Information Processing in Medical Imaging: 27th International Conference, IPMI 2021, Virtual Event, June 28–June 30, 2021, Proceedings (Lecture Notes in Computer Science, 12729) [1st ed. 2021] 3030781909, 9783030781903

This book constitutes the proceedings of the 27th International Conference on Information Processing in Medical Imaging,

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Table of contents :
Preface
Organization
Contents
Registration
HyperMorph: Amortized Hyperparameter Learning for Image Registration
1 Introduction
2 Related Work
3 Methods
3.1 HyperMorph
3.2 Hyperparameter Tuning
3.3 Implementation
4 Experiments
4.1 Experiment 1: HyperMorph Efficiency and Capacity
4.2 Experiment 2: Robustness to Initialization
4.3 Experiment 3: Hyperparameter-Tuning Utility
5 Conclusion
References
Deep Learning Based Geometric Registration for Medical Images: How Accurate Can We Get Without Visual Features?
1 Introduction
1.1 Related Work
1.2 Contribution
2 Methods
2.1 Loopy Belief Propagation for Regularised Registration of Keypoint Graphs
2.2 Geometric Feature Extraction with Graph Convolutional Neural Networks
2.3 Deep Learning Based End-to-End Geometric Registration Framework
2.4 Implementation Details: Keypoints, Visual Features and Integral Loss
3 Experiments and Results
4 Discussion and Conclusion
References
Diffeomorphic Registration with Density Changes for the Analysis of Imbalanced Shapes
1 Introduction
2 Diffeomorphic Registration of Geometric Measures
2.1 Diffeomorphisms and Registration
2.2 Geometric Measure Representation of Shapes
3 Diffeomorphic Registration with Density Changes
3.1 An Augmented Optimal Control Problem
3.2 Numerical Implementation
3.3 Local Density Changes
4 Results
5 Conclusion
References
Causal Models and Interpretability
Estimation of Causal Effects in the Presence of Unobserved Confounding in the Alzheimer's Continuum
1 Introduction
2 Methods
2.1 The Causal Question and Its Associated Graph
2.2 Identifiability in the Presence of an Unobserved Confounder
2.3 Estimating a Substitute Confounder
2.4 Identifiability in the Presence of a Substitute Confounder
2.5 The Outcome Model
3 Experiments
4 Conclusion
References
Multiple-Shooting Adjoint Method for Whole-Brain Dynamic Causal Modeling
1 Introduction
2 Methods
2.1 Notations and Formulation of Problem
2.2 Multiple-Shooting Method
2.3 Adjoint State Method
2.4 Multiple-Shooting Adjoint (MSA) Method
2.5 Dynamic Causal Modeling
3 Experiments
3.1 Validation on Toy Examples
3.2 Application to Whole-Brain Dynamic Causal Modeling with fMRI
4 Conclusion
References
Going Beyond Saliency Maps: Training Deep Models to Interpret Deep Models
1 Introduction
2 Related Work
3 Methods
3.1 Cycle-Consistent Image Simulation
3.2 Coupling Simulators via Conditional Convolution
3.3 Learning Warping Fields
4 Experiments
4.1 Synthetic Experiments
4.2 Visualizing the Effect of Alzheimer's Disease
4.3 Visualizing the Effect of Alcohol Dependence
5 Conclusion
References
Generative Modelling
Enabling Data Diversity: Efficient Automatic Augmentation via Regularized Adversarial Training
1 Introduction
2 Related Work
3 Method
3.1 Preliminaries
3.2 Regularized Adversarial Data Augmentation
3.3 Data Augmentation Space and Models
4 Experiments
4.1 Experiments Setup
4.2 Skin Lesion Diagnosis Result
4.3 Organ-at-Risk Segmentation Result
5 Conclusion
References
Blind Stain Separation Using Model-Aware Generative Learning and Its Applications on Fluorescence Microscopy Images
1 Introduction
2 Methodology
3 Fluorescence Unmixing
4 Experimental Evaluation
4.1 Experimental Setup
4.2 Results and Discussions
5 Conclusions
References
MR Slice Profile Estimation by Learning to Match Internal Patch Distributions
1 Introduction
2 Methods
2.1 Slice Profile
2.2 Slice Profile and Internal Patch Distributions
2.3 Slice Profile and GAN
2.4 Regularization Functions and Other Details
3 Experiments and Results
3.1 Simulations from Isotropic Images
3.2 Incorporating Slice Profile Estimation into SMORE
3.3 Measuring Through-Plane Resolution After Applying SMORE
4 Discussion and Conclusions
References
Shape
Partial Matching in the Space of Varifolds
1 Introduction
2 Partial Matching
2.1 The Varifold Framework for Shape Matching
2.2 Definition of the Partial Matching Dissimilarity
2.3 Normalized Partial Matching Dissimilarity
2.4 Use in the LDDMM Setting
3 Experiments
4 Conclusion
References
Nested Grassmanns for Dimensionality Reduction with Applications to Shape Analysis
1 Introduction
2 Nested Grassmannians
2.1 The Riemannian Geometry of Grassmann Manifolds
2.2 Embedding of Gr(p, m) in Gr(p, n)
2.3 Unsupervised Dimensionality Reduction
