use pytest framework? and show you the ba
Additional functionality for use with fastai’s medical imaging module
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
Open-source python package for the extraction of Radiomics features from 2D and 3D images and binary masks.
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
AI Toolkit for Healthcare Imaging
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
MRQy is a quality assurance and checking tool for quantitative assessment of magnetic resonance imaging (MRI) data.
Front-end View Backend View Table of Contents Description Prerequisites Running Basic Information Measurements User Interface Feedback and usage Descr
Effect of Deep Transfer and Multi task Learning on Sperm Abnormality Detection
Effect of Deep Transfer and Multi task Learning on Sperm Abnormality Detection Introduction This repository includes codes and models of "Effect of De
A Python Tools to imaging the shallow seismic structure
ShallowSeismicImaging Tools to imaging the shallow seismic structure, above 10 km, based on the ZH ratio measured from the ambient seismic noise, and
Airborne Optical Sectioning (AOS) is a wide synthetic-aperture imaging technique
AOS: Airborne Optical Sectioning Airborne Optical Sectioning (AOS) is a wide synthetic-aperture imaging technique that employs manned or unmanned airc
Official Keras Implementation for UNet++ in IEEE Transactions on Medical Imaging and DLMIA 2018
UNet++: A Nested U-Net Architecture for Medical Image Segmentation UNet++ is a new general purpose image segmentation architecture for more accurate i
U-Net: Convolutional Networks for Biomedical Image Segmentation
Deep Learning Tutorial for Kaggle Ultrasound Nerve Segmentation competition, using Keras This tutorial shows how to use Keras library to build deep ne
Official Python implementation of the 'Sparse deconvolution'-v0.3.0
Sparse deconvolution Python v0.3.0 Official Python implementation of the 'Sparse deconvolution', and the CPU (NumPy) and GPU (CuPy) calculation backen
Fusion 360 Add-in that creates a pair of toothed curves that can be used to split a body and create two pieces that slide and lock together.
Fusion-360-Add-In-PuzzleSpline Fusion 360 Add-in that creates a pair of toothed curves that can be used to split a body and create two pieces that sli
Official implementation of NLOS-OT: Passive Non-Line-of-Sight Imaging Using Optimal Transport (IEEE TIP, accepted)
NLOS-OT Official implementation of NLOS-OT: Passive Non-Line-of-Sight Imaging Using Optimal Transport (IEEE TIP, accepted) Description In this reposit
Investigating automatic navigation towards standard US views integrating MARL with the virtual US environment developed in CT2US simulation
AutomaticUSnavigation Investigating automatic navigation towards standard US views integrating MARL with the virtual US environment developed in CT2US
Equivariant Imaging: Learning Beyond the Range Space
Equivariant Imaging: Learning Beyond the Range Space Equivariant Imaging: Learning Beyond the Range Space Dongdong Chen, Julián Tachella, Mike E. Davi
A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.
meddlr Getting Started Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems. Installation To av
small package with utility functions for analyzing (fly) calcium imaging data
fly2p Tools for analyzing two-photon (2p) imaging data collected with Vidrio Scanimage software and micromanger. Loading scanimage data relies on scan
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region
WORD: Revisiting Organs Segmentation in the Whole Abdominal Region. This repository provides the codebase and dataset for our work WORD: Revisiting Or
VoxHRNet - Whole Brain Segmentation with Full Volume Neural Network
VoxHRNet This is the official implementation of the following paper: Whole Brain Segmentation with Full Volume Neural Network Yeshu Li, Jonathan Cui,
Evaluating deep transfer learning for whole-brain cognitive decoding
Evaluating deep transfer learning for whole-brain cognitive decoding This README file contains the following sections: Project description Repository
Neural Nano-Optics for High-quality Thin Lens Imaging
Neural Nano-Optics for High-quality Thin Lens Imaging Project Page | Paper | Data Ethan Tseng, Shane Colburn, James Whitehead, Luocheng Huang, Seung-H
Non-Imaging Transient Reconstruction And TEmporal Search (NITRATES)
Non-Imaging Transient Reconstruction And TEmporal Search (NITRATES) This repo contains the full NITRATES pipeline for maximum likelihood-driven discov
[v1 (ISBI'21) + v2] MedMNIST: A Large-Scale Lightweight Benchmark for 2D and 3D Biomedical Image Classification
MedMNIST Project (Website) | Dataset (Zenodo) | Paper (arXiv) | MedMNIST v1 (ISBI'21) Jiancheng Yang, Rui Shi, Donglai Wei, Zequan Liu, Lin Zhao, Bili
An interactive tool with which to explore the possible imaging performance of candidate ngEHT architectures.
ngEHTexplorer An interactive tool with which to explore the possible imaging performance of candidate ngEHT architectures. Welcome! ngEHTexplorer is a
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,
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
Show Me the Whole World: Towards Entire Item Space Exploration for Interactive Personalized Recommendations
HierarchicyBandit Introduction This is the implementation of WSDM 2022 paper : Show Me the Whole World: Towards Entire Item Space Exploration for Inte
starfish is a Python library for processing images of image-based spatial transcriptomics.
starfish: scalable pipelines for image-based transcriptomics starfish is a Python library for processing images of image-based spatial transcriptomics
Command line utility for converting images to seamless tiles
img2texture Command line utility for converting images to seamless tiles. The resulting tiles can be used as textures in games, compositing and 3D mod
Deep Learning Slide Captcha
滑动验证码深度学习识别 本项目使用深度学习 YOLOV3 模型来识别滑动验证码缺口,基于 https://github.com/eriklindernoren/PyTorch-YOLOv3 修改。 只需要几百张缺口标注图片即可训练出精度高的识别模型,识别效果样例: 克隆项目 运行命令: git cl
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.
SlideGraph+: Whole Slide Image Level Graphs to Predict HER2 Status in Breast Cancer
SlideGraph+: Whole Slide Image Level Graphs to Predict HER2 Status in Breast Cancer A novel graph neural network (GNN) based model (termed SlideGraph+
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)
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
Deep Multi-Magnification Network for multi-class tissue segmentation of whole slide images
Deep Multi-Magnification Network This repository provides training and inference codes for Deep Multi-Magnification Network published here. Deep Multi