腹部CT像上の複数オブジェクトのセグメンテーションのための統計的手法に関する研究

Computer aided diagnosis (CAD) is the use of a computer-generated output as an auxiliary tool for the assistance of efficient interpretation and accurate diagnosis. Medical image segmentation has an essential role in CAD in clinical applications. Generally, the task of medical image segmentation involves multiple objects, such as organs or diffused tumor regions. Moreover, it is very unfavorable to segment these regions from abdominal Computed Tomography (CT) images because of the overlap in intensity and variability in position and shape of soft tissues. In this thesis, a progressive segmentation framework is proposed to extract liver and tumor regions from CT images more efficiently, which includes the steps of multiple organs coarse segmentation, fine segmentation, and liver tumors segmentation. Benefit from the previous knowledge of the shape and its deformation, the Statistical shape model (SSM) method is firstly utilized to segment multiple organs regions robustly. In the process of building an SSM, the correspondence of landmarks is crucial to the quality of the model. To generate a more representative prototype of organ surface, a k-mean clustering method is proposed. The quality of the SSMs, which is measured by generalization ability, specificity, and compactness, was improved. We furtherly extend the shapes correspondence to multiple objects. A non-rigid iterative closest point surface registration process is proposed to seek more properly corresponded landmarks across the multi-organ surfaces. The accuracy of surface registration was improved as well as the model quality. Moreover, to localize the abdominal organs simultaneously, we proposed a random forest regressor cooperating intensity features to predict the position of multiple organs in the CT image. The regions of the organs are substantially restrained using the trained shape models. The accuracy of coarse segmentation using SSMs was increased by the initial information of organ positions.Consequently, a pixel-wise segmentation using the classification of supervoxels is applied for the fine segmentation of multiple organs. The intensity and spatial features are extracted from each supervoxels and classified by a trained random forest. The boundary of the supervoxels is closer to the real organs than the previous coarse segmentation. Finally, we developed a hybrid framework for liver tumor segmentation in multiphase images. To deal with these issues of distinguishing and delineating tumor regions and peripheral tissues, this task is accomplished in two steps: a cascade region-based convolutional neural network (R-CNN) with a refined head is trained to locate the bounding boxes that contain tumors, and a phase-sensitive noise filtering is introduced to refine the following segmentation of tumor regions conducted by a level-set-based framework. The results of tumor detection show the adjacent tumors are successfully separated by the improved cascaded R-CNN. The accuracy of tumor segmentation is also improved by our proposed method. 26 cases of multi-phase CT images were used to validate our proposed method for the segmentation of liver tumors. The average precision and recall rates for tumor detection are 76.8% and 84.4%, respectively. The intersection over union, true positive rate, and false positive rate for tumor segmentation are 72.7%, 76.2%, and 4.75%, respectively.九州工業大学博士学位論文 学位記番号: 工博甲第546号 学位授与年月日: 令和4年3月25日1 Introduction|2 Literature Review|3 Statistical Shape Model Building|4 Multi-organ Segmentation|5 Liver Tumors Segmentation|6 Summary and Outlook九州工業大学令和3年

Attention Gated Networks: Learning to Leverage Salient Regions in Medical Images

We propose a novel attention gate (AG) model for medical image analysis that automatically learns to focus on target structures of varying shapes and sizes. Models trained with AGs implicitly learn to suppress irrelevant regions in an input image while highlighting salient features useful for a specific task. This enables us to eliminate the necessity of using explicit external tissue/organ localisation modules when using convolutional neural networks (CNNs). AGs can be easily integrated into standard CNN models such as VGG or U-Net architectures with minimal computational overhead while increasing the model sensitivity and prediction accuracy. The proposed AG models are evaluated on a variety of tasks, including medical image classification and segmentation. For classification, we demonstrate the use case of AGs in scan plane detection for fetal ultrasound screening. We show that the proposed attention mechanism can provide efficient object localisation while improving the overall prediction performance by reducing false positives. For segmentation, the proposed architecture is evaluated on two large 3D CT abdominal datasets with manual annotations for multiple organs. Experimental results show that AG models consistently improve the prediction performance of the base architectures across different datasets and training sizes while preserving computational efficiency. Moreover, AGs guide the model activations to be focused around salient regions, which provides better insights into how model predictions are made. The source code for the proposed AG models is publicly available.Comment: Accepted for Medical Image Analysis (Special Issue on Medical Imaging with Deep Learning). arXiv admin note: substantial text overlap with arXiv:1804.03999, arXiv:1804.0533

Stratified decision forests for accurate anatomical landmark localization in cardiac images

Accurate localization of anatomical landmarks is an important step in medical imaging, as it provides useful prior information for subsequent image analysis and acquisition methods. It is particularly useful for initialization of automatic image analysis tools (e.g. segmentation and registration) and detection of scan planes for automated image acquisition. Landmark localization has been commonly performed using learning based approaches, such as classifier and/or regressor models. However, trained models may not generalize well in heterogeneous datasets when the images contain large differences due to size, pose and shape variations of organs. To learn more data-adaptive and patient specific models, we propose a novel stratification based training model, and demonstrate its use in a decision forest. The proposed approach does not require any additional training information compared to the standard model training procedure and can be easily integrated into any decision tree framework. The proposed method is evaluated on 1080 3D highresolution and 90 multi-stack 2D cardiac cine MR images. The experiments show that the proposed method achieves state-of-theart landmark localization accuracy and outperforms standard regression and classification based approaches. Additionally, the proposed method is used in a multi-atlas segmentation to create a fully automatic segmentation pipeline, and the results show that it achieves state-of-the-art segmentation accuracy

