Python Brain-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

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

An open software package to develop BCI based brain and cognitive computing technology for recognizing user's intention using deep learning

Brain-Tumor-Detection Building a detection model using a convolutional neural network in Tensorflow & Keras. Used brain MRI images. InceptionResNetV2

The easiest way to the neuroscience world with the shield for RaspberryPi - PIEEG (website). Open-source. Crowdsupply This project is the result of se

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

Recovering-Brain-Structure-Network-Using-Functional-Connectivity Framework: Papers: This repository provides a PyTorch implementation of the models ad

Detect and Classify Brain Tumor using CNN. A system performing detection and classification by using Deep Learning Algorithms using Convolution-Neural Network (CNN).

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

Brain Weight in Humans Variations of head sizes and brain weights in humans Kaggle dataset obtained from this link by Anubhab Swain. Image obtained fr

Organic Alkalinity Sausage Machine A Python toolbox to churn out organic alkalinity calculations with minimal brain engagement. Getting started To mak

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

Deep Learning on SDF for Classifying Brain Biomarkers To reproduce the results f

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

Brain-Tumor-Detection A convolutional neural network model built with Tensorflow & Keras to detect brain tumor and its different variants. Data of the

Brain-Tumor-Classification-with-MRI VGG16 model-based classification project about brain tumor detection. First, you can check what people are doing o

BRATS 2021 Solution For Segmentation Task This repo contains the supported pytorch code and configuration files to reproduce 3D medical image segmenta

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.

Google Brain - Ventilator Pressure Prediction https://www.kaggle.com/c/ventilator-pressure-prediction The ventilator data used in this competition was

BCI-ToolBox 1. Introduction BCI-ToolBox is deep learning pipeline for motor-imagery classification. This repo contains five models: ShallowConvNet, De

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

Brain-Inspired Replay A PyTorch implementation of the continual learning experiments with deep neural networks described in the following paper: Brain

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

BraTS(Brain Tumour Segmentation) using V-Net This project is an approach to dete

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

Allen Institute Visual Behavior Analysis package This repository contains code for analyzing behavioral data from the Allen Brain Observatory: Visual

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

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

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

Winning submission to the 2021 Brain Tumor Segmentation Challenge This repo contains the codes and pretrained weights for the winning submission to th

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

Winning submission to the 2021 Brain Tumor Segmentation Challenge This repo contains the codes and pretrained weights for the winning submission to th

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

Graph WaveNet for brain network analysis This is the implementation of the Graph WaveNet model used in our manuscript: S. Wein , A. Schüller, A. M. To

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

WaveGrad Implementation (PyTorch) of Google Brain's high-fidelity WaveGrad vocoder (paper). First implementation on GitHub with high-quality generatio

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

Multi-template MRI mouse brain atlas (both in vivo and ex vivo) Mouse Brain MRI atlas (both in-vivo and ex-vivo) (repository relocated from the origin

Can fMRI reveal the representation of syntactic structure in the brain? The code base for our paper on understanding syntactic representations in the

Deep Neural Mouse Brain Modeling This is the repository for the ongoing deep neural mouse modeling project, an attempt to characterize the representat

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

Python asymptotic Partial Directed Coherence and Directed Coherence estimation package for brain connectivity analysis. Free software: MIT license Doc

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

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

pyRiemann pyRiemann is a python package for covariance matrices manipulation and classification through Riemannian geometry. The primary target is cla

py_neuromodulation Click this button to run the "Tutorial ML with py_neuro" notebooks: The py_neuromodulation toolbox allows for real time capable pro

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

JBHI-Pytorch This repository contains a reference implementation of the algorithms described in our paper "Self-supervised Multi-modal Hybrid Fusion N

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

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

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

Brain-Image-Segmentation Segmentation of brain tissues in MRI image has a number of applications in diagnosis, surgical planning, and treatment of bra

Equivariant Imaging: Learning Beyond the Range Space Equivariant Imaging: Learning Beyond the Range Space Dongdong Chen, Julián Tachella, Mike E. Davi

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

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 This README file contains the following sections: Project description Repository

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

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