Awesome Medical Image Registration

👋 Hi! This repo is a collection of AWESOME things about 🌟Medical Image Registration🌟, including useful materials, papers, code. Feel free to star and fork.

TODO:

• Add a list organs in medical image registration

Contributing

🏃 We will keep updating it. 🏃

Please feel free to send me pull requests or email ([email protected]) to add links.

Table of Contents

• Related Awesome Lists
• Papers
• Chanllenges
• Software

Related Awesome Lists

• Awesome Optical Flow
• Awesome Image-to-Image Translation
• Awesome Medical Imaging
• Awesome Machine Learning in Biomedical(Healthcare) Imaging

Papers

Table of Contents

• Original and Fancier Network Architecture
  • Original CNN model for Registration
  • Pyramid CNN for Registration
  • Transformer for Registration
  • Iterative Refinement for Registration
• Deep Diffeomorphic Registration
• Joint Affine and Deformable Registration
• Hyperparameter Learning in Registration
• Discrete Registration and Instance Optimization
• Registration on Specific Task
  • Multi-Modality Registration
  • 2D-3D Registration
  • Histological Image Registration
  • Registration with Tumor in Image
  • Cortical Surface Registration
• Foundation Model for Registration
• Registration Related/Based Application
  • Segmentation
  • Template Construction
  • Cardiac Motion Estimation

Original and Fancier Network Architecture

Original CNN model for Registration

• [MICCAI Workshop 2017] End-to-end unsupervised deformable image registration with a convolutional neural network [pdf]
• [CVPR 2018] An Unsupervised Learning Model for Deformable Medical Image Registration [pdf] [code]
• [Arxiv 2018] Inverse-Consistent Deep Networks for Unsupervised Deformable Image Registration [pdf] [code]
• [MICCAI 2019] Unsupervised Deformable Image Registration Using Cycle-Consistent CNN [pdf] [code]
• [TMI 2019] VoxelMorph: A Learning Framework for Deformable Medical Image Registration [pdf] [code]

Pyramid CNN for Registration

• [ICCV 2019] Recursive Cascaded Networks for Unsupervised Medical Image Registration [pdf] [code]
• [MICCAI 2019] Dual-Stream Pyramid Registration Network [pdf] [code]
• [MICCAI 2020] Large Deformation Diffeomorphic Image Registration with Laplacian Pyramid Networks [pdf] [code]
• [TMI 2021] Learning a model-driven variational network for deformable image registration [pdf] [code]
• [MICCAI 2022] NICE-Net: a Non-Iterative Coarse-to-finE registration Network for deformable image registration [pdf] [code]
• [TMI 2023] Self-Distilled Hierarchical Network for Unsupervised Deformable Image Registration [pdf] [code]

Transformer for Registration

• [MedIA 2022] TransMorph: Transformer for unsupervised medical image registration [pdf] [code]
• [MICCAI 2022] Swin-VoxelMorph: A Symmetric Unsupervised Learning Model for Deformable Medical Image Registration Using Swin Transformer [pdf] [code]
• [MICCAI 2022] Deformer: Towards displacement field learning for unsupervised medical image registration [pdf] [code]
• [MICCAI 2022] XMorpher: Full Transformer for Deformable Medical Image Registration via Cross Attention [pdf] [code]
• [CVPR 2022] Affine Medical Image Registration with Coarse-to-Fine Vision Transformer [pdf] [code]
• [TMI 2023] TransMatch: a transformer-based multilevel dual-stream feature matching network for unsupervised deformable image registration [pdf] [code]
• [CVPR 2024] Correlation-aware Coarse-to-fine MLPs for Deformable Medical Image Registration [pdf] [code]

Iterative Refinement for Registration

• [TPAMI 2021] Learning Deformable Image Registration from Optimization: Perspective, Modules, Bilevel Training and Beyond [pdf] [code]
• [MICCAI 2023] PIViT: Large Deformation Image Registration with Pyramid-Iterative Vision Transformer [pdf] [code]
• [CVPR 2024] IIRP-Net: Iterative Inference Residual Pyramid Network for Enhanced Image Registration [pdf] [code]
• [TMI 2024] GroupMorph: Medical Image Registration via Grouping Network with Contextual Fusion [pdf] [code]

Deep Diffeomorphic Registration

• [MICCAI 2018] Unsupervised Learning for Fast Probabilistic Diffeomorphic Registration [pdf] [code]
• [TMI 2019] Learning a Probabilistic Model for Diffeomorphic Registration [pdf]
• [MedIA 2019] Unsupervised Learning of Probabilistic Diffeomorphic Registration for Images and Surfaces [pdf] [code]
• [NeurIPS 2019] Region-specific Diffeomorphic Metric Mapping [pdf] [code]
• [CVPR 2019] Metric Learning for Image Registration [pdf] [code]
• [CVPR 2020] DeepFLASH: An Efficient Network for Learning-based Medical Image Registration [pdf] [code]
• [CVPR 2020] Fast Symmetric Diffeomorphic Image Registration with Convolutional Neural Networks [pdf] [code]
• [ICCV 2023] ICON: Learning Regular Maps Through Inverse Consistency [pdf] [code]
• [CVPR 2023] GradICON: Approximate Diffeomorphisms via Gradient Inverse Consistency [pdf] [code]
• [MedIA 2019] R2Net: Efficient and flexible diffeomorphic image registration using Lipschitz continuous residual networks [pdf] [code]
• [ECCV 2024] NePhi: Neural Deformation Fields for Approximately Diffeomorphic Medical Image Registration [pdf] [code]
• [ArXiv 2024] SITReg: Multi-resolution architecture for symmetric, inverse consistent, and topology preserving image registration [pdf] [code]

