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研究生: 余奕叡
I-Jui YU
論文名稱: 交叉長條生物樣本之AFM數位影像幾何特徵與持久長度估測之研究
Estimation of DNA Persistence Length with Atomic Force Microscopy Imaging
指導教授: 張以全
I-Tsyuen Chang
口試委員: 劉孟昆
Meng-Kun Liu
藍振洋
Chen-Yang Lan
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: 2019
畢業學年度: 107
語文別: 中文
論文頁數: 201
中文關鍵詞: 持久長度DNA影像處理自我交叉數位曲線
外文關鍵詞: Persistence Length, DNA, Image Processing, Self-crossing, Digital curve
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  • 本論文為以DNA數位影像做為樣本,仔細探討估算持久長度(Persistence length)所需的曲線長度(Contour Length)及沿著曲線的切向量(Contour Tangent),並使用交叉DNA樣本的數位影像為研究對象。過去學者在DNA影像估測的研究上皆沒有在有交叉的DNA樣本做探討,本研究則分別考慮有、無交叉的兩類樣本的差異與共同性。
    持久長度為描述長鏈聚合物(Chain Polymer)的剛性強度的指標的一種。在計算持久長度方面需要精準估測DNA曲線輪廓長度以及輪廓切向量。
    在估測輪廓切向量方面,利用AFM攫取的DNA影像,在不同影像解析度下,計算輪廓切向量會有誤差。過去曾經有以中位濾波差分法對估測進行修正,本研究提出中位擬合排序法對估測進行修正。兩者差別主要為中位濾波差分法主要為平均DNA片段內所有切向量,中位擬合排序法在是取DNA片段內所有切向量的中位數。
    本研究也以這兩種方法做為切向量角度估測器,除了加入原本的無交叉影像,也利用過去所研究的自動化交叉走向判斷演算法將交叉影像首次納入研究樣本,並以費里曼鏈碼及形狀數編碼的方式為基礎,重新計算出更準確的新切向量估測器係數,在DNA輪廓切向量計算上提升準確度。
    本論文再將四像素長度估測器所估測出的輪廓長度,合併上述所提的兩種輪廓切向量估測器,進而估測出各至影像樣本的持久長度進行比較探討。


    In this paper, the persistence length is estimated by DNA digital image, and the digital image of the cross sample can be estimated. In the past, scholars did not discuss overlapping DNA samples in the study of DNA imaging estimation.
    The persistence Length is the stiffness of the polymer. Accurate estimation of the length of the DNA curve contour and the contour cut vector are required in calculating the long-lasting length.
    In estimating the contour cut vector, using the DNA image captured by AFM, there is an error in calculating the contour cut vector at different image resolutions. In the past, the median filter difference method was used to correct the estimation. In this study, the median fitting ordering method was proposed to correct the estimation. The difference between the two is mainly that the median filtering difference method is mainly for all the tangent vectors in the average DNA segment, and the median fitting ordering method is to take the median of all the tangent vectors in the DNA segment.
    In this study, the two methods are also used as the tangent vector angle estimator. In addition to adding the self-crossing image, the "automatic cross-direction judgment algorithm" is used to incorporate the cross-image into the research sample for the first time, and the Ferryman chain code is used.
    In this paper, the four-pixel length estimator is used to estimate the contour length, and the two contour cut vector estimators just mentioned are added to estimate the contour cut vector, and then the longest length of each is estimated, and the two are Conduct a comparative discussion.

    論文摘要....................................... I Abstract........................................II 誌謝..............................................III 目錄............................................. IV 圖目錄 .......................................... VIII 表目錄..........................................XVII 符號說明 ..........................................XXI 1緒論........................................ 1 1.1 研究背景介紹 ............................... 1 1.1.1原子力顯微儀........................... 1 .1.2 去氧核糖核酸(DNA) ....................... 4 1.2 文獻回顧................................. 5 1.2.1 持久長度估測........................... 5 1.2.2 輪廓長度估測........................... 6 1.2.3 輪廓切向量估測.......................... 11 1.3 研究動機與目的.............................. 15 2影像處理..................................... 16 2.1 AFM影像特性............................... 16 2.2 影像前處理程序.............................. 16 2.2.1 彩色影像轉灰階.......................... 17 2.2.2 頂帽轉換二值化 ........................ 17 2.2.3 標記聯通成分與橫跨邊界之DNA影像.......... 18 2.2.4 去除雜訊............................. 19 2.2.5 擷取單條DNA影像....................... 19 2.2.6 影像平滑化與二值化....................... 20 2.2.7 剔除交叉兩次以上樣本 .................... 21 2.2.8 影像細線化............................ 22 2.2.9 剔除端點小於2的樣本 .................... 22 .2.10 剪除突刺.............................. 23 2.2.11 復原誤剪的DNA線段 ...................... 23 2.2.12 DNA樣本的長度特徵擷取.................... 24 3 DNA模型與影像模擬.............................. 25 .1 蠕蟲鏈模型................................ 25 4 DNA曲線持久長度估測法........................... 30 4.1 DNA片段模擬程 ............................ 31 .1.1 模擬真實DNA樣本........................ 31 4.1.2 以座標分辨交叉與無交叉樣本.................. 32 4.1.3 DNA模擬樣本數位化...................... 35 4.1.4 以鍊碼紀錄圖像.......................... 36 4.1.5 數位化座標與座標重合..................... 38 4.2 切向量計算方式............................. 46 4.2.1 中位擬合排序法(MFRM)..................... 47 4.2.2 中位濾波差分法(MFDM)..................... 54 4.3 持久長度計算方式............................. 58 5估測結果..................................... 60 5.1 估測係數Tn的收斂與比較...................... 60 5.2持久長度估算 ............................... 100 6 結論與未來展望 ................................. 104 6.1 結論 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 104 6.2 未來展望.................................. 104 參考文獻. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 106 附錄A......................................... 110 A.1 輪廓長度計算方式............................ 110 .1.1 12種細線化片段 ......................... 110 A.1.2 編碼與辨別方式......................... 111 .1.3 估測器架構與係數計算方式 ................... 115 附錄B......................................... 118 B.1 估測器係數Tn的收斂與比較....................... 118 附錄C......................................... 151 C.1 細線化線段交叉區之形貌........................ 151 C.2 交叉DNA影像參數之假設........................ 152 C.3 可能的線段交叉圖形 ........................... 153 C.4 可能的線段交叉走法 ........................... 158 C.5 DNA交叉走向判斷演算法 ........................ 160 C.5.1 掃描細線化交叉線段影像 .................... 160 C.5.2 研盼可能走向 ........................... 161 C.5.3 篩選可能走向 ........................... 162 C.5.4 共用格計票 ............................ 163 C.5.5 決定代表共用格.......................... 164 C.5.6 將交叉影像轉換成鏈碼...................... 167 附錄D......................................... 171 D.1 四像素片段切向量角度 . . . . . . . . . . . . . . . . . . . . . . . . . . 171

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