Deep learning for unsupervised domain adaptation in medical imaging: Recent advancements and future perspectives

Deep learning has demonstrated remarkable performance across various tasks in medical imaging. However, these approaches primarily focus on supervised learning, assuming that the training and testing data are drawn from the same distribution. Unfortunately, this assumption may not always hold true in practice. To address these issues, unsupervised domain adaptation (UDA) techniques have been developed to transfer knowledge from a labeled domain to a related but unlabeled domain. In recent years, significant advancements have been made in UDA, resulting in a wide range of methodologies, including feature alignment, image translation, self-supervision, and disentangled representation methods, among others. In this paper, we provide a comprehensive literature review of recent deep UDA approaches in medical imaging from a technical perspective. Specifically, we categorize current UDA research in medical imaging into six groups and further divide them into finer subcategories based on the different tasks they perform. We also discuss the respective datasets used in the studies to assess the divergence between the different domains. Finally, we discuss emerging areas and provide insights and discussions on future research directions to conclude this survey.Comment: Under Revie

Data efficient unsupervised domain adaptation for cross-modality image segmentation

Deep learning models trained on medical images from a source domain (e.g. imaging modality) often fail when deployed on images from a different target domain, despite imaging common anatomical structures. Deep unsupervised domain adaptation (UDA) aims to improve the performance of a deep neural network model on a target domain, using solely unlabelled target domain data and labelled source domain data. However, current state-of-the-art methods exhibit reduced performance when target data is scarce. In this work, we introduce a new data efficient UDA method for multi-domain medical image segmentation. The proposed method combines a novel VAE-based feature prior matching, which is data-efficient, and domain adversarial training to learn a shared domain-invariant latent space which is exploited during segmentation. Our method is evaluated on a public multi-modality cardiac image segmentation dataset by adapting from the labelled source domain (3D MRI) to the unlabelled target domain (3D CT). We show that by using only one single unlabelled 3D CT scan, the proposed architecture outperforms the state-of-the-art in the same setting. Finally, we perform ablation studies on prior matching and domain adversarial training to shed light on the theoretical grounding of the proposed method.Comment: Accepted by MICCAI 201

Domain Adaptation for Novel Imaging Modalities with Application to Prostate MRI

The need for training data can impede the adoption of novel imaging modalities for deep learning-based medical image analysis. Domain adaptation can mitigate this problem by exploiting training samples from an existing, densely-annotated source domain within a novel, sparsely-annotated target domain, by bridging the differences between the two domains. In this thesis we present methods for adapting between diffusion-weighed (DW)-MRI data from multiparametric (mp)-MRI acquisitions and VERDICT (Vascular, Extracellular and Restricted Diffusion for Cytometry in Tumors) MRI, a richer DW-MRI technique involving an optimized acquisition protocol for cancer characterization. We also show that the proposed methods are general and their applicability extends beyond medical imaging. First, we propose a semi-supervised domain adaptation method for prostate lesion segmentation on VERDICT MRI. Our approach relies on stochastic generative modelling to translate across two heterogeneous domains at pixel-space and exploits the inherent uncertainty in the cross-domain mapping to generate multiple outputs conditioned on a single input. We further extend this approach to the unsupervised scenario where there is no labeled data for the target domain. We rely on stochastic generative modelling to translate across the two domains at pixel space and introduce two loss functions that promote semantic consistency. Finally we demonstrate that the proposed approaches extend beyond medical image analysis and focus on unsupervised domain adaptation for semantic segmentation of urban scenes. We show that relying on stochastic generative modelling allows us to train more accurate target networks and achieve state-of-the-art performance on two challenging semantic segmentation benchmarks

Medical Image Computing and Computer Assisted Intervention – MICCAI 2019 [electronic resource] : 22nd International Conference, Shenzhen, China, October 13–17, 2019, Proceedings, Part II /

