Deep learning image registration library for PyTorch

Last update: Dec 16, 2022

Related tags

Overview

TorchIR: Pytorch Image Registration

TorchIR is a image registration library for deep learning image registration (DLIR). I have integrated several ideas for image registration.

The current version lacks a document, but I have included quite a descriptive tutorial using MNIST data as an example. The example experiments are light-weight and should run on any CPU, although running it on a GPU will increase the speed. The notebook contains a tutorial using MNIST data as an example. Although the code runs faster on a GPU, this tutorial is small enough to run on CPU.

For the tutorial I rely on PyTorch Lightning, which can be installed via:

pip install pytorch-lightning

The pytorch-lightning trainer modules automatically create tensorboard log files. I store them in the ./output/lightning_logs directory. Simply inspect them using:

tensorboard --logdir=./output/lightning_logs

If you use this code for your publications, don't forget to cite my work ;)

[1] Bob D. de Vos, Floris F. Berendsen, Max A. Viergever, Marius Staring and Ivana Išgum, "End-to-end unsupervised deformable image registration with a convolutional neural network," in Deep learning in medical image analysis and multimodal learning for clinical decision support. Springer, Cham, 2017. p. 204-212, doi: 10.1007/978-3-319-67558-9_24 https://link.springer.com/chapter/10.1007%2F978-3-319-67558-9_24

[2] Bob D. de Vos, Floris F. Berendsen, Max A. Viergever, Hessam Sokooti, Marius Staring and Ivana Išgum "A deep learning framework for unsupervised affine and deformable image registration," Medical image analysis, vol. 52, pp. 128-143, Feb. 2019, doi: 10.1016/j.media.2018.11.010 https://www.sciencedirect.com/science/article/pii/S1361841518300495

Please note that the code is still under heavy development and I'd really love your input.

You might also like...

Python implementation of Wu et al (2018)'s registration fusion

reg-fusion Projection of a central sulcus probability map using the RF-ANTs approach (right hemisphere shown). This is a Python implementation of Wu e

26 Nov 12, 2021

UnsupervisedR&R: Unsupervised Pointcloud Registration via Differentiable Rendering

UnsupervisedR&R: Unsupervised Pointcloud Registration via Differentiable Rendering This repository holds all the code and data for our recent work on

118 Dec 6, 2022

Python Implementation of the CoronaWarnApp (CWA) Event Registration

Python implementation of the Corona-Warn-App (CWA) Event Registration This is an implementation of the Protocol used to generate event and location QR

17 Oct 5, 2022

the code of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021)

RMA-Net This repo is the implementation of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021). Paper

205 Nov 9, 2022

[CVPR'21] Locally Aware Piecewise Transformation Fields for 3D Human Mesh Registration

Locally Aware Piecewise Transformation Fields for 3D Human Mesh Registration This repository contains the implementation of our paper Locally Aware Pi

70 Dec 19, 2022

MVP Benchmark for Multi-View Partial Point Cloud Completion and Registration

MVP Benchmark: Multi-View Partial Point Clouds for Completion and Registration [NEWS] 2021-07-12 [NEW 🎉 ] The submission on Codalab starts! 2021-07-1

93 Dec 21, 2022

A robust pointcloud registration pipeline based on correlation.

PHASER: A Robust and Correspondence-Free Global Pointcloud Registration Ubuntu 18.04+ROS Melodic: Overview Pointcloud registration using correspondenc

101 Dec 1, 2022

Compute descriptors for 3D point cloud registration using a multi scale sparse voxel architecture

MS-SVConv : 3D Point Cloud Registration with Multi-Scale Architecture and Self-supervised Fine-tuning Compute features for 3D point cloud registration

42 Jul 25, 2022

You Only Hypothesize Once: Point Cloud Registration with Rotation-equivariant Descriptors

You Only Hypothesize Once: Point Cloud Registration with Rotation-equivariant Descriptors In this paper, we propose a novel local descriptor-based fra

80 Dec 15, 2022

Comments

Rigid Transformation are not defined in RigidIRNet

Respected, Kindly, provide the solution, how to create the class of Rigid transformer in transformer.py. Create the class of RigidIRNet in "https://github.com/BDdeVos/TorchIR/blob/main/torchir/networks/globalnet.py" .

Thanks.

opened by Paluck1Arora2 0
No networks Module on PyPi

PyPi Package torchir==0.1 Does Not Include Networks Package Reproduce: pip3 install torchir in python: from torchir.networks.globalnet import ConvBlock

opened by pweibert 0
Using color images as input for the network

Hello,

I am trying to adapt your work for the alignment of ophthalmological retina images using 3-channel color images. Which changes are necessary to use the framework for this kind of data?