2.4 Supervised Dimensionality Reduction
2.5 Choice of the Distance d
2.6 Analysis of Principal Nested Grassmanns
3 Experiments
3.1 Synthetic Data
3.2 Application to Planar Shape Analysis
4 Conclusion
References
Hierarchical Morphology-Guided Tooth Instance Segmentation from CBCT Images
1 Introduction
2 Methods
2.1 Tooth Centroid and Skeleton Extraction Network
2.2 Multi-task Learning for Tooth Segmentation
2.3 Implementation Details
3 Experimental Results
3.1 Dataset and Evaluation Metrics
3.2 Evaluation and Comparison
3.3 Comparison with the State-of-the-Art Methods
4 Conclusion
References
Cortical Morphometry Analysis Based on Worst Transportation Theory
1 Introduction
2 Theoretic Results
2.1 Optimal Transportation Map
2.2 Worst Transportation Map
2.3 Geometric Variational Method
3 Computational Algorithms
3.1 Basic Concepts from Computational Geometry
3.2 Algorithms Based on Computational Geometry
4 Experiments
5 Conclusion
References
Geodesic B-score for Improved Assessment of Knee Osteoarthritis
1 Introduction
2 Background
2.1 Shape Space
2.2 Geometric Statistics
3 Geodesic B-score
3.1 Generalization
3.2 Sex-Specific Reference
3.3 Algorithmic Treatment
4 Results and Discussion
4.1 Data Description
4.2 Efficiency of Projection Algorithm
4.3 Predictive Validity
5 Conclusion and Future Work
References
Brain Connectivity
Cytoarchitecture Measurements in Brain Gray Matter Using Likelihood-Free Inference
1 Introduction
2 Methods
2.1 Modeling the Brain Gray Matter with a 3-Compartment Model
2.2 An Invertible 3-Compartment Model: dMRI Summary Statistics
2.3 Solving the Inverse Problem via Likelihood Free Inference
3 Results and Discussion
3.1 Simulations
3.2 HCP MGH Results
4 Conclusion
References
Non-isomorphic Inter-modality Graph Alignment and Synthesis for Holistic Brain Mapping
1 Introduction
2 Methodology
3 Experimental Results and Discussion
4 Conclusion
References
Knowledge Transfer for Few-Shot Segmentation of Novel White Matter Tracts
1 Introduction
2 Methods
2.1 Problem Formulation and Classic Fine-Tuning
2.2 Knowledge Transfer for Few-Shot Segmentation of Novel WM Tracts
2.3 A Better Implementation with Warmup
2.4 Implementation Details
3 Results
3.1 Data Description and Experimental Settings
3.2 Evaluation of Segmentation Accuracy
3.3 Impact of the Number of Annotated Training Scans
3.4 Evaluation of Volume Difference
4 Discussion
5 Conclusion
References
Discovering Spreading Pathways of Neuropathological Events in Alzheimer’s Disease Using Harmonic Wavelets
1 Introduction
2 Methods
2.1 Manifold Harmonics
2.2 Construction of Region-Adaptive Harmonic Wavelets
3 Experiments
3.1 Evaluate the Representation Power on Harmonic Wavelets
3.2 Evaluate the Statistic Power of Harmonic Wavelet Fingerprint
4 Conclusions
References
A Multi-scale Spatial and Temporal Attention Network on Dynamic Connectivity to Localize the Eloquent Cortex in Brain Tumor Patients
1 Introduction
2 A Multi-scale Spatial and Temporal Attention Network to Localize the Eloquent Cortex
2.1 Input Dynamic Connectivity Matrices
2.2 Multi-scale Spatial Attention on Convolutional Features
2.3 Temporal Attention Model and Multi-task Learning
3 Experimental Results
3.1 Dataset and Preprocessing
3.2 Localization Results
3.3 Feature Analysis
4 Conclusion
References
Learning Multi-resolution Graph Edge Embedding for Discovering Brain Network Dysfunction in Neurological Disorders
1 Introduction
1.1 Related Work
2 Proposed Method
2.1 Multi-resolution Graph Edge Transform
2.2 Efficient Graph Matrix Transform
2.3 Network Architecture
2.4 Training MENET
3 Experiments
3.1 Datasets
3.2 Experimental Settings
3.3 Structural Brain Connectivity Analysis on ADNI
3.4 Functional Brain Connectivity Analysis on ADHD
3.5 Discussions on Convergence of Scales
4 Conclusion
References
Equivariant Spherical Deconvolution: Learning Sparse Orientation Distribution Functions from Spherical Data
1 Introduction
2 Methods
2.1 Background and Preliminaries
2.2 Equivariant Spherical Deconvolution
3 Experiments
3.1 Noisy Synthetic Benchmark
3.2 The Tractometer Benchmark
3.3 Real-World Multi-shell Human Dataset
4 Discussion
References
Geodesic Tubes for Uncertainty Quantification in Diffusion MRI
1 Introduction
2 Theory
3 Experiments
4 Discussion
References
Structural Connectome Atlas Construction in the Space of Riemannian Metrics
1 Introduction
2 Structural Connectomes as Riemannian Metrics
3 The Geometry of the Manifold of All Metrics
3.1 The Induced Distance Function on the Diffeomorphism Group
4 Computational Anatomy of the Human Connectome
4.1 Estimating the Atlas for a Population of Connectomes
4.2 Implementation Details
