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Medical-image-registration-Resouces

Medical image registration related books, tutorials, papers, datasets, toolboxes and deep learning open source codes

1. Books

Zhenhuan Zhou, et.al: A software guide for medical image segmentation and registration algorithm. 医学图像分割与配准(ITK实现分册) Part Ⅱ introduces the most basic network and architecture of medical registration algorithms (Chinese Version).

2. Tutorials & Workshops

2.1 Tutorials

Learn2Reg MICCAI2019 Big thanks to Yipeng Hu organizing the excellent tutorial.

Autograd Image Registration Laboratory MICCAI2019

Medical Image Registration

2.2 Workshops

WBIR - International Workshop on Biomedical Image Registration WBIR2018, Leiden, Netherlands WBIR2016, Las Vegas NV WBIR2014, London, UK

3. Datasets

Dataset Number Modality Region Format
DIRLAB 10 4D CT Lung .img
LPBA40 40 3D MRI T1 Brain .img+.hdr .nii
IBSR18 18 3D MRI T1 Brain .img+.hdr
EMPIRE 30 4D CT Lung .mhd+.raw
LiTS 131 3D CT Liver .nii

4. Toolbox

Image registration tools survey:A. Klein et al., “Evaluation of 14 nonlinear deformation algorithms applied to human brain MRI registration,” Neuroimage, vol. 46, no. 3, pp. 786–802, 2009.

Tools:

[c++] ITK: Segmentation & Registration Toolkit

[c++ Python and Java] SimpleITK: A simplified layer built on top of ITK

[c++] ANTS: Advanced normalization tools

[c++] Elastix: A toolbox for rigid and nonrigid registration of images

Github repository for deep learning medical image registration:

[Keras] VoxelMorph

[Keras] FAIM

[Tensorflow] Weakly-supervised CNN

[Tensorflow] RegNet3D

[Tensorflow] Recursive-Cascaded-Networks

[Pytorch] Probabilistic Dense Displacement Network

[Pytorch] Linear and Deformable Image Registration

[Pytorch] Inverse-Consistent Deep Networks

[Pytorch] Non-parametric image registration

[Pytorch] One Shot Deformable Medical Image Registration

[Pytorch] Image-and-Spatial Transformer Networks

5. Papers

Links and papers will be continuously updated.

5.1 Survey papers

[1] A. Sotiras, C. Davatzikos, and N. Paragios, “Deformable medical image registration: A survey,” IEEE Trans. Med. Imaging, vol. 32, no. 7, pp. 1153–1190, 2013.

[2] N. J. Tustison, B. B. Avants, and J. C. Gee, “Learning image-based spatial transformations via convolutional neural networks : A review,” Magn. Reson. Imaging, no. January, pp. 0–1, 2019.

[3] G. Haskins, U. Kruger, and P. Yan, “Deep Learning in Medical Image Registration: A Survey,” 2019.

[4] N. Tustison, et.al., “Learning image-based spatial transformations via convolutional neural networks: A review,”2019.

5.2 Traditional medical image registration methods

To be updated

5.3 Learning-based methods

5.3.1 Iterative learning methods

[1] M. Blendowski and M. P. Heinrich, “Combining MRF-based deformable registration and deep binary 3D-CNN descriptors for large lung motion estimation in COPD patients,” Int. J. Comput. Assist. Radiol. Surg., vol. 14, no. 1, pp. 43–52, 2019.

[2] G. Wu, M. Kim, Q. Wang, Y. Gao, S. Liao, and D. Shen, “Unsupervised deep feature learning for deformable registration of MR brain images,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 8150 LNCS, no. PART 2, pp. 649–656, 2013.

[3] K. A. J. Eppenhof and J. P. W. Pluim, “Error estimation of deformable image registration of pulmonary CT scans using convolutional neural networks,” J. Med. Imaging, vol. 5, no. 02, p. 1, 2018.

[4] M. Simonovsky, B. Gutiérrez-Becker, D. Mateus, N. Navab, and N. Komodakis, “A deep metric for multimodal registration,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 9902 LNCS, pp. 10–18, 2016.