Kind regards and thanks for your work on image registration!

opened by AgenoDrei 0
Rigid transformation parameters not equal

Hi, I used torchio to generate some moved 3d image ,which by applying the translation(pixelwise) and rotation(degree) to the still image(without motion), and use the network RigidIRNet to estimate this translation and rotation parameter.

Then I found that although the NCC loss are decreased and the warped image is acceptable, the estimated parameter have a big different compared with the one that I appied beforehand.

May I ask why is the issue for this weird situation ?

opened by jeremysong1106 0

Releases(version_01)

version_01(Nov 15, 2021)

Source code(tar.gz)
Source code(zip)

Owner

Bob de Vos

GitHub Repository

Measures input lag without dedicated hardware, performing motion detection on recorded or live video

What is InputLagTimer? This tool can measure input lag by analyzing a video where both the game controller and the game screen can be seen on a webcam

4 Aug 18, 2022

Codes for ACL-IJCNLP 2021 Paper "Zero-shot Fact Verification by Claim Generation"

Zero-shot-Fact-Verification-by-Claim-Generation This repository contains code and models for the paper: Zero-shot Fact Verification by Claim Generatio

47 Jan 01, 2023

CityLearn Challenge Multi-Agent Reinforcement Learning for Intelligent Energy Management, 2020, PikaPika team

Citylearn Challenge This is the PyTorch implementation for PikaPika team, CityLearn Challenge Multi-Agent Reinforcement Learning for Intelligent Energ

10 Oct 10, 2022

Price-Prediction-For-a-Dream-Home - A machine learning based linear regression trained model for house price prediction.

Price-Prediction-For-a-Dream-Home ROADMAP TO THIS LINEAR REGRESSION BASED HOUSE PRICE PREDICTION PREDICTION MODEL Import all the dependencies of the p

1 Dec 29, 2021

InterFaceGAN - Interpreting the Latent Space of GANs for Semantic Face Editing

InterFaceGAN - Interpreting the Latent Space of GANs for Semantic Face Editing Figure: High-quality facial attributes editing results with InterFaceGA

1.3k Jan 09, 2023

Code for unmixing audio signals in four different stems "drums, bass, vocals, others". The code is adapted from "Jukebox: A Generative Model for Music"

Status: Archive (code is provided as-is, no updates expected) Disclaimer This code is a based on "Jukebox: A Generative Model for Music" Paper We adju

24 Dec 29, 2022

Deep learning image registration library for PyTorch

Related tags

Overview

TorchIR: Pytorch Image Registration

You might also like...

Python implementation of Wu et al (2018)'s registration fusion

UnsupervisedR&R: Unsupervised Pointcloud Registration via Differentiable Rendering

Python Implementation of the CoronaWarnApp (CWA) Event Registration

the code of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021)

[CVPR'21] Locally Aware Piecewise Transformation Fields for 3D Human Mesh Registration

MVP Benchmark for Multi-View Partial Point Cloud Completion and Registration

A robust pointcloud registration pipeline based on correlation.

Compute descriptors for 3D point cloud registration using a multi scale sparse voxel architecture

You Only Hypothesize Once: Point Cloud Registration with Rotation-equivariant Descriptors

Comments

Rigid Transformation are not defined in RigidIRNet

No networks Module on PyPi

Using color images as input for the network

Rigid transformation parameters not equal

Releases(version_01)

version_01(Nov 15, 2021)

Owner

Bob de Vos

Measures input lag without dedicated hardware, performing motion detection on recorded or live video

Codes for ACL-IJCNLP 2021 Paper "Zero-shot Fact Verification by Claim Generation"

CityLearn Challenge Multi-Agent Reinforcement Learning for Intelligent Energy Management, 2020, PikaPika team

Price-Prediction-For-a-Dream-Home - A machine learning based linear regression trained model for house price prediction.

InterFaceGAN - Interpreting the Latent Space of GANs for Semantic Face Editing

Code for unmixing audio signals in four different stems "drums, bass, vocals, others". The code is adapted from "Jukebox: A Generative Model for Music"

Multi Agent Path Finding Algorithms

Evaluation and Benchmarking of Speech Super-resolution Methods

Real-time VIBE: Frame by Frame Inference of VIBE (Video Inference for Human Body Pose and Shape Estimation)

Cartoon-StyleGan2 🙃 : Fine-tuning StyleGAN2 for Cartoon Face Generation

Non-stationary GP package written from scratch in PyTorch

This is official implementaion of paper "Token Shift Transformer for Video Classification".

Python Algorithm Interview Book Review

The repository contain code for building compiler using puthon.

Python framework for Stochastic Differential Equations modeling

Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering

Realtime micro-expression recognition using OpenCV and PyTorch

A large-scale video dataset for the training and evaluation of 3D human pose estimation models

My published benchmark for a Kaggle Simulations Competition

An implementation of the efficient attention module.