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研究生: 蕭名智
Ming-Chih Hsiao
論文名稱: DNA於AFM影像以形狀數編碼之長度估測器
DNA Contour Length Estimator utilizing Shape Number from AFM Imaging
指導教授: 張以全
I-Tsyuen Chang
口試委員: 黃緒哲
Shiuh-Jer Huang
徐繼聖
Gee-Sern Hsu
學位類別: 碩士
Master
系所名稱: 工程學院 - 機械工程系
Department of Mechanical Engineering
論文出版年: 2016
畢業學年度: 104
語文別: 中文
論文頁數: 75
中文關鍵詞: 原子力顯微鏡去氧核醣核酸輪廓長度長度估測器影像處理細線化
外文關鍵詞: AFM, DNA, contour length, length estimator, image processing, thinning
相關次數: 點閱:280下載:3
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本論文研究AFM模擬及實驗所取得的DNA影像,以細線化後的DNA影像為基礎,提出一種利用鏈碼和形狀數編碼,用來計算DNA輪廓長度的方法。DNA長度的計算誤差大部分來自在不同解析度下不同曲率線段,在影像數位化過程中所造成的,因此本論文討論一種可以同時在不同的圖像解析度下,計算出同樣DNA輪廓長度的參數定義方法。於研究中吾人使用DNA於二維平面的蠕蟲鏈模型產生大量不同解析度的AFM模擬影像,根據解析度的不同對設計出的長度估測器進行係數的計算,最後開發出精確、快速且能應用於任何AFM影像解析度的DNA長度估測器。此方法可以應用推廣至不同的長條形生物樣本,以及不限於AFM影像。


This thesis simulates on DNA images acquired from AFM experiments, and proposes a method estimating DNA contour length based on digitized DNA images encoded by chain code and shape number after its image thinning operation. The error in calculating DNA length comes mostly from digitization of line segments with different curvature under various resolution. As a result, this thesis discusses the calculation of DNA contour length with a focus on different pixel resolution images. We apply a two-dimensional worm-like chain model of DNA to produce a large number of simulated AFM images with different resolutions, and according to different resolutions we calculate the coefficients of our designed length estimator. Finally, we developed a length estimator which is precise, rapid, and applicable to any resolution of AFM image using different coefficients.

摘要 I Abstract II 目錄 III 圖目錄 V 表目錄 VII 第一章 介紹 1 1.1 研究背景 1 1.1.1 去氧核糖核酸 1 1.1.2 限制酶 6 1.1.3 聚合酶連鎖反應與AFM 7 1.1.4 原子力顯微鏡 8 1.2 目的與動機 11 1.3 貢獻 13 1.4 文獻回顧 14 第二章 影像處理 19 2.1 AFM影像 19 2.1.1 AFM之影像特性 19 2.1.2 AFM影像之傾斜及偏折 20 2.2 DNA影像處理流程 23 2.2.1 在影像中於多條樣本中擷取單條樣本 23 2.2.2 影像平滑化及二值化 25 2.2.3 剃除交叉重疊樣本 25 2.2.4 細線化 26 2.2.5 剪除突刺 26 2.2.6 復原遭錯誤剪除的DNA線段 27 2.2.7 單條樣本的特徵擷取 28 第三章 輪廓長度計算演算法 30 3.1 12種細線化片段 30 3.2 編碼與辨別方式 31 3.3 估測器架構與係數計算方法 35 第四章 模擬方法與結果討論 38 4.1 DNA模擬影像 39 4.1.1 蠕蟲鏈模型 39 4.1.2 影像數位化流程 40 4.2 估測器係數的計算與收斂情形 44 4.2.1 不同的影像解析度 44 4.2.2 不同數量的模擬影像 49 4.3 估測器精度 54 4.4 實際操作可能遭遇之困難 62 4.4.1 影像處理 62 4.4.2 輪廓長度計算演算法 63 4.4.3 奈米量測與AFM操作 63 第五章 結論與未來工作 68 5.1 結論 68 5.2 未來工作 68 參考文獻 69 附錄A 73 附錄B 75

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