Python Computational-imaging Resources

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

nbsafety adds a layer of protection to computational notebooks by solving the stale dependency problem when executing cells out-of-order

Rotapy Purpose Generate Gaussian 09 input files for the rotamers of an input compound. Distance to the axis of rotation remains constant throughout th

freud Overview The freud Python library provides a simple, flexible, powerful set of tools for analyzing trajectories obtained from molecular dynamics

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

POS-Tagger This repository details the creation of a Part-of-Speech tagger using Trigram Hidden Markov Models to predict word tags in a word sequence.

This package is a python library with tools for the Molecular Simulation - Software Gromos. It allows you to easily set up, manage and analyze simulations in python.

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

Documentation redrawing Python package provinding tools for artistic interactive applications using AI Created by ReDrawing Campinas team for the Open

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

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,

DQC: Differentiable Quantum Chemistry Differentiable quantum chemistry package. Currently only support differentiable density functional theory (DFT)

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

feature-set-comp Compares various time-series feature sets on computational performance, within-set structure, and between-set relationships. Reposito

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

Mathematical modeling is a powerful method for the analysis of complex biological systems. Although there are many researches devoted on produ

pyHype: Computational Fluid Dynamics in Python pyHype is a Python framework for developing parallelized Computational Fluid Dynamics software to solve

MaD GUI Machine Learning and Data Analytics Graphical User Interface MaD GUI is a basis for graphical annotation and computational analysis of time se

MONAI Deploy App SDK offers a framework and associated tools to design, develop and verify AI-driven applications in the healthcare imaging domain.

MUSCO - Multimodal Descriptions of Social Concepts Automatic Modeling of (Highly Abstract) Social Concepts evoked by Art Images This project aims to i

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

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

CS 506 - Computational Tools for Data Science Code, slides, and notes for Boston University CS506 Fall 2021 The Final Project Repository can be found

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

nlcc Install pip install nlcc Must have Open-AI Codex key: export OPENAI_API_KEY=your key here then nlcc key bindings ctrl-w copy to clipboard (Note

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.

MolEncoder Molecular AutoEncoder in PyTorch Install $ git clone https://github.com/cxhernandez/molencoder.git && cd molencoder $ python setup.py insta

Contrastive Learning of Object Representations Supervisor: Prof. Dr. Gemma Roig Institutions: Goethe University CVAI - Computational Vision & Artifici

Hello 🤟 #Team-Greider The team of 20 people for HackBio'2021 Virtual Bioinformatics Internship 💝 🖨️ 👨‍💻 HackBio: https://thehackbio.com 💬 Ask us

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

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.

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

XL-Sum This repository contains the code, data, and models of the paper titled "XL-Sum: Large-Scale Multilingual Abstractive Summarization for 44 Lang

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

JittorVis - Visual understanding of deep learning model.

House-GAN++ Code and instructions for our paper: House-GAN++: Generative Adversarial Layout Refinement Network towards Intelligent Computational Agent

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

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

PICCL: Philosophical Integrator of Computational and Corpus Libraries PICCL offers a workflow for corpus building and builds on a variety of tools. Th

ReproZip ReproZip is a tool aimed at simplifying the process of creating reproducible experiments from command-line executions, a frequently-used comm

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

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

cochlea cochlea is a collection of inner ear models. All models are easily accessible as Python functions. They take sound signal as input and return

YouTokenToMe YouTokenToMe is an unsupervised text tokenizer focused on computational efficiency. It currently implements fast Byte Pair Encoding (BPE)

Scattertext 0.1.0.0 A tool for finding distinguishing terms in corpora and displaying them in an interactive HTML scatter plot. Points corresponding t

Colibri Core by Maarten van Gompel, [email protected], Radboud University Nijmegen Licensed under GPLv3 (See http://www.gnu.org/licenses/gpl-3.0.html

Ucto for Python This is a Python binding to the tokeniser Ucto. Tokenisation is one of the first step in almost any Natural Language Processing task,

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