5 Results
6 Conclusions
References
A Higher Order Manifold-Valued Convolutional Neural Network with Applications to Diffusion MRI Processing
1 Introduction
2 Preliminary
3 Manifold-Valued Volterra Series and Convolution
3.1 Manifold-Valued Volterra Series
3.2 Manifold-Valued Deep Network Based on MVVS/MVC
3.3 The Cases of Sn and SPD(n)
4 Experiments
4.1 Parkinson's Disease vs. Controls Classification
4.2 fODF Reconstruction
5 Conclusion
References
Representation Learning
Representation Disentanglement for Multi-modal Brain MRI Analysis
1 Introduction
2 Related Works
3 Proposed Method
3.1 Representation Disentanglement by Image-to-image Translation
3.2 Fusing Disentangled Representations for Downstream Tasks
4 Experiments
4.1 Datasets
4.2 Experimental Settings
4.3 Evaluation on Disentangled Representation
4.4 Evaluation on Downstream Tasks
5 Conclusion
References
Variational Knowledge Distillation for Disease Classification in Chest X-Rays
1 Introduction
2 Related Work
3 Methodology
3.1 Preliminaries
3.2 Disease Classification by Conditional Variational Inference
3.3 Knowledge Distillation from EHRs
3.4 Empirical Objective Function
3.5 Implementation with Neural Networks
4 Experiments
4.1 Datasets
4.2 Experimental Settings
4.3 Results
5 Conclusion
References
Information-Based Disentangled Representation Learning for Unsupervised MR Harmonization
1 Introduction
2 Method
2.1 The Disentangling Framework
2.2 Creating a Consistent Anatomical Space
2.3 Learning from an Information Bottleneck
2.4 Domain Adaptation
3 Experiments and Results
3.1 Datasets and Preprocessing
3.2 Qualitative and Quantitative Evaluation
3.3 Domain Adaptation
4 Discussion and Conclusion
References
A3DSegNet: Anatomy-Aware Artifact Disentanglement and Segmentation Network for Unpaired Segmentation, Artifact Reduction, and Modality Translation
1 Introduction
2 Methodology
2.1 Network Architecture
2.2 Network Learning and Loss Functions
2.3 Anatomy-Aware Modality Translation
2.4 3D Segmentation
3 Experiments
3.1 Dataset and Experiment Setup
3.2 Ablation Study
3.3 Comparison with State-of-the-Art
4 Conclusions
References
Unsupervised Learning of Local Discriminative Representation for Medical Images
1 Introduction
2 Related Work
3 Methods
3.1 Local Discrimination Learning
3.2 Prior-Guided Anatomical Structure Clustering
4 Experiments and Discussion
4.1 Network Architectures and Initialization
4.2 Experiments for Learning Local Discrimination
4.3 Experiments for Clustering Structures Based on Prior Knowledge
5 Conclusion
References
TopoTxR: A Topological Biomarker for Predicting Treatment Response in Breast Cancer
1 Introduction
1.1 Related Work
2 Methodology
2.1 Background: Persistent Homology
2.2 Persistence Cycles and Their Computation
2.3 Topological-Cycle-Driven 3D CNN
3 Experimental Results
3.1 Discussion and TopoTxR Feature Interpretation
4 Conclusion
References
Segmentation
Segmenting Two-Dimensional Structures with Strided Tensor Networks
1 Introduction
2 Methods
2.1 Overview
2.2 Tensor Notation
2.3 Image Segmentation Using Linear Models
2.4 Strided Tensor Networks
2.5 Optimisation
3 Data and Experiments
3.1 Data
3.2 Experiments
3.3 Results
4 Discussion and Conclusions
References
Distributional Gaussian Process Layers for Outlier Detection in Image Segmentation
1 Introduction
1.1 Related Work
1.2 Contributions
2 Hierarchical GP with Wasserstein-2 Kernels
3 Convolutionally Warped DistGP and Activation Function
4 Imposing Lipschitz Conditions in Convolutionally Warped DistGP
4.1 Proving Lipschitz Bounds in a DistGP Layer
5 DistGP-Based Segmentation Network and OOD Detection
6 Evaluation on Brain MRI
6.1 Data and Pre-processing
6.2 Brain Tissue Segmentation on Normal MRI Scans
6.3 Outlier Detection in MRI Scans with Tumors
7 Discussion
References
Deep Label Fusion: A 3D End-To-End Hybrid Multi-atlas Segmentation and Deep Learning Pipeline
1 Introduction
2 Materials
3 Method
3.1 Deep Label Fusion
3.2 Alternative Methods for Comparisons
4 Experiments and Results
5 Conclusion
References
Feature Library: A Benchmark for Cervical Lesion Segmentation
1 Introduction
2 Related Works
2.1 Automated Cervical Lesion Segmentation
2.2 Colposcopic Image Datasets
3 CINEMA Dataset
4 Benchmark Method
5 Experiments
5.1 Ablation Study
5.2 Comparison with Baselines
6 Conclusion
References
Generalized Organ Segmentation by Imitating One-Shot Reasoning Using Anatomical Correlation
1 Introduction
2 Related Work
3 Proposed Method
3.1 One-Shot Reasoning Using OrganNet
3.2 Pyramid Reasoning Modules
4 Experiments and Results
4.1 Dataset and Evaluation Metric
4.2 Implementation Details
