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
Automatic labeling, conversion of different data set formats, sample size statistics, model cascade

Simple Gadget Collection for Object Detection Tasks Automatic image annotation Conversion between different annotation formats Obtain statistical info

llt 4 Aug 24, 2022
TrackFormer: Multi-Object Tracking with Transformers

TrackFormer: Multi-Object Tracking with Transformers This repository provides the official implementation of the TrackFormer: Multi-Object Tracking wi

Tim Meinhardt 321 Dec 29, 2022
Implementing Graph Convolutional Networks and Information Retrieval Mechanisms using pure Python and NumPy

Implementing Graph Convolutional Networks and Information Retrieval Mechanisms using pure Python and NumPy

Noah Getz 3 Jun 22, 2022
Code and data for "TURL: Table Understanding through Representation Learning"

TURL This Repo contains code and data for "TURL: Table Understanding through Representation Learning". Environment and Setup Data Pretraining Finetuni

SunLab-OSU 63 Nov 23, 2022
Modification of convolutional neural net "UNET" for image segmentation in Keras framework

ZF_UNET_224 Pretrained Model Modification of convolutional neural net "UNET" for image segmentation in Keras framework Requirements Python 3.*, Keras

209 Nov 02, 2022
Official PyTorch implementation of RIO

Image-Level or Object-Level? A Tale of Two Resampling Strategies for Long-Tailed Detection Figure 1: Our proposed Resampling at image-level and obect-

NVIDIA Research Projects 17 May 20, 2022
Optimizing synthesizer parameters using gradient approximation

Optimizing synthesizer parameters using gradient approximation NASH 2021 Hackathon! These are some experiments I conducted during NASH 2021, the Neura

Jordie Shier 10 Feb 10, 2022
Implementation of OmniNet, Omnidirectional Representations from Transformers, in Pytorch

Omninet - Pytorch Implementation of OmniNet, Omnidirectional Representations from Transformers, in Pytorch. The authors propose that we should be atte

Phil Wang 48 Nov 21, 2022
Supporting code for the Neograd algorithm

Neograd This repo supports the paper Neograd: Gradient Descent with a Near-Ideal Learning Rate, which introduces the algorithm "Neograd". The paper an

Michael Zimmer 12 May 01, 2022
The PyTorch implementation for paper "Neural Texture Extraction and Distribution for Controllable Person Image Synthesis" (CVPR2022 Oral)

ArXiv | Get Start Neural-Texture-Extraction-Distribution The PyTorch implementation for our paper "Neural Texture Extraction and Distribution for Cont

Ren Yurui 111 Dec 10, 2022
Train emoji embeddings based on emoji descriptions.

emoji2vec This is my attempt to train, visualize and evaluate emoji embeddings as presented by Ben Eisner, Tim Rocktäschel, Isabelle Augenstein, Matko

Miruna Pislar 17 Sep 03, 2022
[ICLR2021oral] Rethinking Architecture Selection in Differentiable NAS

DARTS-PT Code accompanying the paper ICLR'2021: Rethinking Architecture Selection in Differentiable NAS Ruochen Wang, Minhao Cheng, Xiangning Chen, Xi

Ruochen Wang 86 Dec 27, 2022
Code for the paper "Next Generation Reservoir Computing"

Next Generation Reservoir Computing This is the code for the results and figures in our paper "Next Generation Reservoir Computing". They are written

OSU QuantInfo Lab 105 Dec 20, 2022
🔥 Cogitare - A Modern, Fast, and Modular Deep Learning and Machine Learning framework for Python

Cogitare is a Modern, Fast, and Modular Deep Learning and Machine Learning framework for Python. A friendly interface for beginners and a powerful too

Cogitare - Modern and Easy Deep Learning with Python 76 Sep 30, 2022
To SMOTE, or not to SMOTE?

To SMOTE, or not to SMOTE? This package includes the code required to repeat the experiments in the paper and to analyze the results. To SMOTE, or not

Amazon Web Services 1 Jan 03, 2022
A curated list of awesome neural radiance fields papers

Awesome Neural Radiance Fields A curated list of awesome neural radiance fields papers, inspired by awesome-computer-vision. How to submit a pull requ

Yen-Chen Lin 3.9k Dec 27, 2022
Cascaded Pyramid Network (CPN) based on Keras (Tensorflow backend)

ML2 Takehome Project Reimplementing the paper: Cascaded Pyramid Network for Multi-Person Pose Estimation Dataset The model uses the COCO dataset which

Vo Van Tu 1 Nov 22, 2021
Cross-Image Region Mining with Region Prototypical Network for Weakly Supervised Segmentation

Cross-Image Region Mining with Region Prototypical Network for Weakly Supervised Segmentation The code of: Cross-Image Region Mining with Region Proto

LiuWeide 16 Nov 26, 2022
Official code for "EagerMOT: 3D Multi-Object Tracking via Sensor Fusion" [ICRA 2021]

EagerMOT: 3D Multi-Object Tracking via Sensor Fusion Read our ICRA 2021 paper here. Check out the 3 minute video for the quick intro or the full prese

Aleksandr Kim 276 Dec 30, 2022
[ACM MM 2021] TSA-Net: Tube Self-Attention Network for Action Quality Assessment

Tube Self-Attention Network (TSA-Net) This repository contains the PyTorch implementation for paper TSA-Net: Tube Self-Attention Network for Action Qu

ShunliWang 18 Dec 23, 2022