123 Repositories
Python hyperspectral-imaging Libraries
"MST++: Multi-stage Spectral-wise Transformer for Efficient Spectral Reconstruction" (CVPRW 2022) & (Winner of NTIRE 2022 Challenge on Spectral Reconstruction from RGB)
MST++: Multi-stage Spectral-wise Transformer for Efficient Spectral Reconstruction (CVPRW 2022) Yuanhao Cai, Jing Lin, Zudi Lin, Haoqian Wang, Yulun Z
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
Framework for Spectral Clustering on the Sparse Coefficients of Learned Dictionaries
Dictionary Learning for Clustering on Hyperspectral Images Overview Framework for Spectral Clustering on the Sparse Coefficients of Learned Dictionari
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
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 (
Adaptive Dropblock Enhanced GenerativeAdversarial Networks for Hyperspectral Image Classification
This repo holds the codes of our paper: Adaptive Dropblock Enhanced GenerativeAdversarial Networks for Hyperspectral Image Classification, which is ac
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
Pytorch implement of 'Unmixing based PAN guided fusion network for hyperspectral imagery'
Pgnet There's a improved version compared with the publication in Tgrs with the modification in the deduction of the PDIN block: https://arxiv.org/abs
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,
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
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
Band-Adaptive Spectral-Spatial Feature Learning Neural Network for Hyperspectral Image Classification
Band-Adaptive Spectral-Spatial Feature Learning Neural Network for Hyperspectral Image Classification
Codes to calculate solar-sensor zenith and azimuth angles directly from hyperspectral images collected by UAV. Works only for UAVs that have high resolution GNSS/IMU unit.
UAV Solar-Sensor Angle Calculation Table of Contents About The Project Built With Getting Started Prerequisites Installation Datasets Contributing Lic
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
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
Calibrated Hyperspectral Image Reconstruction via Graph-based Self-Tuning Network.
mask-uncertainty-in-HSI This repository contains the testing code and pre-trained models for the paper Calibrated Hyperspectral Image Reconstruction v
Code for the paper: Fusformer: A Transformer-based Fusion Approach for Hyperspectral Image Super-resolution
Fusformer Code for the paper: "Fusformer: A Transformer-based Fusion Approach for Hyperspectral Image Super-resolution" Plateform Python 3.8.5 + Pytor
PyTorch Implementation of SSTNs for hyperspectral image classifications from the IEEE T-GRS paper "Spectral-Spatial Transformer Network for Hyperspectral Image Classification: A FAS Framework."
PyTorch Implementation of SSTN for Hyperspectral Image Classification Paper links: SSTN published on IEEE T-GRS. Also, you can directly find the imple
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
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
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
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.
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
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
Spectralformer: Rethinking hyperspectral image classification with transformers
Spectralformer: Rethinking hyperspectral image classification with transformers Danfeng Hong, Zhu Han, Jing Yao, Lianru Gao, Bing Zhang, Antonio Plaza
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
Large-scale Hyperspectral Image Clustering Using Contrastive Learning, CIKM 21 Workshop
Spectral-spatial contrastive clustering (SSCC) Yaoming Cai, Yan Liu, Zijia Zhang, Zhihua Cai, and Xiaobo Liu, Large-scale Hyperspectral Image Clusteri
Spectralformer: Rethinking hyperspectral image classification with transformers
The code in this toolbox implements the "Spectralformer: Rethinking hyperspectral image classification with transformers". More specifically, it is detailed as follow.
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
HyperBlend is a new type of hyperspectral image simulator based on Blender.
HyperBlend version 0.1.0 This is the HyperBlend leaf spectra simulator developed in Spectral Laboratory of University of Jyväskylä. You can use and mo
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
paper: Hyperspectral Remote Sensing Image Classification Using Deep Convolutional Capsule Network
DC-CapsNet This is a tensorflow and keras based implementation of DC-CapsNet for HSI in the Remote Sensing Letters R. Lei et al., "Hyperspectral Remot
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
Graph Regularized Residual Subspace Clustering Network for hyperspectral image clustering
Graph Regularized Residual Subspace Clustering Network for hyperspectral image clustering
[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
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
PyTorch implementation of our method for adversarial attacks and defenses in hyperspectral image classification.
Self-Attention Context Network for Hyperspectral Image Classification PyTorch implementation of our method for adversarial attacks and defenses in hyp
Semi-Supervised Graph Prototypical Networks for Hyperspectral Image Classification, IGARSS, 2021.
Semi-Supervised Graph Prototypical Networks for Hyperspectral Image Classification, IGARSS, 2021. Bobo Xi, Jiaojiao Li, Yunsong Li and Qian Du. Code f
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.
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
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
[MICCAI'20] AlignShift: Bridging the Gap of Imaging Thickness in 3D Anisotropic Volumes
AlignShift NEW: Code for our new MICCAI'21 paper "Asymmetric 3D Context Fusion for Universal Lesion Detection" will also be pushed to this repository
SCICO is a Python package for solving the inverse problems that arise in scientific imaging applications.
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]
Dense Deep Unfolding Network with 3D-CNN Prior for Snapshot Compressive Imaging, ICCV2021 [PyTorch Code]
The friendly PIL fork (Python Imaging Library)
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
Python wrappers for external BART computational imaging tools and internal libraries
bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo
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