The six-volume set LNCS 11764, 11765, 11766, 11767, 11768, and 11769 constitutes the refereed proceedings of the 22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019, held in Shenzhen, China, in October 2019. The 539 revised full papers presented were carefully reviewed and selected from 1730 submissions in a double-blind review process. The papers are organized in the following topical sections: Part I: optical imaging; endoscopy; microscopy. Part II: image segmentation; image registration; cardiovascular imaging; growth, development, atrophy and progression. Part III: neuroimage reconstruction and synthesis; neuroimage segmentation; diffusion weighted magnetic resonance imaging; functional neuroimaging (fMRI); miscellaneous neuroimaging. Part IV: shape; prediction; detection and localization; machine learning; computer-aided diagnosis; image reconstruction and synthesis. Part V: computer assisted interventions; MIC meets CAI. Part VI: computed tomography; X-ray imaging.Image Segmentation -- Searching Learning Strategy with Reinforcement Learning for 3D Medical Image Segmentation -- Comparative Evaluation of Hand-Engineered and Deep-Learned Features for Neonatal Hip Bone Segmentation in Ultrasound -- Unsupervised Quality Control of Image Segmentation based on Bayesian Learning -- One Network To Segment Them All: A General, Lightweight System for Accurate 3D Medical Image Segmentation -- 'Project & Excite' Modules for Segmentation of Volumetric Medical Scans -- Assessing Reliability and Challenges of Uncertainty Estimations for Medical Image Segmentation -- Learning Cross-Modal Deep Representations for Multi-Modal MR Image Segmentation -- Extreme Points Derived Confidence Map as a Cue For Class-Agnostic Segmentation Using Deep Neural Network -- Hetero-Modal Variational Encoder-Decoder for Joint Modality Completion and Segmentation -- Instance Segmentation from Volumetric Biomedical Images without Voxel-Wise Labeling -- Optimizing the Dice Score and Jaccard Index for Medical Image Segmentation: Theory & Practice -- Dual Adaptive Pyramid Network for Cross-Stain Histopathology Image Segmentation -- HD-Net: Hybrid Discriminative Network for Prostate Segmentation in MR Images -- PHiSeg: Capturing Uncertainty in Medical Image Segmentation -- Neural Style Transfer Improves 3D Cardiovascular MR Image Segmentation on Inconsistent Data -- Supervised Uncertainty Quantification for Segmentation with Multiple Annotations -- 3D Tiled Convolution for Effective Segmentation of Volumetric Medical Images -- Hyper-Pairing Network for Multi-Phase Pancreatic Ductal Adenocarcinoma Segmentation -- Statistical intensity- and shape-modeling to automate cerebrovascular segmentation from TOF-MRA data -- Segmentation of Vessels in Ultra High Frequency Ultrasound Sequences using Contextual Memory -- Accurate Esophageal Gross Tumor Volume Segmentation in PET/CT using Two-Stream Chained 3D Deep Network Fusion -- Mixed-Supervised Dual-Network for Medical Image Segmentation -- Fully Automated Pancreas Segmentation with Two-stage 3D Convolutional Neural Networks -- Globally Guided Progressive Fusion Network for 3D Pancreas Segmentation -- Automatic Segmentation of Muscle Tissue and Inter-muscular Fat in Thigh and Calf MRI Images -- Resource Optimized Neural Architecture Search for 3D Medical Image Segmentation -- Radiomics-guided GAN for Segmentation of Liver Tumor without Contrast Agents -- Liver Segmentation in Magnetic Resonance Imaging via Mean Shape Fitting with Fully Convolutional Neural Networks -- Unsupervised Domain Adaptation via Disentangled Representations: Application to Cross-Modality Liver Segmentation -- Automatic Segmentation of Vestibular Schwannoma from T2-Weighted MRI by Deep Spatial Attention with Hardness-Weighted Loss -- Learning Shape Representation on Sparse Point Clouds for Volumetric Image Segmentation -- Collaborative Multi-agent Learning for MR Knee Articular Cartilage Segmentation -- 3D U2-Net: A 3D Universal U-Net for Multi-Domain Medical Image Segmentation -- Impact of Adversarial Examples on Deep Learning Segmentation Models -- Multi-Resolution Path CNN with Deep Supervision for Intervertebral Disc Localization and Segmentation -- Automatic paraspinal muscle segmentation in patients with lumbar pathology using deep convolutional neural network -- Constrained Domain Adaptation for Segmentation -- Image Registration -- Image-and-Spatial Transformer Networks for Structure-Guided Image Registration -- Probabilistic Multilayer Regularization Network for Unsupervised 3D Brain Image Registration -- A deep learning approach to MR-less spatial normalization for tau PET images -- TopAwaRe: Topology-Aware Registration -- Multimodal Data Registration for Brain Structural Association Networks -- Dual-Stream Pyramid Registration Network -- A Cooperative Autoencoder for Population-Based Regularization of CNN Image Registration -- Conditional Segmentation in Lieu of Image Registration -- On the applicability of registration uncertainty -- DeepAtlas: Joint Semi-Supervised Learning of Image Registration and Segmentation -- Linear Time Invariant Model based Motion Correction (LiMo-Moco) of Dynamic Radial Contrast Enhanced MRI -- Incompressible image registration using divergence-conforming B-splines -- Cardiovascular Imaging -- Direct Quantification for Coronary Artery Stenosis Using Multiview