Python Biomedical-imaging Resources

Small Lesion Segmentation in Brain MRIs with Subpixel Embedding PyTorch implementation of Small Lesion Segmentation in Brain MRIs with Subpixel Embedd

AlignShift NEW: Code for our new MICCAI'21 paper "Asymmetric 3D Context Fusion for Universal Lesion Detection" will also be pushed to this repository

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]

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

BioLAMA BioLAMA is biomedical factual knowledge triples for probing biomedical LMs. The triples are collected and pre-processed from three sources: CT

MVGCN MVGCN: a novel multi-view graph convolutional network (MVGCN) framework for link prediction in biomedical bipartite networks. Developer: Fu Hait

bartpy Python bindings for BART. Overview This repo contains code to generate an updated Python wrapper for the Berkeley Advance Reconstruction Toolbo

Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN

Mask-RCNN on Mycobacterium tuberculosis This is an example of object detection on Mycobacterium Tuberculosis using Mask RCNN. Implement of Mask R-CNN

WobblyStitcher Introduction A scalable implementation of WobblyStitcher Dependencies $ python -m pip install numpy scikit-image Visualization ImageJ

Medical image preprocessing and augmentation toolkit for deep learning. Part of the PyTorch Ecosystem.

Named Entity Recognition with Small Strongly Labeled and Large Weakly Labeled Data arXiv This is the code base for weakly supervised NER. We provide a

News The code of MCTrans has been released. if you are interested in contributing to the standardization of the medical image analysis community, plea

ml4h is a toolkit for machine learning on clinical data of all kinds including genetics, labs, imaging, clinical notes, and more

Deep Optics for Single-shot High-dynamic-range Imaging Code associated with the paper "Deep Optics for Single-shot High-dynamic-range Imaging" CVPR, 2

NCRF Prerequisites Data Whole slide images Annotations Patch images Model Training Testing Tissue mask Probability map Tumor localization FROC evaluat

Deep Neural Networks Improve Radiologists' Performance in Breast Cancer Screening Introduction This is an implementation of the model used for breast

Adaptive Segmentation Mask Attack This repository contains the implementation of the Adaptive Segmentation Mask Attack (ASMA), a targeted adversarial

UNet for segmenting salt deposits from seismic images with PyTorch. General We, tugstugi and xuyuan, have participated in the Kaggle competition TGS S

The Medical Detection Toolkit contains 2D + 3D implementations of prevalent object detectors such as Mask R-CNN, Retina Net, Retina U-Net, as well as a training and inference framework focused on dealing with medical images.

U Net Lowered with Keras Complete U-net Implementation with keras Original Paper Link : https://arxiv.org/abs/1505.04597 Special Implementations : The

What is nnDetection? Simultaneous localisation and categorization of objects in medical images, also referred to as medical object detection, is of hi

LMs for biomedical KG completion This repository contains code to run the experiments described in: Scientific Language Models for Biomedical Knowledg

English | 中文说明 CBLUE AI (Artificial Intelligence) is playing an indispensabe role in the biomedical field, helping improve medical technology. For fur

SumGNN: Multi-typed Drug Interaction Prediction via Efficient Knowledge Graph Summarization This is the code for our paper ``SumGNN: Multi-typed Drug

MultiResUNet Rethinking the U-Net architecture for multimodal biomedical image segmentation This repository contains the original implementation of "M

Trove Trove is a research framework for building weakly supervised (bio)medical named entity recognition (NER) and other entity attribute classifiers

Welcome to MedicalTorch MedicalTorch is an open-source framework for PyTorch, implementing an extensive set of loaders, pre-processors and datasets fo

Cornell Biomedical Knowledge Hub (CBKH) CBKG integrates data from 18 publicly available biomedical databases. The current version of CBKG contains a t

CheXbert: Combining Automatic Labelers and Expert Annotations for Accurate Radiology Report Labeling Using BERT CheXbert is an accurate, automated dee

Domain Generalization for Medical Imaging Classification with Linear Dependency Regularization The code release of paper 'Domain Generalization for Me

InVesalius InVesalius generates 3D medical imaging reconstructions based on a sequence of 2D DICOM files acquired with CT or MRI equipments. InVesaliu

Medical-Transformer Pytorch Code for the paper "Medical Transformer: Gated Axial-Attention for Medical Image Segmentation" About this repo: This repo

Meshroom is a free, open-source 3D Reconstruction Software based on the AliceVision Photogrammetric Computer Vision framework. Learn more details abou

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

This repository contains custom pipes and models related to using spaCy for scientific documents. In particular, there is a custom tokenizer that adds

Documentation: https://raamana.github.io/neuropredict/ News As of v0.6, neuropredict now supports regression applications i.e. predicting continuous t

nilearn Nilearn enables approachable and versatile analyses of brain volumes. It provides statistical and machine-learning tools, with instructive doc

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