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

Interactive medical image segmentation - towards integrating human guidance and deep learning

Medical image segmentation is an essential step in many clinical workflows involving diagnostics and patient treatment planning. Deep learning has advanced the field of medical image segmentation, particularly with respect to automating contouring. However, some anatomical structures, such as tumours, are challenging for fully automated methods. When automatic methods fail, manual contouring is required. In such cases, semi-automatic tools can support clinicians in contouring tasks. The objective of this thesis was to leverage clinicians’ expert knowledge when performing segmentation tasks, allowing for interactions along the segmentation workflow and improving deep learning predictions. In this thesis, a deep learning approach is proposed that produces a 3D segmentation of a structure of interest based on a user-provided input. If trained on a diverse set of structures, state-of-the-art performance was achieved for structures included in the training set. More importantly, the model was also able to generalize and make predictions for unseen structures that were not represented in the training set. Various avenues to guide user interaction and leverage multiple user inputs more effectively were also investigated. These further improved the segmentation performance and demonstrated the ability to accurately segment a broad range of anatomical structures. An evaluation by clinicians demonstrated that time spent contouring was reduced when using the contextual deep learning tool as compared to conventional contouring tools. This evaluation also revealed that the majority of contouring time is observation time, which is only indirectly affected by the segmentation approach. This suggests, that user interface design and guiding the user’s attention to critical areas can have a large impact on time taken on the contouring task. Overall, this thesis proposes an interactive deep learning segmentation method, demonstrates its clinical impact, and highlights the potential synergies between clinicians and artificial intelligence

Improving Radiotherapy Targeting for Cancer Treatment Through Space and Time

Radiotherapy is a common medical treatment in which lethal doses of ionizing radiation are preferentially delivered to cancerous tumors. In external beam radiotherapy, radiation is delivered by a remote source which sits several feet from the patient\u27s surface. Although great effort is taken in properly aligning the target to the path of the radiation beam, positional uncertainties and other errors can compromise targeting accuracy. Such errors can lead to a failure in treating the target, and inflict significant toxicity to healthy tissues which are inadvertently exposed high radiation doses. Tracking the movement of targeted anatomy between and during treatment fractions provides valuable localization information that allows for the reduction of these positional uncertainties. Inter- and intra-fraction anatomical localization data not only allows for more accurate treatment setup, but also potentially allows for 1) retrospective treatment evaluation, 2) margin reduction and modification of the dose distribution to accommodate daily anatomical changes (called `adaptive radiotherapy\u27), and 3) targeting interventions during treatment (for example, suspending radiation delivery while the target it outside the path of the beam). The research presented here investigates the use of inter- and intra-fraction localization technologies to improve radiotherapy to targets through enhanced spatial and temporal accuracy. These technologies provide significant advancements in cancer treatment compared to standard clinical technologies. Furthermore, work is presented for the use of localization data acquired from these technologies in adaptive treatment planning, an investigational technique in which the distribution of planned dose is modified during the course of treatment based on biological and/or geometrical changes of the patient\u27s anatomy. The focus of this research is directed at abdominal sites, which has historically been central to the problem of motion management in radiation therapy

FPGA-Based Portable Ultrasound Scanning System with Automatic Kidney Detection

Bedsides diagnosis using portable ultrasound scanning (PUS) offering comfortable diagnosis with various clinical advantages, in general, ultrasound scanners suffer from a poor signal-to-noise ratio, and physicians who operate the device at point-of-care may not be adequately trained to perform high level diagnosis. Such scenarios can be eradicated by incorporating ambient intelligence in PUS. In this paper, we propose an architecture for a PUS system, whose abilities include automated kidney detection in real time. Automated kidney detection is performed by training the Viola–Jones algorithm with a good set of kidney data consisting of diversified shapes and sizes. It is observed that the kidney detection algorithm delivers very good performance in terms of detection accuracy. The proposed PUS with kidney detection algorithm is implemented on a single Xilinx Kintex-7 FPGA, integrated with a Raspberry Pi ARM processor running at 900 MHz

AUTOMATIC LIVER SEGMENTATION FROM CT SCANS USING INTENSITY ANALYSIS AND LEVEL-SET ACTIVE CONTOURS

Liver segmentation from CT scans is still a challenging task due to the liver characteristics in terms of shape and intensity variability. In this work, we propose an automatic segmentation method of the liver from CT data sets. The framework consists of three main steps: liver shape model localization, liver intensity range estimation and localized active contouring. We proposed an adaptive multiple thresholding technique to estimate the range of the liver intensities. First, multiple thresholding is used to extract the dense tissue from the whole CT scan. A localization step is then used to find the approximate location of the liver in the CT scan, to localize a constructed mean liver shape model. A liver intensity-range estimation step is then applied within the localized shape model ROI. The localized shape model and the estimated liver intensity range are used to build the initial mask. A level set based active contour algorithm is used to deform the initial mask to the liver boundaries in the CT scan. The proposed method was evaluated on two public data sets: SLIVER07 and 3D-IRCAD. The experiments showed that the proposed method is able to segment to liver in all CT scans in the two data sets accurately

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

A comparative evaluation for liver segmentation from spir images and a novel level set method using signed pressure force function

Thesis (Doctoral)--Izmir Institute of Technology, Electronics and Communication Engineering, Izmir, 2013Includes bibliographical references (leaves: 118-135)Text in English; Abstract: Turkish and Englishxv, 145 leavesDeveloping a robust method for liver segmentation from magnetic resonance images is a challenging task due to similar intensity values between adjacent organs, geometrically complex liver structure and injection of contrast media, which causes all tissues to have different gray level values. Several artifacts of pulsation and motion, and partial volume effects also increase difficulties for automatic liver segmentation from magnetic resonance images. In this thesis, we present an overview about liver segmentation methods in magnetic resonance images and show comparative results of seven different liver segmentation approaches chosen from deterministic (K-means based), probabilistic (Gaussian model based), supervised neural network (multilayer perceptron based) and deformable model based (level set) segmentation methods. The results of qualitative and quantitative analysis using sensitivity, specificity and accuracy metrics show that the multilayer perceptron based approach and a level set based approach which uses a distance regularization term and signed pressure force function are reasonable methods for liver segmentation from spectral pre-saturation inversion recovery images. However, the multilayer perceptron based segmentation method requires a higher computational cost. The distance regularization term based automatic level set method is very sensitive to chosen variance of Gaussian function. Our proposed level set based method that uses a novel signed pressure force function, which can control the direction and velocity of the evolving active contour, is faster and solves several problems of other applied methods such as sensitivity to initial contour or variance parameter of the Gaussian kernel in edge stopping functions without using any regularization term

Cloud-Based Benchmarking of Medical Image Analysis

Medical imagin