[5] S. Miao et al., “Dilated FCN for multi-agent 2D/3D medical image registration,” 32nd AAAI Conf. Artif. Intell. AAAI 2018, pp. 4694–4701, 2018.

[6] A. Sedghi et al., “Semi-Supervised Deep Metrics for Image Registration,” 2018.

[7] X. Cheng, L. Zhang, and Y. Zheng, “Deep similarity learning for multimodal medical images,” Comput. Methods Biomech. Biomed. Eng. Imaging Vis., vol. 6, no. 3, pp. 248–252, 2018.

[8] V. A. Z. B et al., Data Driven Treatment Response Assessment and Preterm, Perinatal, and Paediatric Image Analysis, vol. 11076. Springer International Publishing, 2018.

[9] K. Ma et al., “Multimodal Image Registration with Deep Context Reinforcement Learning,” 2017, vol. 10433, no. 1, pp. 728–736.

[10] J. Krebs et al., “Robust non-rigid registration through agent-based action learning,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 10433 LNCS, pp. 344–352, 2017.

[11] G. Haskins et al., “Learning deep similarity metric for 3D MR–TRUS image registration,” Int. J. Comput. Assist. Radiol. Surg., vol. 14, no. 3, pp. 417–425, 2019.

[12] R. Liao et al., “An artificial agent for robust image registration,” 31st AAAI Conf. Artif. Intell. AAAI 2017, pp. 4168–4175, 2017.

5.3.2 Supervised learning methods

[1] X. Cao, J. Yang, L. Wang, Z. Xue, Q. Wang, and D. Shen, “Deep learning based inter-modality image registration supervised by intra-modality similarity,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 11046 LNCS, pp. 55–63, 2018.

[2] X. Cao et al., “Deformable Image Registration Based on Similarity-Steered CNN Regression,” vol. 10433, pp. 728–736, 2017.

[3] Y. Hu, M. Modat, E. Gibson, N. Ghavami, E. Bonmati, and C. M. Moore, “LABEL-DRIVEN WEAKLY-SUPERVISED LEARNING FOR MULTIMODAL DEFORMABLE IMAGE REGISTRATION Centre for Medical Image Computing , University College London , UK Institute of Biomedical Engineering , University of Oxford , UK Division of Surgery and Interventional,” 2018 IEEE 15th Int. Symp. Biomed. Imaging (ISBI 2018), no. Isbi, pp. 1070–1074, 2018.

[4] M. Ito and F. Ino, “An automated method for generating training sets for deep learning based image registration,” BIOIMAGING 2018 - 5th Int. Conf. Bioimaging, Proceedings; Part 11th Int. Jt. Conf. Biomed. Eng. Syst. Technol. BIOSTEC 2018, vol. 2, no. January, pp. 140–147, 2018.

[5] X. Yang, R. Kwitt, and M. Niethammer, “Fast predictive image registration,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 10008 LNCS, pp. 48–57, 2016.

[6] S. Miao, Z. J. Wang, Y. Zheng, and R. Liao, “Real-time 2D/3D registration via CNN regression,” Proc. - Int. Symp. Biomed. Imaging, vol. 2016-June, pp. 1430–1434, 2016.

[7] H. Uzunova, M. Wilms, H. Handels, and J. Ehrhardt, “Training CNNs for image registration from few samples with model-based data augmentation,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 10433 LNCS, pp. 223–231, 2017.

[8] H. Sokooti, B. de Vos, F. Berendsen, B. P. F. Lelieveldt, I. Iˇsgum, and M. Staring, “Nonrigid image registration using multi-scale 3d convolutional neural networks,” vol. 10433, pp. 728–736, Oct. 2017.

[9] X. Yang, “UNCERTAINTY QUANTIFICATION, IMAGE SYNTHESIS AND DEFORMATION PREDICTION FOR IMAGE REGISTRATION,” UNC, 2017.

[10] K. A. J. Eppenhof and J. P. W. Pluim, “Pulmonary CT Registration Through Supervised Learning With Convolutional Neural Networks,” IEEE Trans. Med. Imaging, vol. 38, no. 5, pp. 1097–1105, 2019.

[11] P. Yan, S. Xu, A. R. Rastinehad, and B. J. Wood, “Adversarial image registration with application for MR and TRUS image fusion,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 11046 LNCS, pp. 197–204, 2018.

