Python Structural-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

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

Molecular Nodes 🧬 🔬 💻 Buy Me a Coffee to Keep Development Going! Join a Community of Blender SciVis People! What is Molecular Nodes? Molecular Node

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

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.

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 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

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 (

This repository contains the code for TABS, a 3D CNN-Transformer hybrid automated brain tissue segmentation algorithm using T1w structural MRI scans. TABS relies on a Res-Unet backbone, with a Vision Transformer embedded between the encoder and decoder layers.

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

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

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 Dependencies numpy==1.18.5 scikit_image==0.16.2 torchvision==0.8.1 torch==1.7.0 runstats==1.8.0 p

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

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

package tests docs license stats support This repository contains FEDOT - an open-source framework for automated modeling and machine learning (AutoML

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

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.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.

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

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

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

A collection of graph classification methods, covering embedding, deep learning, graph kernel and factorization papers

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

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

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

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

VolumeGAN - 3D-aware Image Synthesis via Learning Structural and Textural Representations 3D-aware Image Synthesis via Learning Structural and Textura

script-SV-genotyping These are the scripts used for the project of ‘Assembly of a pan-genome for global cattle reveals missing sequence and novel stru

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

An easy to use elastic 3D structural engineering finite element analysis library for Python.

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

CCasGNN A new framework, collaborative cascade prediction based on graph neural networks (CCasGNN) to jointly utilize the structural characteristics,

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

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

slientruss3d : Python for stable truss analysis tool Desciption slientruss3d is a python package which can solve the resistances, internal forces and

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

Structural Guidance for Transformer Language Models This repository accompanies the paper, Structural Guidance for Transformer Language Models, publis

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

structural-probes Codebase for testing whether hidden states of neural networks encode discrete structures. Based on the paper A Structural Probe for

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

LexPOS_ko Generating Korean Slogans with phonetic and structural repetition Generating Slogans with Linguistic Features LexPOS is a sequence-to-sequen

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

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

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

ShallowSeismicImaging Tools to imaging the shallow seismic structure, above 10 km, based on the ZH ratio measured from the ambient seismic noise, and

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

===================================== README: Inpainting based PatchMatch ===================================== @Author: Younesse ANDAM @Conta

AOS: Airborne Optical Sectioning Airborne Optical Sectioning (AOS) is a wide synthetic-aperture imaging technique that employs manned or unmanned airc

counterfactual-tpp This is a repository containing code and real data for the paper Counterfactual Temporal Point Processes. Pre-requisites This code

Python Causal Impact Causal inference using Bayesian structural time-series models. This package aims at defining a python equivalent of the R CausalI

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

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

Sparse deconvolution Python v0.3.0 Official Python implementation of the 'Sparse deconvolution', and the CPU (NumPy) and GPU (CuPy) calculation backen

3DFEM Python 3D finite element code This python code allows for solving 3D structural problems using the finite element method. New features will be a

NLOS-OT Official implementation of NLOS-OT: Passive Non-Line-of-Sight Imaging Using Optimal Transport (IEEE TIP, accepted) Description In this reposit

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 Dongdong Chen, Julián Tachella, Mike E. Davi

AlphaFold Analyser This program produces high quality visualisations of predicted structures produced by AlphaFold. These visualisations allow the use

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

fly2p Tools for analyzing two-photon (2p) imaging data collected with Vidrio Scanimage software and micromanger. Loading scanimage data relies on scan

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) This repo contains the full NITRATES pipeline for maximum likelihood-driven discov

Structural Constraints on Information Content in Human Brain States Code accompanying the paper "The information content of brain states is explained

xtbreak estimating and testing for many known and unknown structural breaks in time series and panel data. For an overview of xtbreak test see xtbreak

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

ngEHTexplorer An interactive tool with which to explore the possible imaging performance of candidate ngEHT architectures. Welcome! ngEHTexplorer is a

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

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

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

Role-based network embedding via structural features reconstruction with degree-regularized constraint Train python main.py --dataset brazil-flights

starfish: scalable pipelines for image-based transcriptomics starfish is a Python library for processing images of image-based spatial transcriptomics

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

Graph Neural Networks with Learnable Structural and Positional Representations Source code for the paper "Graph Neural Networks with Learnable Structu

PurNet Project for the TIP 2021 Paper "Salient Object Detection with Purificatory Mechanism and Structural Similarity Loss" Abstract Image-based salie

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)

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