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研究生: 戴芝軒
Zhi-Xuan Dai
論文名稱: 原子力顯微鏡生物樣本數位切向量精準估測之研究
Accurate Estimation for Digital Curve Tangent Vector of Biological Samples from AFM systems
指導教授: 張以全
I-Tsyuen Chang
口試委員: 田維欣
Wei-Hsin Tien
劉孟昆
Meng-Kun Liu
施博仁
Po-Jen Shih
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: 2018
畢業學年度: 106
語文別: 中文
論文頁數: 152
中文關鍵詞: 原子力顯微鏡影像處理去氧核糖核酸蠕蟲鏈模型持久長度
外文關鍵詞: Worm-like chain, Freeman chain code
相關次數: 點閱:167下載:2
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  • 本研究利用原子力顯微鏡(Atomic Force Microscope, AFM)量測去氧核醣核酸(deoxy- ribonucleicacid, DNA)影像,再將DNA影像進行影像處理後,利用一種由8連通費 里曼鏈碼(Freeman chain code)延伸出來的切向量估測進行曲線擬合,估算DNA的 輪廓切向量。持久長度(Persistence Length)是一種力學性質,可用來表示DNA分子 鏈的剛性,能夠預估DNA的輪廓彎曲情形。在計算DNA的持久長度時,需要精 準的曲線輪廓長度(Contour Length)以及精準的輪廓切向量,才能有準確的估測結 果。原子力顯微鏡被使用在長條狀高分子生物(Long Chain Biopolymer)樣本的成像 上,例如:DNA,但在不同的影像解析度下,計算輪廓切向量會產生誤差。為了修 正DNA的輪廓切向量誤差,本研究利用AFM攫取的DNA影像,經過一系列的影像 處理,將二值化影像細線化至單一像素寬後,針對單一像素寬的DNA影像,進行 輪廓切向量的估測,再對應原始DNA輪廓切向量估測結果進行修正,最後可得到 準確的DNA輪廓切向量。


    A tangent vector estimator extended from the 4-pixel 8-connected Freeman chain code is used to fit the curve of DNA image taken by AFM in this research. Persistence length is a kind of physical property that is able to represent the rigidity of molecule chain of DNA. Precise contour length and accurate contour tangent are both required for estimation of accurate persistence length. However, because of the different image resolutions, the calculation of the contour tangent will have the error. In order to eliminate the contour tangent error of the curve of the DNA image, an estimation method of contour tangent for digitized images is developed in this study. Using this method can effectively eliminate the error of contour tangent which caused by the image resolution, and measure the precise contour tangent.

    1 介紹 1.1 研究背景 1.2 目的與動機 1.3 文獻回顧 2 影像處理 2.1 AFM之影像特性 2.2 影像處理步驟 3 切向量估測方法 3.1 數位化切向量估測法 4 DNA片段模擬 4.1 蠕蟲鏈模型 4.2 蒙地卡羅法 4.3 DNA片段模擬流程 5 估測結果 5.1 蠕蟲鏈模型實驗量測結果 5.2 DNA影像實驗量測結果 6 結論與未來工作 6.1 結論 6.2 未來工作