Learning -- Bayesian Optimization on Large Graphs via a Graph Convolutional Generative Model: Application in Cardiac Model Personalization -- Discriminative Coronary Artery Tracking via 3D CNN in Cardiac CT Angiography -- Multi-modality Whole-Heart and Great Vessel Segmentation in Congenital Heart Disease using Deep Neural Networks and Graph Matching -- Harmonic Balance Techniques in Cardiovascular Fluid Mechanics -- Deep learning within a priori temporal feature spaces for large-scale dynamic MR image reconstruction: Application to 5-D cardiac MR Multitasking -- k-t NEXT: Dynamic MR Image Reconstruction Exploiting Spatio-temporal Correlations -- Model-based reconstruction for highly accelerated first-pass perfusion cardiac MRI -- Learning Shape Priors for Robust Cardiac MR Segmentation from Multi-view images -- Right Ventricle Segmentation in Short-Axis MRI Using A Shape Constrained Dense Connected U-net -- Self-Supervised Learning for Cardiac MR Image Segmentation by Anatomical Position Prediction -- A Fine-Grain Error Map Prediction and Segmentation Quality Assessment Framework for Whole-Heart Segmentation -- Cardiac Segmentation from LGE MRI Using Deep Neural Network Incorporating Shape and Spatial Priors -- Curriculum semi-supervised segmentation -- A Multi-modal Network for Cardiomyopathy Death Risk Prediction with CMR Images and Clinical Information -- 3D Cardiac Shape Prediction with Deep Neural Networks: Simultaneous Use of Images and Patient Metadata -- Discriminative Consistent Domain Generation for Semi-supervised Learning -- Uncertainty-aware Self-ensembling Model for Semi-supervised 3D Left Atrium Segmentation -- MSU-Net: Multiscale Statistical U-Net for Real-time 3D Cardiac MRI Video Segmentation -- The Domain Shift Problem of Medical Image Segmentation and Vendor-Adaptation by Unet-GAN -- Cardiac MRI Segmentation with Strong Anatomical Guarantees -- Decompose-and-Integrate Learning for Multi-class Segmentation in Medical Images -- Missing Slice Imputation in Population CMR Imaging via Conditional Generative Adversarial Nets -- Unsupervised Standard Plane Synthesis in Population Cine MRI via Cycle-Consistent Adversarial Networks -- Data Efficient Unsupervised Domain Adaptation for Cross-Modality Image Segmentation -- Recurrent Aggregation Learning for Multi-View Echocardiographic Sequences Segmentation -- Echocardiography View Classification Using Quality Transfer Star Generative Adversarial Networks -- Dual-view Joint Estimation of Left Ventricular Ejection Fraction with Uncertainty Modelling in Echocardiograms -- Frame Rate Up-Conversion in Echocardiography Using a Conditioned Variational Autoencoder and Generative Adversarial Model -- Annotation-Free Cardiac Vessel Segmentation via Knowledge Transfer from Retinal Images -- DeepAAA: clinically applicable and generalizable detection of abdominal aortic aneurysm using deep learning -- Texture-based classification of significant stenosis in CCTA multi-view images of coronary arteries -- Fourier Spectral Dynamic Data Assimilation: Interlacing CFD with 4D flow MRI -- Quality Control-Driven Image Segmentation Towards Reliable Automatic Image Analysis in Large-Scale Cardiovascular Magnetic Resonance Aortic Cine Imaging -- HFA-Net: 3D Cardiovascular Image Segmentation with Asymmetrical Pooling and Content-Aware Fusion -- Spectral CT based training dataset generation and augmentation for conventional CT vascular segmentation -- Context-Aware Inductive Bias Learning for Vessel Border Detection in Multi-modal Intracoronary Imaging -- Growth, Development, Atrophy and Progression -- Neural parameters estimation for brain tumor growth modeling -- Learning-Guided Infinite Network Atlas Selection for Predicting Longitudinal Brain Network Evolution from a Single Observation -- Deep Probabilistic Modeling of Glioma Growth -- Surface-Volume Consistent Construction of Longitudinal Atlases for the Early Developing Brains -- Variational Autoencoder for Regression: Application to Brain Aging Analysis -- Early Development of Infant Brain Complex Network -- Revealing Developmental Regionalization of Infant Cerebral Cortex Based on Multiple Cortical Properties -- Continually Modeling Alzheimer's Disease Progression via Deep Multi-Order Preserving Weight Consolidation -- Disease Knowledge Transfer across Neurodegenerative Diseases.The six-volume set LNCS 11764, 11765, 11766, 11767, 11768, and 11769 constitutes the refereed proceedings of the 22nd International Conference on Medical Image Computing and Computer-Assisted Intervention, MICCAI 2019, held in Shenzhen, China, in October 2019. The 539 revised full papers presented were carefully reviewed and selected from 1730 submissions in a double-blind review process. The papers are organized in the following topical sections: Part I: optical imaging; endoscopy; microscopy. Part II: image segmentation; image registration; cardiovascular imaging; growth, development, atrophy and progression. Part III: neuroimage reconstruction and synthesis; neuroimage segmentation; diffusion weighted magnetic resonance imaging; functional neuroimaging (fMRI); miscellaneous neuroimaging. Part IV: shape; prediction; detection and localization; machine learning; computer-aided diagnosis; image reconstruction and synthesis. Part V: computer assisted interventions; MIC meets CAI. Part VI: computed tomography; X-ray imaging