Joint Affine and Deformable Registration

• [CVPR 2019] Networks for Joint Affine and Non-Parametric Image Registration [pdf] [code]
• [JBHI 2020] Unsupervised 3D End-to-End Medical Image Registration with Volume Tweening Network [pdf] [code]
• [MICCAI 2021] SAME: Deformable Image Registration based on Self-supervised Anatomical Embeddings [pdf] [code]
• [MICCAI 2023] Non-iterative Coarse-to-Fine Transformer Networks for Joint Affine and Deformable Image Registration [pdf] [code]
• [Arxiv 2023] SAME++: Deformable Image Registration based on Self-supervised Anatomical Embeddings [pdf] [code]

Hyperparameter learning in Registration

• [IPMI 2021] HyperMorph: Amortized Hyperparameter Learning for Image Registration [pdf] [code]
• [MICCAI 2021] Conditional Deformable Image Registration with Convolutional Neural Network [pdf] [code]
• [TPAMI 2021] Learning Deformable Image Registration from Optimization: Perspective, Modules, Bilevel Training and Beyond [pdf] [code]
• [MedIA 2023] Hyper-Convolutions via Implicit Kernels for Medical Image Analysis [pdf] [code]
• [TIP 2023] Automated learning for deformable medical image registration by jointly optimizing network architectures and objective functions [pdf] [code]

Discrete Registration and Instance Optimization

• [MICCAI 2019] Closing the Gap between Deep and Conventional Image Registration using Probabilistic Dense Displacement Networks [pdf] [code]
• [MICCAI 2020] Highly accurate and memory efficient unsupervised learning-based discrete CT registration using 2.5 D displacement search [pdf] [code]
• [MICCAI Workshop 2021] Fast 3D registration with accurate optimisation and little learning for Learn2Reg 2021 [pdf] [code]
• [MICCAI Workshop 2022] Voxelmorph++ going beyond the cranial vault with keypoint supervision and multi-channel instance optimisation [pdf] [code]
• [MICCAI 2023] SAMConvex: Fast Discrete Optimization for CT Registration using Self-supervised Anatomical Embedding and Correlation Pyramid [pdf] [code]
• [TMI 2024] ConvexAdam: Self-Configuring Dual-Optimisation-Based 3D Multitask Medical Image Registration [pdf] [code]

Registration on Specific Task

Multi-Modality Registration

• [IPMI 2019] Unsupervised deformable registration for multi-modal images via disentangled representations [pdf]
• [MICCAI 2019] Synthesis and inpainting-based MR-CT registration for image-guided thermal ablation of liver tumors [pdf]
• [MICCAI 2020] Adversarial uni-and multi-modal stream networks for multimodal image registration [pdf]
• [NeurIPS 2020] CoMIR: Contrastive multimodal image representation for registration [pdf] [code]
• [TPMAI 2021] SymReg-GAN: symmetric image registration with generative adversarial networks [pdf]
• [MedIA 2022] Deformable MR-CT image registration using an unsupervised, dual-channel network for neurosurgical guidance [pdf]
• [MICCAI 2022] ContraReg: Contrastive Learning of Multi-modality Unsupervised Deformable Image Registration [pdf] [code]
• [MICCAI 2023] DISA: DIfferentiable Similarity Approximation for Universal Multimodal Registration [pdf] [code]
• [CVPR 2024] Modality-Agnostic Structural Image Representation Learning for Deformable Multi-Modality Medical Image Registration [pdf]

2D-3D Registration

• [MICCAI 2020] Fluid Registration Between Lung CT and Stationary Chest Tomosynthesis Images [pdf] [code]
• [MICCAI 2020] Generalizing spatial transformers to projective geometry with applications to 2D/3D registration [pdf] [code]
• [MICCAI 2022] LiftReg: Limited Angle 2D/3D Deformable Registration [pdf] [code]
• [MICCAI 2023] X-ray to ct rigid registration using scene coordinate regression [pdf] [code]
• [MICCAI 2023] A patient-specific self-supervised model for automatic X-Ray/CT registration [pdf] [code]
• [CVPR 2024] Intraoperative 2D/3D Image Registration via Differentiable X-ray Rendering [pdf] [code]