4.3 Comparison with One-Shot Segmentation Methods: Better Performance
4.4 Comparison with Supervised 3D U-Nets: Less Labeling Cost
4.5 Ablation Study on Network Design
4.6 Visual Analysis
4.7 Generalization to Non-organ Segmentation
5 Conclusions and Future Work
References
EnMcGAN: Adversarial Ensemble Learning for 3D Complete Renal Structures Segmentation
1 Introduction
2 Methodology
2.1 Multi-windowing Committee for Multiple Fine-Grained Representation
2.2 Multi-condition GAN for Shape Constraints
2.3 Adversarial Weighted Ensemble for Personalized Fine Fusion
3 Materials and Configurations
4 Results and Analysis
4.1 Comparative Study Shows Superiority
4.2 Ablation Study Shows Improvements of the Innovations
4.3 Framework Analysis
5 Conclusion
References
Segmentation with Multiple Acceptable Annotations: A Case Study of Myocardial Segmentation in Contrast Echocardiography
1 Introduction
2 Related Work
3 Method
4 Experiment
4.1 Dataset
4.2 Training DNN with Extended Dice Loss
4.3 Extended Dice as a Superior Evaluation Metric
5 Conclusion
References
A New Bidirectional Unsupervised Domain Adaptation Segmentation Framework
1 Introduction
2 Method
2.1 Problem Definition
2.2 DRPL Framework with Domain-Aware Pattern Encoder
2.3 Loss Functions for DRPL-based BiUDA Framework
3 Experiments
4 Discussion
5 Conclusion
References
3D Nucleus Instance Segmentation for Whole-Brain Microscopy Images
1 Introduction
2 Problem Formulation
3 Proposed Model
3.1 Encoder
3.2 Reconstruction Branch
3.3 Identity Propagation Branch
4 Experiments
4.1 Dataset
4.2 Experiment Setup
4.3 Results
5 Conclusion
References
Teach Me to Segment with Mixed Supervision: Confident Students Become Masters
1 Introduction
2 Related Work
3 Methodology
3.1 Multi-branch Architecture
3.2 Supervised Learning
3.3 Not So-Supervised Branch
3.4 Distilling Strong Knowledge
3.5 Shannon-Entropy Minimization
3.6 Link Between Entropy and Pseudo-mask Supervision
3.7 Joint Objective
4 Experimental Setting
4.1 Results
References
Sequential Modelling
Future Frame Prediction for Robot-Assisted Surgery
1 Introduction
2 Method
2.1 Problem Formulation
2.2 Decomposed Video Encoding Network
2.3 Ternary Latent Variable
2.4 Learning Process
3 Experimental Results
3.1 Dataset and Evaluation Metrics
3.2 Implementation Details
3.3 Results
4 Conclusion and Future Work
References
Velocity-To-Pressure (V2P) - Net: Inferring Relative Pressures from Time-Varying 3D Fluid Flow Velocities
1 Introduction
2 Methodology
2.1 Background
2.2 V2P-Net:
3 Experiments
4 Results and Discussion:
5 Conclusion
References
Lighting Enhancement Aids Reconstruction of Colonoscopic Surfaces
1 Introduction
2 Background: SLAM and Colonoscopic Reconstruction
2.1 SLAM Mechanism
2.2 The Lighting Problem in Colonoscopic Surface Reconstruction
3 Method
3.1 Adaptive Gamma Correction
3.2 RNN Network
3.3 Training Strategy
4 Experiments
4.1 Implementation Details
4.2 Visual Effect
4.3 Application in Colonoscopic Surface Reconstruction
5 Discussion and Conclusion
References
Mixture Modeling for Identifying Subtypes in Disease Course Mapping
1 Introduction
2 Related Work
3 Method
3.1 Disease Course Mapping Model
3.2 Mixture of Disease Course Mapping Models
3.3 Tempered Scheme
3.4 Initialization Method
4 Results and Discussion
4.1 Simulated Data
4.2 Applications on Alzheimer's Disease Data
References
Learning Transition Times in Event Sequences: The Temporal Event-Based Model of Disease Progression
1 Introduction
2 Theory
2.1 Temporal Event-Based Model
2.2 Inference
2.3 Staging
3 Experiments and Results
3.1 Alzheimer's Disease Data
3.2 Model Training
3.3 TEBM Parameters
3.4 Alzheimer's Disease Timeline
3.5 Individual Trajectories
3.6 Prediction of Progression Rate
3.7 Comparative Model Performance
3.8 Performance with Missing Data
4 Discussion
References
Learning with Few or Low Quality Labels
Knowledge Distillation with Adaptive Asymmetric Label Sharpening for Semi-supervised Fracture Detection in Chest X-Rays
1 Introduction
2 Method
2.1 Knowledge Distillation Learning
2.2 Adaptive Asymmetric Label Sharpening
2.3 Implementation Details
3 Experiments
3.1 Experimental Settings
3.2 Comparison with Baseline Methods
3.3 Ablation Study
4 Conclusion
References
Semi-Supervised Screening of COVID-19 from Positive and Unlabeled Data with Constraint Non-Negative Risk Estimator
1 Introduction
2 Related Work
2.1 Automated COVID-19 Screening
2.2 Positive Unlabeled Learning
3 Methodology
3.1 Learning Set-Up
3.2 Unbiased PU Learning
3.3 Constraint Non-Negative PU Learning
3.4 Theoretical Analyses
4 Experiments
4.1 Setup
4.2 Results
4.3 Insight Analyses
5 Conclusion
References