[12] S. S. Mohseni Salehi, S. Khan, D. Erdogmus, and A. Gholipour, “Real-Time Deep Pose Estimation With Geodesic Loss for Image-to-Template Rigid Registration,” IEEE Trans. Med. Imaging, vol. 38, no. 2, pp. 470–481, 2019.

[13] J. M. Sloan, K. A. Goatman, and J. P. Siebert, “Learning rigid image registration utilizing convolutional neural networks for medical image registration,” BIOIMAGING 2018 - 5th Int. Conf. Bioimaging, Proceedings; Part 11th Int. Jt. Conf. Biomed. Eng. Syst. Technol. BIOSTEC 2018, vol. 2, no. Biostec, pp. 89–99, 2018.

[14] M. Graziani, V. Andrearczyk, and M. Henning, Understanding and Interpreting Machine Learning in Medical Image Computing Applications, vol. 11038. Springer International Publishing, 2018.

[15] L. V. Jun, M. Yang, J. Zhang, and X. Wang, “Respiratory motion correction for free-breathing 3D abdominal MRI using CNN-based image registration: a feasibility study,” Br. J. Radiol., vol. 91, no. 1083, pp. 1–9, 2018.

[16] Y. Hu et al., “Adversarial deformation regularization for training image registration neural networks,” arXiv, vol. 11070 LNCS, pp. 774–782, 2018.

[17] Rohe and Xavier, “SVF-Net: Learning Deformable Image Registration Using Shape Matching Marc-Michel,” vol. 10433, pp. 728–736, Oct. 2017.

[18] Y. Hu et al., “Weakly-supervised convolutional neural networks for multimodal image registration,” Med. Image Anal., vol. 49, pp. 1–13, 2018.

[19] A. Hering, S. Kuckertz, S. Heldmann, and M. P. Heinrich, “Enhancing Label-Driven Deep Deformable Image Registration with Local Distance Metrics for State-of-the-Art Cardiac Motion Tracking,” Inform. aktuell, pp. 309–314, 2019.

[20] J. Zheng, S. Miao, Z. Jane Wang, and R. Liao, “Pairwise domain adaptation module for CNN-based 2-D/3-D registration,” J. Med. Imaging, vol. 5, no. 02, p. 1, 2018.

[21] J. Fan, X. Cao, P. T. Yap, and D. Shen, “BIRNet: Brain image registration using dual-supervised fully convolutional networks,” Med. Image Anal., vol. 54, pp. 193–206, 2019.

[22] E. Chee and Z. Wu, “AIRNet: Self-Supervised Affine Registration for 3D Medical Images using Neural Networks,” pp. 1–13, 2018.

5.3.3 Unsupervised learning methods

[1] S. Ghosal and N. Ray, [“Deep deformable registration: Enhancing accuracy by fully convolutional neural net,” ](Deep Deformable Registration: Enhancing Accuracy by Fully Convolutional Neural Net)Pattern Recognit. Lett., vol. 94, pp. 81–86, 2017.

[2] Q. Liu and H. Leung, “Tensor-based descriptor for image registration via unsupervised network,” 20th Int. Conf. Inf. Fusion, Fusion 2017 - Proc., 2017.

[3] C. Shu, X. Chen, Q. Xie, and H. Han, “An unsupervised network for fast microscopic image registration,” no. March, p. 48, 2018.

[4] L. Sun and S. Zhang, “Deformable MRI-Ultrasound Registration Using 3D Convolutional Neural Network,” shuib, vol. 11042, pp. 21–28, 2018.

[5] J. Neylon, Y. Min, D. A. Low, and A. Santhanam, “A neural network approach for fast, automated quantification of DIR performance:,” Med. Phys., vol. 44, no. 8, pp. 4126–4138, 2017.

[6] D. Kuang and T. Schmah, “FAIM -- A ConvNet Method for Unsupervised 3D Medical Image Registration,” pp. 1–9, 2018.

[7] Pingge Jiang, J. A. Shackleford, and D. of E. and C. Engineering, “Cnn driven sparse multi-level b-spline image registration,” no. December, pp. 9281–9289, 2012.

