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研究生: 柯雁芬
Ko, Yen-Fen
論文名稱: 半暹羅U-Net神經網路於電阻抗斷層掃描之心肺影像分割
Separation of lung and heart functions in electrical impedance tomography using semi-Siamese U-Net
指導教授: 鄭國順
Cheng, Kuo-Sheng
學位類別: 博士
Doctor
系所名稱: 工學院 - 生物醫學工程學系
Department of BioMedical Engineering
論文出版年: 2021
畢業學年度: 109
語文別: 英文
論文頁數: 92
中文關鍵詞: 電阻抗斷層掃描U-Net半暹羅U-Net通氣分佈通氣/灌流
外文關鍵詞: Electrical impedance tomography, U-Net, semi-Siamese U-Net, ventilation distribution, V/Q
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  • 生醫電阻抗斷層掃描近年來廣泛應用在臨床呼吸相關研究,其根據胸腔中不同組織電特性,經由影像重建演算法建構出電阻係數在空間中分佈之新式醫學成像技術。其基於組織電特性量測原理,具備非侵入性和無輻射性之醫學成像技術,適合長時間連續監測且即時響應肺臟通氣狀態。
    電阻抗成像是屬於高度非線性不適定逆問題,空間解析度不足是長久以來的缺陷,要重建出清晰且高品質的電阻抗斷層影像有它的挑戰性。本研究透過深度學習方法,以U-Net 為基礎並根據生醫電阻抗斷層影像的特性量身設計專為電阻抗成像所用之網路架構,訓練專化的電阻抗模型重建影像;研究中提出的半暹羅U-Net 模型其新穎網路結構分別以多重分離任務和多重損失權重手法,來達到同步學習辨識隱含在生醫電阻抗斷層影像中不同特性的阻抗變化。
    透過兩階段1.)基於有限元素的仿生假體與生醫電阻抗模擬實驗,2.)人體電阻抗斷層影像資料測試模型的分割能力。以獨立的測試資料集評估訓練後的模型,平均絕對誤差以及DICE 相似係數評估模型的分割能力,同時實現經典的U-Net模型做為比較的基礎模型。基於有限元素仿生之電阻抗實驗訓練模型的結果,心臟和肺臟相關的阻抗影像分割效能相較於經典的U-Net:DICE 相似係數相對改善達11.37%以及3.2%;平均絕對誤差相對改善3.16%以及5.54%。將第一階段所訓練的模型應用於自動化分割心與肺電阻抗斷層影像之人體實驗,結果證實所提出的深度學習方法,僅透過模擬資料學習的模型,亦具備良好泛化性,實現在真實世界分割心與肺阻抗影像的能力。本研究所提出的半暹羅U-Net 模型實現生醫電阻抗斷層影像重建,提高重建影像的空間解析度,改善電阻抗斷層影像的品質,為電阻抗斷層影像長久以來空間解析度問題提供一種全新的改善方法。
    半暹羅 U-Net 模型實現同步分離肺與心相關的功能性阻抗影像,所提供的訊息在呼吸相關研究中開闢新的臨床應用機會,使用電阻抗斷層掃描協助急性呼吸窘迫症候群或是其它通氣/灌流不匹配的心肺疾病患者,於呼吸治療的過程中視覺化即時監測局部肺臟通氣/灌流之阻抗變化。