Deep MCEM for Weakly-Supervised Learning to Jointly Segment and Recognize Objects Using Very Few Expert Segmentations
1 Introduction and Related Work
2 Methods
2.1 DNN-Based Variational Model for Object Segmentation
2.2 DNN-Based Statistical Model to Recognize a Segmented Object
2.3 MCEM for Weakly-Supervised Segmenter-Recognizer Learning
2.4 Efficient MH Sampling of Missing Segmentations and Encodings
2.5 Deep-MCEM Based Inference Strategy for Test Images
3 Results and Discussion
4 Conclusion
References
Weakly Supervised Deep Learning for Aortic Valve Finite Element Mesh Generation from 3D CT Images
1 Introduction
2 Methods
2.1 Possible Problem Formulation: Meshing from Segmentation
2.2 Proposed Problem Formulation: Mesh Template Matching
2.3 Deformation Field
3 Experiments and Results
3.1 Data Acquisition and Preprocessing
3.2 Implementation Details
3.3 Evaluation Metrics
3.4 Comparison with an Image Intensity Gradient-Based Approach
3.5 Comparison with Other Deformation Strategies
3.6 FEA Results
3.7 Limitations and Future Works
4 Conclusion
References
Continual Active Learning for Efficient Adaptation of Machine Learning Models to Changing Image Acquisition
1 Introduction
2 Method
2.1 CASA Training Scheme
2.2 Pseudo-domain Module
2.3 Task Module
2.4 Training Memory
2.5 Outlier Memory and Pseudo-domain Identification
3 Experiments and Results
3.1 Data Set
3.2 Methods Compared in the Evaluation
3.3 Experimental Setup
3.4 Model Accuracy Across Domains
3.5 Evaluation of the Memory and Pseudo-Domains
4 Conclusion
References
Multimodal Self-supervised Learning for Medical Image Analysis
1 Introduction
2 Related Work
3 Method
3.1 Multimodal Puzzle Construction
3.2 Puzzle-Solving with Sinkhorn Networks
3.3 Cross-modal Generation
4 Experimental Results
4.1 Datasets
4.2 Transfer Learning ResultsWe Evaluate on realistic data in this section, using a 5-fold cross validation approach.
4.3 Low-Shot Learning Results
4.4 Cross-modal Generation Results
5 Conclusion and Future Work
References
Uncertainty Quantification and Generative Modelling
Spatially Varying Label Smoothing: Capturing Uncertainty from Expert Annotations
1 Introduction
2 Spatially Varying Label Smoothing
2.1 Multi-rater SVLS
3 Experiments
3.1 Datasets
3.2 Implementation Details and Baselines
4 Results
4.1 Evaluation Metrics
4.2 Multi-class Image Segmentation
4.3 Multiple Expert Annotations
5 Discussion
References
Quantile Regression for Uncertainty Estimation in VAEs with Applications to Brain Lesion Detection
1 Introduction
2 Background
2.1 Variance Shrinkage Problem in Variational Autoencoders
2.2 Conditional Quantile Regression
3 Proposed Approach: Uncertainty Estimation for Autoencoders with Quantile Regression (QR-VAE)
4 Experiments and Results
4.1 Simulations
4.2 Unsupervised Lesion Detection
5 Conclusion
References
A Probabilistic Framework for Modeling the Variability Across Federated Datasets
1 Introduction
2 State of the Art
3 Federated Multi-views PPCA
3.1 Problem Setup
3.2 Modeling Assumptions
3.3 Proposed Framework
4 Applications
4.1 Materials
4.2 Benchmark
4.3 Results
5 Conclusions
References
Is Segmentation Uncertainty Useful?
1 Introduction
2 Modelling Segmentation Uncertainty
3 Probabilistic Segmentation Networks
4 Experiments
4.1 Data
4.2 Model Tuning and Training
4.3 Uncertainty Estimation
4.4 Sampling Segmentation Masks
4.5 Uncertainty Estimates for Active Learning
5 Discussion and Conclusion
References
Deep Learning
Principled Ultrasound Data Augmentation for Classification of Standard Planes
1 Introduction
2 Methods
3 Experiments and Results
4 Conclusion
References
Adversarial Regression Learning for Bone Age Estimation
1 Introduction
2 Related Work
3 Method
3.1 Motivation
3.2 Problem
3.3 Adversarial Regression Learning
3.4 Overall Objective
4 Experiments
4.1 Datasets
4.2 Implementation Details
4.3 Evaluation
5 Discussion
6 Conclusion
References
Learning Image Quality Assessment by Reinforcing Task Amenable Data Selection
1 Introduction
2 Method
2.1 Image Quality Assessment by Task Amenability
2.2 The Reinforcement Learning Algorithm
2.3 Image Quality Assessment with Reinforcement Learning
3 Experiment
4 Result
5 Discussion and Conclusion
References
Collaborative Multi-agent Reinforcement Learning for Landmark Localization Using Continuous Action Space
1 Introduction
2 Method
3 Experimental Setup
4 Results
5 Discussion
6 Conclusion
References
Author Index
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Information Processing in Medical Imaging: 27th International Conference, IPMI 2021, Virtual Event, June 28–June 30, 2021, Proceedings (Lecture Notes in Computer Science, 12729) [1st ed. 2021]
 3030781909, 9783030781903

