Python Biomedical-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

LinkBERT: A Knowledgeable Language Model Pretrained with Document Links This repo provides the model, code & data of our paper: LinkBERT: Pretraining

SOFIMA SOFIMA (Scalable Optical Flow-based Image Montaging and Alignment) is a tool for stitching, aligning and warping large 2d, 3d and 4d microscopy

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

SciFive SciFive provided a Text-Text framework for biomedical language and natural language in NLP. Under the T5's framework and desrbibed in the pape

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

Hyper-Convolution Networks for Biomedical Image Segmentation Code for our WACV 2022 paper "Hyper-Convolution Networks for Biomedical Image Segmentatio

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 (

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

This is a Kaggle competition in which we have to identify if the given lesion image is malignant or not for Melanoma which is a type of skin cancer.

GreaseLM: Graph REASoning Enhanced Language Models This repo provides the source code & data of our paper "GreaseLM: Graph REASoning Enhanced Language

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

STonKGs STonKGs is a Sophisticated Transformer that can be jointly trained on biomedical text and knowledge graphs. This multimodal Transformer combin

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

Biomedical Entity Linking This repo provides the code for the paper BERT might be Overkill: A Tiny but Effective Biomedical Entity Linker based on Res

A set of Python codes for the generation of biomedical ontologies from the MeSH keywords of the PubMed scholarly publications

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.

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by

Machine Learning use case in the field of Healthcare. In this project MONAI and pytorch frameworks are used for 3D Liver segmentation.

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization), a tool that improves the previous neural network-based NER tool by

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

BERN2 We present BERN2 (Advanced Biomedical Entity Recognition and Normalization

ehtim (eht-imaging) Python modules for simulating and manipulating VLBI data and producing images with regularized maximum likelihood methods. This ve

U-Net Implementation By Christopher Ley This is my interpretation and implementation of the famous paper "U-Net: Convolutional Networks for Biomedical

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

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

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

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

BT-Unet: A-Self-supervised-learning-framework-for-biomedical-image-segmentation-using-Barlow-Twins Deep learning has brought most profound contributio

Robust Place Recognition using an Imaging Lidar A place recognition package using high-resolution imaging lidar. For best performance, a lidar equippe

A toolkit for computational pathology and machine learning. View documentation Please cite our paper Installation There are several ways to install Pa

Simulation of moving particles under microscopic imaging Install scipy numpy scikit-image tiffile Run python simulation.py Read result https://imagej

CBio-NAMER CBioNAMER (Nested nAMed Entity Recognition for Chinese Biomedical Text) is our method used in CBLUE (Chinese Biomedical Language Understand

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

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

Tools for curating biomedical training data for large-scale language modeling

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

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

Introduction The field of connectomics aims to reconstruct the wiring diagram of the brain by mapping the neural connections at the level of individua

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

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

RobustBioNLP Improving the robustness and performance of biomedical NLP models through adversarial training In this repository you can find suppliment

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

Medical Image Segmentation with Guided Attention This repository contains the code of our paper: "'Multi-scale self-guided attention for medical image

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

Flexible-CLmser: Regularized Feedback Connections for Biomedical Image Segmentation The skip connections in U-Net pass features from the levels of enc

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

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

waltlabtools A collection of tools for biomedical research assay analysis in Python. Key Features Analysis for assays such as digital ELISA, including

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

BMVC 2021 BI-GConv: Boundary-Aware Input-Dependent Graph Convolution for Biomedical Image Segmentation Necassary Dependencies: PyTorch 1.2.0 Python 3.

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

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

Kimimaro: Skeletonize Densely Labeled Images # Produce SWC files from volumetric images. kimimaro forge labels.npy --progress # writes to ./kimimaro_o

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

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