    Electrical impedance tomography (EIT) is widely used for bedside monitoring of lung ventilation status. Its goal is to reflect the internal conductivity changes and estimate the electrical properties of the tissues in the thorax. However, poor spatial resolution affects EIT image reconstruction to the extent that the heart and lung-related impedance images are barely distinguishable. Several studies have attempted to tackle this problem, and approaches based on decomposition of EIT images using linear transformations have been developed. Recently, U-Net has become a prominent architecture for semantic segmentation. In this paper, we propose a novel semi-Siamese U-Net specifically tailored for EIT application. It is based on the state-of-the-art U-Net, whose structure is modified and extended, forming shared encoder with parallel decoders and has multi-task weighted losses added to adapt to the individual separation tasks. The trained semi-Siamese U-Net model was evaluated with a test dataset, and the results were compared with those of the classical U-Net in terms of Dice similarity coefficient and mean absolute error.
    Results showed that compared with the classical U-Net, semi-Siamese U-Net exhibited performance improvements of 11.37% and 3.2% in Dice similarity coefficient, and 3.16% and 5.54% in mean absolute error, in terms of heart and lung-impedance image separation, respectively.
    EIT is a non-invasive technique that constitutes a promising tool for the real-time imaging and long-term monitoring of the ventilation distribution at bedside. However, clinical monitoring and diagnostic evaluations depend on various methods to assess ventilation-dependent parameters useful for ventilation therapy. This study developed an automatic, robust, and rapidly accessible method for lung segmentation that can be used to define appropriate regions-of-interest (ROIs) within EIT images.
    Approach: To date, available methods for patients with lung defects have the disadvantage of not being able to identify lung regions because of their poor ventilation responses. Furthermore, the challenges related to the identification of lung areas in EIT images are attributed to the low spatial resolution of EIT. In this study, a U-Net-based automatic lung segmentation model is used as a postprocessor to transform the original EIT image to a lung ROI image and refine the inherent conductivity distribution of the original EIT image. It is different from conventional approaches in that the trained U-Net network can perform an automatic segmentation of conductivity changes in EIT images without requiring prior information.
    Main results: The experimental design of this study was based on a finite element method phantom used to assess the feasibility and effectiveness of the proposed method, and the evaluation of the trained models on the test dataset was performed using the Dice similarity coefficient and the mean absolute error.
    Significance: The use of a deep-learning-based approach attained automatic and convenient segmentation of lung ROIs into distinguishable images, which represents a direct benefit for regional lung ventilation-dependent parameter extraction and analysis. However, further investigations and validation are warranted in real human datasets with different physiology conditions with CT cross-section dataset to refine the suggested model.

    中文摘要 I Abstract III Acknowledgments VI Contents VII List of Figures IX List of Tables XII Chapter 1 1 Introduction 1 1.1 History of EIT 1 1.2 Lung EIT 2 1.3 ARDS 3 1.4 Lung EIT limitations 7 1.5 Primary research questions 8 1.6 Dissertation organization 13 Chapter 2 14 LITERATURE REVIEW 14 2.1 Separating methods 14 2.2 Commonly Used Approach 17 2.3 Drawbacks of previous studies 18 2.4 Empirical Mode Decomposition 20 2.5 AI-based imaging methods used in EIT 22 Chapter 3 25 Specialized Deep Learning Method 25 3.1 U-Net 25 3.2 U-Net for biomedical image segmentation 26 3.3 U-Net variants 28 Chapter 4 31 RESEARCH FRAMEWORK 31 Chapter 5 36 Material and Methods 36 5.1 Proposed architecture 36 5.2 Multi-weighted loss 39 5.3 Dataset preparation 42 5.4 Training of semi-Siamese U-Net 46 5.5 Experiments 48 5.6 Real human EIT data application 51 Chapter 6 52 Results 52 6.1 Performance Trade-Offs for Selection of Model for Fine Tuning 52 6.2 Superiority of performance of semi-Siamese U-Net over that of U-Net 53 6.3 Number of epochs 58 6.4 Predicted results 60 6.5 Real human EIT data application 62 Chapter 7 67 Discussions 67 7.1 Semi-Siamese U-Net for separation tasks in simulation thorax EIT 68 7.2 Automatic lung and heart segmentation in EIT using semi-Siamese U-Net approach 70 Chapter 8 74 Conclusions 74 8.1 Semi-Siamese U-Net for separation tasks in simulation thorax EIT 74 8.2 Automatic lung and heart segmentation in EIT using semi-Siamese U-Net approach 75 References 78 Publications 92

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