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LNCS 12729

Aasa Feragen Stefan Sommer Julia Schnabel Mads Nielsen (Eds.)

Information Processing in Medical Imaging 27th International Conference, IPMI 2021 Virtual Event, June 28–June 30, 2021 Proceedings

Lecture Notes in Computer Science Founding Editors Gerhard Goos Karlsruhe Institute of Technology, Karlsruhe, Germany Juris Hartmanis Cornell University, Ithaca, NY, USA

Editorial Board Members Elisa Bertino Purdue University, West Lafayette, IN, USA Wen Gao Peking University, Beijing, China Bernhard Steffen TU Dortmund University, Dortmund, Germany Gerhard Woeginger RWTH Aachen, Aachen, Germany Moti Yung Columbia University, New York, NY, USA

12729

More information about this subseries at http://www.springer.com/series/7412

Aasa Feragen · Stefan Sommer · Julia Schnabel · Mads Nielsen (Eds.)

Information Processing in Medical Imaging 27th International Conference, IPMI 2021 Virtual Event, June 28–June 30, 2021 Proceedings

Editors Aasa Feragen Technical University of Denmark Kgs Lyngby, Denmark

Stefan Sommer University of Copenhagen Copenhagen, Denmark

Julia Schnabel King’s College London London, UK

Mads Nielsen University of Copenhagen Copenhagen, Denmark

ISSN 0302-9743 ISSN 1611-3349 (electronic) Lecture Notes in Computer Science ISBN 978-3-030-78190-3 ISBN 978-3-030-78191-0 (eBook) https://doi.org/10.1007/978-3-030-78191-0 LNCS Sublibrary: SL6 – Image Processing, Computer Vision, Pattern Recognition, and Graphics © Springer Nature Switzerland AG 2021 This work is subject to copyright. All rights are reserved by the Publisher, whether the whole or part of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission or information storage and retrieval, electronic adaptation, computer software, or by similar or dissimilar methodology now known or hereafter developed. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publication does not imply, even in the absence of a specific statement, that such names are exempt from the relevant protective laws and regulations and therefore free for general use. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authors or the editors give a warranty, expressed or implied, with respect to the material contained herein or for any errors or omissions that may have been made. The publisher remains neutral with regard to jurisdictional claims in published maps and institutional affiliations. This Springer imprint is published by the registered company Springer Nature Switzerland AG The registered company address is: Gewerbestrasse 11, 6330 Cham, Switzerland

Preface

The Information Processing in Medical Imaging (IPMI) conferences have a long history and broad reach. Since 1969, the conferences have taken place on either side of the Atlantic, and the very first IPMI in Asia occurred fifty years later in Hong Kong. IPMI 2021, the twenty-seventh conference in the series, was scheduled to happen in Denmark on the island of Bornholm in the Baltic Sea. However, in the spring and summer of 2021, the COVID-19 pandemic remained a challenge in large parts of the world. Though swift and extensive vaccination programs promised to soon reclaim normality, uncertainty related to international travel made a large physical gathering impossible. Therefore, IPMI 2021 was the first in the conference series to take place not in Asia, the USA, or Europe, but entirely virtually. All these decades have established traditions that give the IPMI conferences a very special feel and help to promote the series’ hallmarks: IPMI places the utmost importance on high-quality submissions coupled with presentations and thorough discussions of the presented contributions. To facilitate this, the venues are often chosen in remote locations and the conferences have discussion groups, social activities, and unlimited discussion time for each presentation. In 2021, we were challenged with organizing a conference that kept as many of these aspects as possible in a virtual venue. We made every effort to retain the IPMI traditions and ideas while navigating the restrictions of a virtual conference. IPMI 2021 built on the traditional study groups to extend the discussions to both papers presented orally and in poster sessions. The virtual setting allowed study groups to meet before the conference to start the discussions and network in the groups. During the conference, poster sessions ran twice to accommodate time-zone differences. In addition to live talks, oral presenters had posters where participants could meet and discuss the paper and presentations according to their time-zone preference, with no restrictions on duration. Gitte Moos Knudsen, Professor at the Department of Neurology and Chair of the Neurobiology Research Unit, Copenhagen University Hospital, gave the keynote at IPMI 2021. And of course the conference included the traditional IPMI soccer match, this time without a physical ball. IPMI 2021 received 204 submissions, of which 200 papers went into peer review and were reviewed by at least 3 reviewers each. Following the reviewing process, each paper that received at least one “accept” was read by one or more members of the Paper Selection Committee, and most of these papers were discussed at the paper selection meeting. 59 submissions were accepted for publication and presentation at the conference, resulting in a 30% acceptance rate. At the conference, 19 oral presentations and 40 posters were presented on topics ranging from brain connectivity, image registration and segmentation, causal models and interpretability, representation learning, computer-assisted intervention, differential geometry, and shape analysis. One of the defining priorities throughout the organization was diversity. In particular, all committees had at least 40% representation of either gender, and we also strived for

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Preface

a diverse reviewing pool. We are excited to note that among the accepted papers we find first authors from Asia, Africa, North America and Europe – a trend that we hope will continue. The François Erbsmann Prize is awarded to a young scientist of age 35 or below, who is the first author of a paper, giving his/her first oral presentation at IPMI. The prize was awarded to one of the 18 eligible oral presenters, and awards were given for the best poster presentations. The IPMI 2021 organizing team would like to send a special thanks to both the Scientific Committee and the Paper Selection Committee: the 166 reviewers did an excellent job in reviewing the submitted papers. The Paper Selection Committee - Polina Golland, Martin Styner, Albert Chung, Ender Konukoglu, Marleen de Bruijne, Dorin Comaniciu, Ipek Oguz, and Demian Wassermann - reached decisions for each paper based on the reviews and thorough discussions in the committee. Due to the pandemic, the paper selection meeting was virtual as well. This, however, proved no obstacle for the work: the committee worked efficiently through a number of long hours on Zoom to decide on the final list of accepted papers. We would like to thank the IPMI board for giving us the opportunity to host IPMI 2021, and for valuable discussions on how to handle the difficult situation regarding the COVID-19 pandemic. This in particular applies to Albert Chung, who in addition to being chairman of the IPMI board was also the organizer of IPMI 2019. Albert has been invaluable in sharing experiences on organizational aspects and in discussing how to organize the first virtual IPMI. IPMI 2021 was supported financially by the Carlsberg Foundation, the Lundbeck Foundation, the Otto Mønsted Foundation, and Springer. We are extremely grateful for the support which has allowed us to offer a number of IPMI scholarships for participants needing financial assistance to attend IPMI as well as a general reduction in registration fees. Furthermore, we wish to thank our universities – the University of Copenhagen, the Technical University of Denmark, and King’s College London - for generous organizational and administrative support. We have been delighted to organize IPMI 2021 and present the range of excellent scientific work covered in this volume. We hope IPMI 2021 offered the best possible experience for a first time virtual IPMI. Perhaps IPMI 2021 will be the only virtual conference in the series, or perhaps some form of virtuality will persist or reappear in future IPMIs. We did our very best to organize the conference in a very difficult time. May 2021

