Deep learning image registration library for PyTorch

Related tags

Deep LearningTorchIR
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
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

Dan Gale 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

Mohamed El Banani 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

MaZderMind 17 Oct 5, 2022
the code of the paper: Recurrent Multi-view Alignment Network for Unsupervised Surface Registration (CVPR 2021)
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

Wanquan Feng 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

sfwang 70 Dec 19, 2022
MVP Benchmark for Multi-View Partial Point Cloud Completion and Registration
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

PL 93 Dec 21, 2022
A robust pointcloud registration pipeline based on correlation.
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

ETHZ ASL 101 Dec 1, 2022
Compute descriptors for 3D point cloud registration using a multi scale sparse voxel architecture
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

null 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

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

Haiping Wang 80 Dec 15, 2022
Comments
  • Rigid Transformation are not defined in RigidIRNet

    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

    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

    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

    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)
Owner
Bob de Vos
Bob de Vos
GitHub Repository
codes for "Scheduled Sampling Based on Decoding Steps for Neural Machine Translation" (long paper of EMNLP-2022)

Scheduled Sampling Based on Decoding Steps for Neural Machine Translation (EMNLP-2021 main conference) Contents Overview Background Quick to Use Furth

Adaxry 13 Jul 25, 2022
Seeing if I can put together an interactive version of 3b1b's Manim in Streamlit

streamlit-manim Seeing if I can put together an interactive version of 3b1b's Manim in Streamlit Installation I had to install pango with sudo apt-get

Adrien Treuille 6 Aug 03, 2022
Data and code for the paper "Importance of Kernel Bandwidth in Quantum Machine Learning"

Reproducibility materials for "Importance of Kernel Bandwidth in Quantum Machine Learning" Repo structure: code contains Python scripts used to genera

Ruslan Shaydulin 3 Oct 23, 2022
Official code for 'Pixel-wise Energy-biased Abstention Learning for Anomaly Segmentationon Complex Urban Driving Scenes'

PEBAL This repo contains the Pytorch implementation of our paper: Pixel-wise Energy-biased Abstention Learning for Anomaly Segmentationon Complex Urba

Yu Tian 115 Dec 29, 2022
Performant, differentiable reinforcement learning

deluca Performant, differentiable reinforcement learning Notes This is pre-alpha software and is undergoing a number of core changes. Updates to follo

Google 114 Dec 27, 2022
This repository contains an implementation of ConvMixer for the ICLR 2022 submission "Patches Are All You Need?".

Patches Are All You Need? 🤷 This repository contains an implementation of ConvMixer for the ICLR 2022 submission "Patches Are All You Need?". Code ov

ICLR 2022 Author 934 Dec 30, 2022
ML-based medical imaging using Azure

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

Microsoft Azure 68 Dec 23, 2022
Pure python implementation reverse-mode automatic differentiation

MiniGrad A minimal implementation of reverse-mode automatic differentiation (a.k.a. autograd / backpropagation) in pure Python. Inspired by Andrej Kar

Kenny Song 76 Sep 12, 2022
Beyond Image to Depth: Improving Depth Prediction using Echoes (CVPR 2021)

Beyond Image to Depth: Improving Depth Prediction using Echoes (CVPR 2021) Kranti Kumar Parida, Siddharth Srivastava, Gaurav Sharma. We address the pr

Kranti Kumar Parida 33 Jun 27, 2022
A PyTorch implementation of "Signed Graph Convolutional Network" (ICDM 2018).

SGCN ⠀ A PyTorch implementation of Signed Graph Convolutional Network (ICDM 2018). Abstract Due to the fact much of today's data can be represented as

Benedek Rozemberczki 251 Nov 30, 2022
Image-Adaptive YOLO for Object Detection in Adverse Weather Conditions

Image-Adaptive YOLO for Object Detection in Adverse Weather Conditions Accepted by AAAI 2022 [arxiv] Wenyu Liu, Gaofeng Ren, Runsheng Yu, Shi Guo, Jia

liuwenyu 245 Dec 16, 2022
Face Depixelizer based on "PULSE: Self-Supervised Photo Upsampling via Latent Space Exploration of Generative Models" repository.

NOTE We have noticed a lot of concern that PULSE will be used to identify individuals whose faces have been blurred out. We want to emphasize that thi

Denis Malimonov 2k Dec 29, 2022
Pythonic particle-based (super-droplet) warm-rain/aqueous-chemistry cloud microphysics package with box, parcel & 1D/2D prescribed-flow examples in Python, Julia and Matlab

PySDM PySDM is a package for simulating the dynamics of population of particles. It is intended to serve as a building block for simulation systems mo

Atmospheric Cloud Simulation Group @ Jagiellonian University 32 Oct 18, 2022
A PyTorch implementation of "Capsule Graph Neural Network" (ICLR 2019).

CapsGNN ⠀⠀ A PyTorch implementation of Capsule Graph Neural Network (ICLR 2019). Abstract The high-quality node embeddings learned from the Graph Neur

Benedek Rozemberczki 1.2k Jan 02, 2023
Earth Vision Foundation

EVer - A Library for Earth Vision Researcher EVer is a Pytorch-based Python library to simplify the training and inference of the deep learning model.

Zhuo Zheng 34 Nov 26, 2022
GLIP: Grounded Language-Image Pre-training

GLIP: Grounded Language-Image Pre-training Updates 12/06/2021: GLIP paper on arxiv https://arxiv.org/abs/2112.03857. Code and Model are under internal

Microsoft 862 Jan 01, 2023
Visualize Camera's Pose Using Extrinsic Parameter by Plotting Pyramid Model on 3D Space

extrinsic2pyramid Visualize Camera's Pose Using Extrinsic Parameter by Plotting Pyramid Model on 3D Space Intro A very simple and straightforward modu

JEONG HYEONJIN 106 Dec 28, 2022
KITTI-360 Annotation Tool is a framework that developed based on python(cherrypy + jinja2 + sqlite3) as the server end and javascript + WebGL as the front end.

KITTI-360 Annotation Tool is a framework that developed based on python(cherrypy + jinja2 + sqlite3) as the server end and javascript + WebGL as the front end.

86 Dec 12, 2022
On-device wake word detection powered by deep learning.

Porcupine Made in Vancouver, Canada by Picovoice Porcupine is a highly-accurate and lightweight wake word engine. It enables building always-listening

Picovoice 2.8k Dec 29, 2022
ConE: Cone Embeddings for Multi-Hop Reasoning over Knowledge Graphs

ConE: Cone Embeddings for Multi-Hop Reasoning over Knowledge Graphs This is the code of paper ConE: Cone Embeddings for Multi-Hop Reasoning over Knowl

MIRA Lab 33 Dec 07, 2022