[8] E. Ferrante, O. Oktay, B. Glocker, and D. H. Milone, “On the adaptability of unsupervised CNN-based deformable image registration to unseen image domains,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 11046 LNCS, pp. 294–302, 2018.

[9] G. Balakrishnan, A. Zhao, M. R. Sabuncu, J. Guttag, and A. V. Dalca, “VoxelMorph: A Learning Framework for Deformable Medical Image Registration,” IEEE Trans. Med. Imaging, pp. 1–1, 2019.

[10] B. D. de Vos, F. F. Berendsen, M. A. Viergever, H. Sokooti, M. Staring, and I. Išgum, “A deep learning framework for unsupervised affine and deformable image registration,” Med. Image Anal., vol. 52, pp. 128–143, 2019.

[11] X. Cao, J. Yang, L. Wang, Z. Xue, Q. Wang, and D. Shen, “Deep learning based inter-modality image registration supervised by intra-modality similarity,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 11046 LNCS, pp. 55–63, 2018.

[12] C. Stergios et al., “Linear and deformable image registration with 3D convolutional neural networks,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 11040 LNCS, pp. 13–22, 2018.

[13] J. Zhang, “Inverse-Consistent Deep Networks for Unsupervised Deformable Image Registration,” vol. 1, pp. 1–13, 2018.

[14] H. Li and Y. Fan, “Non-rigid image registration using self-supervised fully convolutional networks without training data,” Proc. - Int. Symp. Biomed. Imaging, vol. 2018-April, pp. 1075–1078, 2018.

[15] G. Balakrishnan, A. Zhao, M. R. Sabuncu, A. V. Dalca, and J. Guttag, “An Unsupervised Learning Model for Deformable Medical Image Registration,” in 2018 IEEE/CVF Conference on Computer Vision and Pattern Recognition, 2018, pp. 9252–9260.

[16] B. D. de Vos, F. F. Berendsen, M. A. Viergever, M. Staring, and I. Išgum, “End-to-end unsupervised deformable image registration with a convolutional neural network,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 10553 LNCS, pp. 204–212, 2017.

[17] J. Fan, X. Cao, Z. Xue, and P. Yap, Adversarial Similarity Network for Evaluating Image Alignment in Deep Learning Based Registration, vol. 8149. Springer International Publishing, 2018.

[18] A. V. Dalca, G. Balakrishnan, J. Guttag, and M. R. Sabuncu, “Unsupervised learning for fast probabilistic diffeomorphic registration,” Lect. Notes Comput. Sci. (including Subser. Lect. Notes Artif. Intell. Lect. Notes Bioinformatics), vol. 11070 LNCS, pp. 729–738, 2018.

[19] A. Sheikhjafari, K. Punithakumar, and N. Ray, “Unsupervised Deformable Image Registration with Fully Connected Generative Neural Network,” Midl, no. Midl 2018, pp. 1–9, 2018.

5.3.4 Most recently papers

[1] X. Hu, M. Kang, W. Huang, M. R. Scott, R. Wiest, and M. Reyes, Dual-Stream Pyramid Registration Network, vol. 2. Springer International Publishing, 2019.

[2] D. Wei et al., “Synthesis and Inpainting-Based MR-CT Registration for Image-Guided Thermal Ablation of Liver Tumors,” vol. 2, pp. 1–10, 2019.

[3] T. Estienne et al., “U-ReSNet: Ultimate Coupling; of Registration and Segmentation with Deep Nets,” vol. 2, pp. 329–337, 2019.

[4] L. Liu, X. Hu, L. Z. B, and P. Heng, Probabilistic Multilayer Regularization Network for Unsupervised 3D Brain Image Registration. Springer International Publishing, 2019.

[5] M. P. Heinrich, “Closing the Gap between Deep and Conventional Image Registration using Probabilistic Dense Displacement Networks,” pp. 1–9, 2019.

[6] A. Sheikhjafari, K. Punithakumar, and N. Ray, “Unsupervised Deformable Image Registration with Fully Connected Generative Neural Network,” Midl, no. Midl 2018, pp. 1–9, 2018.