Histological Image Registration

• [TMI 2020] ANHIR: Automatic Non-rigid Histological Image Registration Challenge, IEEE Transactions on Medical Imaging [pdf] [code]
• [Nature Communications 2023] Virtual alignment of pathology image series for multi-gigapixel whole slide image [pdf] [code]
• [TMI 2024] Unsupervised Non-rigid Histological Image Registration Guided by Keypoint Correspondences Based on Learnable Deep Features with Iterative Training [pdf] [code]

Registration with Tumor in Image

• [MICCAI 2022] Unsupervised Deformable Image Registration with Absent Correspondences in Pre-operative and Post-Recurrence Brain Tumor MRI Scans [pdf] [code]
• [ICCV 2023] Preserving Tumor Volumes for Unsupervised Medical Image Registration [pdf] [code]

Cortical Surface Registration

• [MICCAI Workshop 2020] Unsupervised Learning for Spherical Surface Registration [pdf] [code]
• [NeuroImage 2020] Cortical surface registration using unsupervised learning [pdf] [code]
• [TMI 2021] S3Reg: Superfast Spherical Surface Registration Based on Deep Learning [pdf] [code]
• [MICCAI 2022] A Deep-Discrete Learning Framework for Spherical Surface Registration [pdf] [code]
• [MICCAI Workshop 2022] GeoMorph: Geometric Deep Learning for Cortical Surface Registration [pdf] [code]
• [MICCAI Workshop 2023] Unsupervised Learning of Cortical Surface Registration Using Spherical Harmonics [pdf]
• [MedIA 2024] SUGAR: Spherical ultrafast graph attention framework for cortical surface registration [pdf] [code]
• [MedIA 2024] Longitudinally consistent registration and parcellation of cortical surfaces using semi-supervised learning [pdf] [code]
• [MedIA 2024] JOSA: Joint surface-based registration and atlas construction of brain geometry and function [pdf] [code]

Foundation Model for Registration

• [TMI 2022] SynthMorph: learning contrast-invariant registration without acquired images [pdf] [code]
• [ArXiv 2023] UAE: Universal Anatomical Embedding on Multi-modality Medical Images [pdf] [code]
• [MICCAI 2024] uniGradICON: A Foundation Model for Medical Image Registration [pdf] [code]
• [Arxiv 2024] Learning General-purpose Biomedical Volume Representations using Randomized Synthesis [pdf][code]
• [Arxiv 2024] UniMo: Universal Motion Correction For Medical Images without Network Retraining [pdf] [code]

Registration Related/Based Application

Segmentation

• [CVPR 2019] Data Augmentation Using Learned Transformations for One-Shot Medical Image Segmentation [pdf] [code]
• [MICCAI 2019] DeepAtlas: Joint Semi-Supervised Learning of Image Registration and Segmentation [pdf] [code]
• [MedIA 2022] Atlas-ISTN: joint segmentation, registration and atlas construction with image-and-spatial transformer networks [pdf] [code]

Template Construction

• [NeurIPS 2019] Learning conditional deformable templates with convolutional networks [pdf] [code]
• [ICCV 2021] Generative Adversarial Registration for Improved Conditional Deformable Templates [pdf] [code]
• [CVPR 2022] Aladdin: Joint Atlas Building and Diffeomorphic Registration Learning with Pairwise Alignment [pdf] [code]
• [CVPR 2022] Topology-preserving shape reconstruction and registration via neural diffeomorphic flow [pdf] [code]
• [NeurIPS 2022] Geo-SIC: Learning Deformable Geometric Shapes in Deep Image Classifiers [pdf] [code]

Cardiac Motion Estimation

• [MICCAI 2018] Joint learning of motion estimation and segmentation for cardiac MR image sequences [pdf] [code]
• [CVPR 2021] DeepTag: An unsupervised deep learning method for motion tracking on cardiac tagging magnetic resonance images [pdf] [code]
• [TMI 2022] MulViMotion: Shape-aware 3D Myocardial Motion Tracking from Multi-View Cardiac MRI [pdf] [code]
• [MedIA 2023] Generative myocardial motion tracking via latent space exploration with biomechanics-informed prior [pdf] [code]
• [MICCAI 2024] TLRN: Temporal Latent Residual Networks For Large Deformation Image Registration [pdf] [code]

Chanllenges

• Oncoreg
• Learn2Reg 2024
• Learn2Reg 2023
• Learn2Reg 2022
• Learn2Reg 2021
• Learn2Reg 2020
• AutomatiC Registration Of Breast cAncer Tissue (ACROBAT)
• Automatic Non-rigid Histological Image Registration (ANHIR)
• Robust Non-rigid Registration Challenge for Expansion Microscopy (RnR-ExM)
• Correction of Brain shift with Intra-Operative Ultrasound (CuRIOUS 2019)
• Correction of Brain shift with Intra-Operative Ultrasound (CuRIOUS 2018)

Software

• ANTs
• NiftyReg
• LDDMM
• DeedsBCV
• Elastix
• FireANTs (GPU)