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Awesome Medical Image Registration Awesome

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

For researchers who are new to registration, it is recommended to read papers in chronological order to study the evolution of research trends.

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

Table of Contents

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

Classic
  • [MedIA 2011] MIND: Modality independent neighborhood descriptor for multi-modal deformable registration [pdf]
  • [MedIA 2012] DRAMMS: Deformable registration via attribute matching and mutual-saliency weighting [pdf]
  • [MICCAI 2013] Towards realtime multimodal fusion for image-guided interventions using self-similarities [pdf]
  • [MedIA 2014] Automatic ultrasound–MRI registration for neurosurgery using the 2D and 3D LC2 Metric [pdf]
Learning-based
  • [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]
  • [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

Software