[7] Y. Hu, E. Gibson, D. C. Barratt, M. Emberton, J. A. Noble, and T. Vercauteren, Conditional Segmentation in Lieu of Image Registration, vol. 2. Springer International Publishing, 2019.

[8] S. Zhou, Z. X. B, C. Chen, X. Chen, and D. Liu, Fast and Accurate Electron Microscopy Image Registration with 3D Convolution. Springer International Publishing, 2019.

[9] R. K. Nielsen, S. Darkner, and A. Feragen, TopAwaRe : Topology-Aware Registration, vol. 2. Springer International Publishing, 2019.

[10] J. Luo et al., On the Ambiguity of Registration Uncertainty, vol. 2. Springer International Publishing, 2018.

[11] Z. Xu and M. Niethammer, DeepAtlas: Joint Semi-Supervised Learning of Image Registration and Segmentation. Springer International Publishing, 2019.

[12] M. C. H. Lee, O. Oktay, A. Schuh, M. Schaap, and B. Glocker, Image-and-Spatial Transformer Networks for Structure-Guided Image Registration, vol. 2. Springer International Publishing, 2019.

[13] B. Li et al., “A hybrid deep learning framework for integrated segmentation and registration: evaluation on longitudinal white matter tract changes,” pp. 1–9, 2019.

[14] M. S. Elmahdy, J. M. Wolterink, H. Sokooti, I. Išgum, and M. Staring, “Adversarial optimization for joint registration and segmentation in prostate CT radiotherapy,” pp. 1–9, 2019.

[15] W. Zhu et al., “NeurReg: Neural Registration and Its Application to Image Segmentation,” WACV,2020.

[16] S. Zhao, Y. Dong, E. I.-C. Chang, and Y. Xu, “Recursive Cascaded Networks for Unsupervised Medical Image Registration,” ICCV2019, 2019.

[17] W. Zhu et al., “Neural Multi-Scale Self-Supervised Registration for Echocardiogram Dense Tracking,” pp. 1–9, 2019.

[18] R. Sandkühler, S. Andermatt, G. Bauman, S. Nyilas, C. Jud, and P. C. Cattin, “Recurrent Registration Neural Networks for Deformable Image Registration,” pp. 1–11, 2019.

[19] Z. Shen, X. Han, Z. Xu, and M. Niethammer, “Networks for Joint Affine and Non-parametric Image Registration,” CVPR2019, pp. 4224–4233, 2019.

[20] B. D. de Vos, F. F. Berendsen, M. A. Viergever, H. Sokooti, M. Staring, and I. Išgum, “A deep learning framework for unsupervised affine and deformable image registration,” Med. Image Anal., vol. 52, pp. 128–143, 2019.

[21] T. Lau, J. Luo, S. Zhao, E. I.-C. Chang, and Y. Xu, “Unsupervised 3D End-to-End Medical Image Registration with Volume Tweening Network,” pp. 1–14, 2019.

[22] J. Fan, X. Cao, Q. Wang, P. Yap, and D. Shen, “Adversarial Learning for Mono- or Multi-Modal Registration,” Medical image analysis, 2019.

6. Conferences and Journals

6.1 Conferences

① Biomedical image:

MICCAI: International Conference on Medical Image Computing and Computer Assisted Intervention

IPMI: Information Processing in Medical Imaging

ISBI: International Symposium on Biomedical Imaging

Medical Imaging SPIE

② C.v. c.s Conferences:

CVPR: IEEE International Conference on Computer Vision and Pattern Recognition

ICCV: IEEE International Conference on Computer Vision

ECCV: European Conference on Computer Vision

NeurIPS: Conference on Neural Information Processing Systems

AAAI: Association for the Advancement of Artificial Intelligence

ICML: International Conference on Machine Learning

ICPR: International Conference on Pattern Recognition

IJCNN: International Joint Conference on Neural Networks

ICIP: IEEE International Conference on Image Processing

IJCAI: International Joint Conferences on Artificial Intelligence

WACV: Winter Conference on Applications of Computer Vision

6.2 Journals

MIA: Medical Image Analysis

TIP: IEEE Transactions on Image Processing

TBME: IEEE Transactions on Biomedical Engineering

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