Morphological and multi-level geometrical descriptor analysis in CT and MRI volumes for automatic pancreas segmentation

Automatic pancreas segmentation in 3D radiological scans is a critical, yet challenging task. As a prerequisite for computer-aided diagnosis (CADx) systems, accurate pancreas segmentation could generate both quantitative and qualitative information towards establishing the severity of a condition, and thus provide additional guidance for therapy planning. Since the pancreas is an organ of high inter-patient anatomical variability, previous segmentation approaches report lower quantitative accuracy scores in comparison to abdominal organs such as the liver or kidneys. This paper presents a novel approach for automatic pancreas segmentation in magnetic resonance imaging (MRI) and computer tomography (CT) scans. This method exploits 3D segmentation that, when coupled with geometrical and morphological characteristics of abdominal tissue, classifies distinct contours in tight pixel-range proximity as “pancreas” or “non-pancreas”. There are three main stages to this approach: (1) identify a major pancreas region and apply contrast enhancement to differentiate between pancreatic and surrounding tissue; (2) perform 3D segmentation via continuous max-flow and min-cuts approach, structured forest edge detection, and a training dataset of annotated pancreata; (3) eliminate non-pancreatic contours from resultant segmentation via morphological operations on area, structure and connectivity between distinct contours. The proposed method is evaluated on a dataset containing 82 CT image volumes, achieving mean Dice Similarity coefficient (DSC) of 79.3 ± 4.4%. Two MRI datasets containing 216 and 132 image volumes are evaluated, achieving mean DSC 79.6 ± 5.7% and 81.6 ± 5.1% respectively. This approach is statistically stable, reflected by lower metrics in standard deviation in comparison to state-of-the-art approaches

Automatic Pancreas Segmentation and 3D Reconstruction for Morphological Feature Extraction in Medical Image Analysis

The development of highly accurate, quantitative automatic medical image segmentation techniques, in comparison to manual techniques, remains a constant challenge for medical image analysis. In particular, segmenting the pancreas from an abdominal scan presents additional difficulties: this particular organ has very high anatomical variability, and a full inspection is problematic due to the location of the pancreas behind the stomach. Therefore, accurate, automatic pancreas segmentation can consequently yield quantitative morphological measures such as volume and curvature, supporting biomedical research to establish the severity and progression of a condition, such as type 2 diabetes mellitus. Furthermore, it can also guide subject stratification after diagnosis or before clinical trials, and help shed additional light on detecting early signs of pancreatic cancer. This PhD thesis delivers a novel approach for automatic, accurate quantitative pancreas segmentation in mostly but not exclusively Magnetic Resonance Imaging (MRI), by harnessing the advantages of machine learning and classical image processing in computer vision. The proposed approach is evaluated on two MRI datasets containing 216 and 132 image volumes, achieving a mean Dice similarity coefficient (DSC) of 84:1 4:6% and 85:7 2:3% respectively. In order to demonstrate the universality of the approach, a dataset containing 82 Computer Tomography (CT) image volumes is also evaluated and achieves mean DSC of 83:1 5:3%. The proposed approach delivers a contribution to computer science (computer vision) in medical image analysis, reporting better quantitative pancreas segmentation results in comparison to other state-of-the-art techniques, and also captures detailed pancreas boundaries as verified by two independent experts in radiology and radiography. The contributions’ impact can support the usage of computational methods in biomedical research with a clinical translation; for example, the pancreas volume provides a prognostic biomarker about the severity of type 2 diabetes mellitus. Furthermore, a generalisation of the proposed segmentation approach successfully extends to other anatomical structures, including the kidneys, liver and iliopsoas muscles using different MRI sequences. Thus, the proposed approach can incorporate into the development of a computational tool to support radiological interpretations of MRI scans obtained using different sequences by providing a “second opinion”, help reduce possible misdiagnosis, and consequently, provide enhanced guidance towards targeted treatment planning

Computational Anatomy for Multi-Organ Analysis in Medical Imaging: A Review

The medical image analysis field has traditionally been focused on the development of organ-, and disease-specific methods. Recently, the interest in the development of more 20 comprehensive computational anatomical models has grown, leading to the creation of multi-organ models. Multi-organ approaches, unlike traditional organ-specific strategies, incorporate inter-organ relations into the model, thus leading to a more accurate representation of the complex human anatomy. Inter-organ relations are not only spatial, but also functional and physiological. Over the years, the strategies 25 proposed to efficiently model multi-organ structures have evolved from the simple global modeling, to more sophisticated approaches such as sequential, hierarchical, or machine learning-based models. In this paper, we present a review of the state of the art on multi-organ analysis and associated computation anatomy methodology. The manuscript follows a methodology-based classification of the different techniques 30 available for the analysis of multi-organs and multi-anatomical structures, from techniques using point distribution models to the most recent deep learning-based approaches. With more than 300 papers included in this review, we reflect on the trends and challenges of the field of computational anatomy, the particularities of each anatomical region, and the potential of multi-organ analysis to increase the impact of 35 medical imaging applications on the future of healthcare.Comment: Paper under revie