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研究生: 陳昱丞
Yu-Cheng Chen
論文名稱: 用於乳癌病理影像分割與診斷的深度學習模型開發
Development of Deep learning Models for Segmentation of Histopathological Images in Breast Cancer Diagnosis
指導教授: 王靖維
Ching-Wei Wang
口試委員: 陳燕麟
Yan-Lin Chen
鄭世平
Shig-Ping Cheng
武敬和
Ching-Ho Wu
許維君
Wei-Chun Hsu
王靖維
Ching-Wei Wang
學位類別: 碩士
Master
系所名稱: 應用科技學院 - 醫學工程研究所
Graduate Institute of Biomedical Engineering
論文出版年: 2019
畢業學年度: 107
語文別: 中文
論文頁數: 35
中文關鍵詞: 深度學習卷積神經網路醫學影像乳癌診斷全卷積式神經網路
外文關鍵詞: Deep Learning, Convolutional Neural Network, Medical Imaging, Breast cancer Diagnosis, Fully Convolutional Networks
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  • 乳癌為女性中最為常見的癌症,主要由病理學家檢查病人之病理切片作為診斷方式。然而乳癌的人工診斷與分類十分的耗時,並且需要經驗豐富的病理學家來進行診斷,因此本研究將深度學習用於乳癌病理切片分割、良惡性組織辨識。

    關於以深度學習進行乳癌的分割與組織辨識,大多數現有的研究著重於良性與惡性乳腺腫瘤的二元分類。而我們則是以四種不同生物標記(E-cadherin, P63, CK14與 CK5/6)的整張切片影像為依據,將乳癌分為正常乳腺組織、上皮增生、非典型乳腺導管癌、原位導管癌與浸潤性導管癌五個階段並在病理學家的監督下標註H\&E切片影像。我們以此由四種生物標記的切片為依據所標註出之整張H\&E切片影像來訓練深度學習卷積神經網絡(全卷積神經網路),已達辨識良惡性組織並將乳癌組織分割的成果。

    我們使用訓練完成的模型進行測試,最佳的模型測試的結果經過混淆矩陣量化分析後能夠在分割乳癌組織上達到準確率0.8768、精確率0.8477、召回率0.8037和綜合評價指標0.8137。在覆蓋率量化分析上,分割乳癌組織上達到覆蓋率50\%的比例為0.9248。這項研究結果顯示深度學習模型能夠達成自動化的乳癌影像分割與良惡性組織辨識,隨著更深入的研究,也可將其於臨床上使用,對於不論是學術研究或是醫療診斷都能夠有很大的貢獻。


    Breast cancer, the most common cancer in women, is primarily diagnosed with inspection of histopathological slides by pathologists. Manual diagnosis and classification of breast cancer is time consuming and needs experienced pathologists,and thus this research use deep learning for segmentation of breast cancer histopathological image and recognition of benign or malignancy tissue.

    About the detection and classification of breast cancer by Deep Learning. Most of the existing works focus only on binary classification of breast tumor (benign and malignant).We used whole slide images of four different biomarkers (E-cadherin, P63, CK14, and CK5/6) to categorize breast cancer stages into five different categories:normal breast tissue, Epithelial Hyperplasia, Atypical Ductal Carcinoma, Ductal Carcinoma Insitu and Invasive Ductal Carcinoma. Based on these four biomarkers we manually annotated H\&E slide under supervision of Pathologists. By using H\&E whole slide images which are annotated based on the four biomarkers, we trained the deep learning convolutional neural network (Fully Convolutional Network) to segment breast cancer tissue and recognize benign and malignancy tissue.

    Our model was able to detect and classify different tissue of breast cancer with accuracy of 0.8768,precision of 0.8477,recall of 0.8037 and F-measure of 0.8137.In the evaluation of coverage ,the ratio of segmentation result which cover 50\% of the breast cancer tissue is 0.9248. These findings suggest that deep learning models can automate the process of segmentation and the recognition between benign and malignancy tissue and with further research it can be used for clinical use .

    摘要. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . I Abstract . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . II 致謝. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . III 目錄. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . IV 圖目錄. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . VI 表目錄. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . VII 第一章 緒論. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 1 1.1 研究動機. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.2 研究目標. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.3 論文貢獻. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 2 1.4 論文架構. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 3 第二章 研究背景. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 4 2.1 乳癌病理切片影像與五種染色方法. . . . . . . . . . . . . . . . . . . . . . . . . 4 2.2 深度學習應用於乳癌病理影像分類與預測. . . . . . . . . . . . . . . . . . . . . . 5 2.2.1 深度學習應用於病理影像的研究回顧. . . . . . . . . . . . . . . . . . . . . 5 2.2.2 全卷積神經網路. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 6 第三章 研究方法. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3.1 數據準備. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 3.2 數據預處理. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 10 3.2.1 影像標註方法與標註影像製作. . . . . . . . . . . . . . . . . . . . . . . 10 3.2.2 標註型態. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 3.3 全卷積神經網路架構、訓練與測試. . . . . . . . . . . . . . . . . . . . . . . . 15 3.3.1 全卷積神經網路架構. . . . . . . . . . . . . . . . . . . . . . . . . . 15 3.3.2 全卷積神經網路訓練. . . . . . . . . . . . . . . . . . . . . . . . . . 16 3.3.3 測試方法. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17 第四章 實驗結果與分析. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 4.1 乳癌病理影像量化分析. . . . . . . . . . . . . . . . . . . . . . . . . . . . 19 4.1.1 實驗資料. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 20 4.1.2 混淆矩陣. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 21 4.1.3 覆蓋率. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 23 4.1.4 量化分析結果. . . . . . . . . . . . . . . . . . . . . . . . . . . 24 4.2 乳癌病理影像分割結果與分析. . . . . . . . . . . . . . . . . . . . . . . . . 28 第五章 結論與未來展望. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 5.1 結論. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . .32 5.2 未來發展. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 參考文獻. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33

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