A flexible ML framework built to simplify medical image reconstruction and analysis experimentation.

Overview

meddlr

Getting Started

Meddlr is a config-driven ML framework built to simplify medical image reconstruction and analysis problems.

Installation

To avoid cuda-related issues, downloading torch, torchvision, and cupy (optional) must be done prior to downloading other requirements.

# Create and activate the environment.
conda create -n meddlr_env python=3.7
conda activate meddlr_env

# Install cuda-dependant libraries. Change cuda version as needed.
# Below we show examples for cuda-10.1
conda install pytorch torchvision cudatoolkit=10.1 -c pytorch
pip install cupy-cuda101

# Install as package in virtual environment (recommended):
git clone https://github.com/ad12/meddlr.git
cd dl-ss-recon && python -m pip install -e '.[dev]'

# For all contributors, install development packages.
make dev

Contributing

See CONTRIBUTING.md for more information.

Acknowledgements

Meddlr's design for rapid experimentation and benchmarking is inspired by detectron2.

About

If you use Meddlr for your work, please consider citing the following work:

@article{desai2021noise2recon,
  title={Noise2Recon: A Semi-Supervised Framework for Joint MRI Reconstruction and Denoising},
  author={Desai, Arjun D and Ozturkler, Batu M and Sandino, Christopher M and Vasanawala, Shreyas and Hargreaves, Brian A and Re, Christopher M and Pauly, John M and Chaudhari, Akshay S},
  journal={arXiv preprint arXiv:2110.00075},
  year={2021}
}
Owner
Arjun Desai
Arjun Desai
Yolox-bytetrack-sample - Python sample of MOT (Multiple Object Tracking) using YOLOX and ByteTrack

yolox-bytetrack-sample YOLOXとByteTrackを用いたMOT(Multiple Object Tracking)のPythonサン

KazuhitoTakahashi 12 Nov 09, 2022
Yolov5 deepsort inference,使用YOLOv5+Deepsort实现车辆行人追踪和计数,代码封装成一个Detector类,更容易嵌入到自己的项目中

使用YOLOv5+Deepsort实现车辆行人追踪和计数,代码封装成一个Detector类,更容易嵌入到自己的项目中。

813 Dec 31, 2022
INSPIRED: A Transparent Dialogue Dataset for Interactive Semantic Parsing

INSPIRED: A Transparent Dialogue Dataset for Interactive Semantic Parsing Existing studies on semantic parsing focus primarily on mapping a natural-la

7 Aug 22, 2022
A library for differentiable nonlinear optimization.

Theseus A library for differentiable nonlinear optimization built on PyTorch to support constructing various problems in robotics and vision as end-to

Meta Research 1.1k Dec 30, 2022
An algorithm study of the 6th iOS 10 set of Boost Camp Web Mobile

알고리즘 스터디 🔥 부스트캠프 웹모바일 6기 iOS 10조의 알고리즘 스터디 입니다. 개인적인 사정 등으로 S034, S055만 참가하였습니다. 스터디 목적 상진: 코테 합격 + 부캠끝나고 아침에 일어나기 위해 필요한 사이클 기완: 꾸준하게 자리에 앉아 공부하기 +

2 Jan 11, 2022
BossNAS: Exploring Hybrid CNN-transformers with Block-wisely Self-supervised Neural Architecture Search

BossNAS This repository contains PyTorch evaluation code, retraining code and pretrained models of our paper: BossNAS: Exploring Hybrid CNN-transforme

Changlin Li 127 Dec 26, 2022
Pytorch Geometric Tutorials

Pytorch Geometric Tutorials

Antonio Longa 648 Jan 08, 2023
Convolutional Neural Network for Text Classification in Tensorflow

This code belongs to the "Implementing a CNN for Text Classification in Tensorflow" blog post. It is slightly simplified implementation of Kim's Convo

Denny Britz 5.5k Jan 02, 2023
2D Human Pose estimation using transformers. Implementation in Pytorch

PE-former: Pose Estimation Transformer Vision transformer architectures perform very well for image classification tasks. Efforts to solve more challe

Panteleris Paschalis 23 Oct 17, 2022
SpecAugmentPyTorch - A Pytorch (support batch and channel) implementation of GoogleBrain's SpecAugment: A Simple Data Augmentation Method for Automatic Speech Recognition

SpecAugment An implementation of SpecAugment for Pytorch How to use Install pytorch, version=1.9.0 (new feature (torch.Tensor.take_along_dim) is used

IMLHF 3 Oct 11, 2022
Python版OpenCVのTracking APIのサンプルです。DaSiamRPNアルゴリズムまで対応しています。

OpenCV-Object-Tracker-Sample Python版OpenCVのTracking APIのサンプルです。   Requirement opencv-contrib-python 4.5.3.56 or later Algorithm 2021/07/16時点でOpenCVには以

KazuhitoTakahashi 36 Jan 01, 2023
Machine learning for NeuroImaging in Python

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

919 Dec 25, 2022
Nsdf: A mesh SDF with just some code we can directly paste into our raymarcher

nsdf Representing SDFs of arbitrary meshes has been a bit tricky so far. Express

Jan Ivanecky 5 Feb 18, 2022
WormMovementSimulation - 3D Simulation of Worm Body Movement with Neurons attached to its body

Generate 3D Locomotion Data This module is intended to create 2D video trajector

1 Aug 09, 2022
A curated list of awesome Machine Learning frameworks, libraries and software.

Awesome Machine Learning A curated list of awesome machine learning frameworks, libraries and software (by language). Inspired by awesome-php. If you

Joseph Misiti 57.1k Jan 03, 2023
Examples of how to create colorful, annotated equations in Latex using Tikz.

The file "eqn_annotate.tex" is the main latex file. This repository provides four examples of annotated equations: [example_prob.tex] A simple one ins

SyNeRCyS Research Lab 3.2k Jan 05, 2023
Transformer Huffman coding - Complete Huffman coding through transformer

Transformer_Huffman_coding Complete Huffman coding through transformer 2022/2/19

3 May 19, 2022
a minimal terminal with python 😎😉

Meterm a terminal with python 😎 How to use Clone Project: $ git clone https://github.com/motahharm/meterm.git Run: in Terminal: meterm.exe Or pip ins

Motahhar.Mokfi 5 Jan 28, 2022
This repository contains the segmentation user interface from the OpenSurfaces project, extracted as a lightweight tool

OpenSurfaces Segmentation UI This repository contains the segmentation user interface from the OpenSurfaces project, extracted as a lightweight tool.

Sean Bell 66 Jul 11, 2022
Code for ICLR2018 paper: Improving GAN Training via Binarized Representation Entropy (BRE) Regularization - Y. Cao · W Ding · Y.C. Lui · R. Huang

code for "Improving GAN Training via Binarized Representation Entropy (BRE) Regularization" (ICLR2018 paper) paper: https://arxiv.org/abs/1805.03644 G

21 Oct 12, 2020