Stefan Sommer Aasa Feragen Julia Schnabel Mads Nielsen

Organization

Conference Chairs Stefan Sommer Aasa Feragen Julia Schnabel Mads Nielsen

University of Copenhagen, Denmark Technical University of Denmark, Denmark King’s College London, UK University of Copenhagen, Denmark

Communications and Local Organization Nanna Højholt

University of Copenhagen, Denmark

Paper Selection Committee Polina Golland Martin Styner Albert Chung Ender Konukoglu Marleen de Bruijne Dorin Comaniciu Ipek Oguz Demian Wassermann

Massachusetts Institute of Technology, USA University of North Carolina at Chapel Hill, USA The Hong Kong University of Science and Technology, Hong Kong ETH Zurich, Switzerland Erasmus MC the Netherlands, and University of Copenhagen, Denmark Siemens Healthineers, USA Vanderbilt, USA Inria, France

Scientific Committee Adrian V. Dalca Akshay Pai Alexis Arnaudon Alice Barbara Tumpach Alison Noble Anand Joshi Andrea Fuster Andrew King Anna Calissano Anuj Srivastava Archana Venkataraman Arrate Munoz Barrutia Ayushi Sinha

Massachusetts Institute of Technology, USA Cerebriu, Denmark Imperial College London, UK University of Lille, France University of Oxford, UK University of Southern California, USA Eindhoven University of Technology, the Netherlands King’s College London, UK Politecnico di Milano, Italy Florida State University, USA Johns Hopkins University, USA Universidad Carlos III de Madrid, Spain Philips Research, USA

viii

Organization

Baba Vemuri Beatriz Paniagua Ben Glocker Bennett A. Landman Benoit Dawant Bjoern Menze Boklye Kim Boudewijn Lelieveldt Bulat Ibragimov Carl-Fredrik Westin Carole H. Sudre Caroline Petitjean Catie Chang Chantal Tax Chao Chen Chen Chen Chen Qin Christof Seiler Chuyang Ye Claire Cury Clara Sanchez Gutierrez Daniel Alexander Daniel Rueckert Darko Stern Diana Mateus Dou Qi Dzung Pham Ehsan Adeli Elizabeth A. Krupinski Enzo Ferrante Erik B. B. Dam Ernst Schwartz Ertunc Erdil Esther E. Bron Esther Puyol-Antón Francois-Xavier Vialard Frithjof Kruggel Gary E. Christensen Gemma Piella Ghada Zamzmi Guido Gerig Harshita Sharma Herve Lombaert Hongzhi Wang Isabelle Bloch Islem Rekik

University of Florida, USA Kitware, USA Imperial College London, UK Vanderbilt University, USA Vanderbilt University, USA Technical University of Munich, Germany University of Michigan, USA Leiden University Medical Center, the Netherlands University of Copenhagen, Denmark Harvard University, USA University College London, UK Université de Rouen, France Vanderbilt University, USA Cardiff University, UK Stony Brook University, USA Imperial College London, UK Imperial College London, UK Maastricht University, the Netherlands Beijing Institute of Technology, China Inria, France Radboud UMC, the Netherlands University College London, UK Imperial College London, UK Technical University of Graz, Austria Centrale Nantes, France The Chinese University of Hong Kong, Hong Kong Henry M. Jackson Foundation, USA Stanford University, USA University of Arizona, USA CONICET, Argentina University of Copenhagen, Denmark Medical University of Vienna, Austria ETH Zurich, Switzerland Erasmus MC, the Netherlands King’s College London, UK University of Paris-Est, France UC Irvine, USA University of Iowa, USA Pompeu Fabra University, Spain NIH, USA New York University, USA University of Oxford, UK Microsoft Research-Inria Joint Centre, France IBM Research, USA Télécom Paris, France Istanbul Technical University, Turkey

Organization

Ivan Ezhov Ivor J. A. Simpson James S. Duncan James Gee Jan Kybic Jana Hutter Jens Petersen Jeppe Thagaard Jerry L. Prince Jesper L. Hinrich John Ashburner Jon Sporring Joseph Reinhardt Justin Haldar Kaleem Siddiqi Karl Rohr Karthik Gopinath Kayhan Batmanghelich Kilian Pohl Klaus H. Maier-Hein Laura Igual Laurent Risser Lei Du Lei Li Li Shen Li Tang Lilla Zöllei Linwei Wang Luping Zhou M. Jorge Cardoso Magdalini Paschali Mahdieh Khanmohammadi Marc Niethammer Marco Lorenzi Marco Pizzolato Maria A. Zuluaga Mathilde Bateson Matthew Toews Mattias Heinrich Michela Antonelli Mingchen Gao Mingxia Liu Moo Chung Natasha Lepore Nicola Rieke Nina Miolane

ix

Technical University of Munich, Germany University of Sussex, UK Yale University, USA University of Pennsylvania, USA Czech Technical University in Prague, Czech Republic King’s College London, UK University of Copenhagen, Denmark Visiopharm, Denmark Johns Hopkins University, USA University of Copenhagen, Denmark University College London, UK University of Copenhagen, Denmark University of Iowa, USA University of Southern California, USA McGill University, Canada University of Heidelberg, Germany ETS Montreal, Canada University of Pittsburgh, USA SRI, USA German Cancer Research Center (DKFZ), Germany Universitat de Barcelona, Spain CNRS, France Northwestern Polytechnical University, USA Shanghai Jiao Tong University, China University of Pennsylvania, USA University of Iowa, USA Massachusetts General Hospital, USA Rochester Institute of Technology, USA University of Sydney, Australia King’s College London, UK Technische Universität München, Germany University of Stavanger, Norway UNC, USA Inria, France Technical University of Denmark, Denmark EURECOM, France ETS Montreal, Canada École de technologie supérieure, Canada University of Luebeck, Germany King’s College London, UK University at Buffalo, USA UNC, USA University of Wisconsin at Madison, USA Children’s Hospital Los Angeles, USA NVIDIA, Germany Stanford University, USA

x

Organization

Nooshin Ghavami Olivier Commowick Olivier Salvado Paul A. Yushkevich Pengcheng Shi Pew-Thian Yap Pierre-Louis Bazin Qingyu Zhao Raghavendra Selvan Rasmus R. Paulsen Razvan V. Marinescu Reyer Zwiggelaar Roland Kwitt Ross Whitaker Roxane Licandro Sami S. Brandt Sara Garbarino Sarah Gerard Shanshan Wang Shireen Elhabian Shuo Li Sidsel Winther Silas N. Ørting Simon K. Warfield Sophia Bano Stefan Klein Steffen Czolbe Steve Pizer Sune Darkner Suyash P. Awate Sylvain Bouix Talha Qaiser Tessa Cook Tianming Liu Tim Cootes Tim Dyrby Tobias Heimann Ulas Bagci Vedrana A. Dahl Veronika A. Zimmer Wenqi Li Xavier Pennec Xiaoran Chen Xiaoxiao Li Yalin Wang Yi Hong Yixuan Yuan Yong Fan Yonggang Shi

King’s College London, UK Inria, France Australian e-Health Research Centre, Australia University of Pennsylvania, USA Rochester Institute of Technology, USA University of North Carolina at Chapel Hill, USA University of Amsterdam, the Netherlands Stanford University, USA University of Copenhagen, Denmark Technical University of Denmark, Denmark Massachusetts Institute of Technology, USA University of Aberystwyth, UK University of Salzburg, Austria University of Utah, USA TU Wien, Austria IT University of Copenhagen, Denmark Università di Genova, Italy Harvard Medical School, USA Shenzhen Institute of Advanced Technology, China University of Utah, USA University of Western Ontario, Canada Technical University of Denmark, Denmark University of Copenhagen, Denmark Harvard University, USA University College London, UK Erasmus MC, the Netherlands University of Copenhagen, Denmark University of North Carolina, USA University of Copenhagen, Denmark Indian Institute of Technology Bombay, India Brigham and Women’s Hospital, USA Imperial College London, UK University of Pennsylvania, USA University of Georgia, USA University of Manchester, UK Technical University of Denmark, Denmark Siemens Healthineers, Germany Northwestern University, USA Technical University of Denmark, Denmark King’s College London, UK NVIDIA, UK Inria, France ETH Zurich, Switzerland Princeton University, USA Arizona State University, USA Shanghai Jiao Tong University, China City University of Hong Kong, Hong Kong University of Pennsylvania, USA University of Southern California, USA

Organization

xi

IPMI 2021 Board Albert Chung Martin Styner James Duncan Stephen Pizer Chris Taylor Gary Christensen Gabor Szekely Jerry Prince William Wells Sebastien Ourselin Marleen de Bruijne Randy Brill Andrew Todd-Pokropek Polina Golland Alison Noble Richard Leahy

The Hong Kong University of Science and Technology, Hong Kong University of North Carolina, USA Yale University, USA University of North Carolina at Chapel Hill, USA University of Manchester, UK University of Iowa, USA ETH Zurich, Switzerland Johns Hopkins University, USA Harvard Medical School, USA King’s College London, UK Erasmus MC, the Netherlands Vanderbilt University, USA University College London, UK Massachusetts Institute of Technology, USA Oxford University, UK University of Southern California, USA

Contents

Registration HyperMorph: Amortized Hyperparameter Learning for Image Registration . . . . Andrew Hoopes, Malte Hoffmann, Bruce Fischl, John Guttag, and Adrian V. Dalca

3

Deep Learning Based Geometric Registration for Medical Images: How Accurate Can We Get Without Visual Features? . . . . . . . . . . . . . . . . . . . . . . . . . . . . Lasse Hansen and Mattias P. Heinrich

18

Diffeomorphic Registration with Density Changes for the Analysis of Imbalanced Shapes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Hsi-Wei Hsieh and Nicolas Charon

31

Causal Models and Interpretability Estimation of Causal Effects in the Presence of Unobserved Confounding in the Alzheimer’s Continuum . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Sebastian Pölsterl and Christian Wachinger Multiple-Shooting Adjoint Method for Whole-Brain Dynamic Causal Modeling . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Juntang Zhuang, Nicha Dvornek, Sekhar Tatikonda, Xenophon Papademetris, Pamela Ventola, and James S. Duncan Going Beyond Saliency Maps: Training Deep Models to Interpret Deep Models . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Zixuan Liu, Ehsan Adeli, Kilian M. Pohl, and Qingyu Zhao

45

58

71

Generative Modelling Enabling Data Diversity: Efficient Automatic Augmentation via Regularized Adversarial Training . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . Yunhe Gao, Zhiqiang Tang, Mu Zhou, and Dimitris Metaxas

85

Blind Stain Separation Using Model-Aware Generative Learning and Its Applications on Fluorescence Microscopy Images . . . . . . . . . . . . . . . . . . . . . . . . . . Xingyu Li

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Contents

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