    [1] “deoxyribonucleic acid (dna) wiki https://zh.wikipedia.org/wiki/2018.
    [2] J.L.M.R.K.R.BruceAlberts,AlexanderJohnsonandP.Walter,MolecularBiology of the Cell, 4th edition. New York: Garland Science, 2002.
    [3] J. M. Butler, Forensic DNA Typing. Elsevier, 2001.
    [4] M. Mandelkern, J. G. Elias, D. Eden, and D. M. Crothers, “The dimensions of dna
    in solution,” Journal of molecular biology, vol. 152, no. 1, pp. 153–161, 1981.
    [5] S. Gregory, K. Barlow, K. McLay, R. Kaul, D. Swarbreck, A. Dunham, C. Scott, K. Howe, K. Woodfine, C. Spencer, et al., “The dna sequence and biological anno- tation of human chromosome 1,” Nature, vol. 441.
    [6] Wiki, “Dna structure.” Wikimedia, 2016.
    [7] “A-b-z-dna side view.” via Wikimedia Commons, March 2005.
    [8] “Afm原理與應用.” 科袖網, 2017.
    [9] “原子力顯微鏡(afm)的使用和成像技巧.” CoreCMS Alpha, 2017.
    [10] 蔡毓楨, 原子力顯微鏡實作訓練教材. 國家圖書館, 2007.
    [11] D. Y. Abramovitch, S. B. Andersson, L. Y. Pao, and G. Schitter, “A tutorial on the mechanisms, dynamics, and control of atomic force microscopes,” in American Control Conference, 2007. ACC’07, pp. 3488–3502, IEEE, 2007.
    [12] Y. Lyubchenko, L. Shlyakhtenko, R. Harrington, P. Oden, and S. Lindsay, “Atomic force microscopy of long dna: imaging in air and under water.,” Proceedings of the National Academy of Sciences, vol. 90, no. 6, pp. 2137–2140, 1993.
    [13] H.G.Hansma,“Surfacebiologyofdnabyatomicforcemicroscopy,”Annualreview of physical chemistry, vol. 52, no. 1, pp. 71–92, 2001.
    [14] C. Rivetti, M. Guthold, and C. Bustamante, “Scanning force microscopy of dna de- posited onto mica: Equilibrationversuskinetic trapping studied by statistical polymer chain analysis,” Journal of molecular biology, vol. 264, no. 5, pp. 919–932, 1996.
    [15] T. Spisz, Y. Fang, R. H. Reeves, C. Seymour, I. N. Bankman, and J. H. Hoh, “Au- tomated sizing of dna fragments in atomic force microscope images,” Medical and Biological Engineering and Computing, vol. 36, no. 6, pp. 667–672, 1998.
    [16] E. Ficarra, L. Benini, E. Macii, and G. Zuccheri, “Automated dna fragments recog- nition and sizing through afm image processing,” IEEE Transactions on Information Technology in Biomedicine, vol. 9, no. 4, pp. 508–517, 2005.
    [17] C. Rivetti, “A simple and optimized length estimator for digitized dna contours,” Cytometry Part A, vol. 75, no. 10, pp. 854–861, 2009.
    [18] C. Rivetti, C. Walker, and C. Bustamante, “Polymer chain statistics and confor- mational analysis of dna molecules with bends or sections of different flexibility,” Journal of molecular biology, vol. 280, no. 1, pp. 41–59, 1998.
    [19] J. Bednar, P. Furrer, V. Katritch, A. Stasiak, J. Dubochet, and A. Stasiak, “Deter- mination of dna persistence length by cryo-electron microscopy. separation of the static and dynamic contributions to the apparent persistence length of dna,” Journal of molecular biology, vol. 254, no. 4, pp. 579–594, 1995.
    [20] E. Ficarra, D. Masotti, E. Macii, L. Benini, G. Zuccheri, and B. Samor`ı, “Auto- matic intrinsic dna curvature computation from afm images,” IEEE transactions on biomedical engineering, vol. 52, no. 12, pp. 2074–2086, 2005.
    [21] D. M. S. L.-M. Z. Leonenko, D. Cramb, “Atomic force microscopy at the interface of chemistry and biology,” Recent Research Developments in Physical Chemistry, vol. Vol. 6, pp. pp.75–89, 2002.
    [22] S. B. Gray, “Local properties of binary images in two dimensions,” IEEE Transac- tions on Computers, vol. 100, no. 5, pp. 551–561, 1971.
    [23] W. K. Pratt, “Geometrical image modification,” Digital Image Processing: PIKS Scientific Inside, Fourth Edition, pp. 387–417, 2007.
    [24] H. Papasaika-Hanusch, “Digital image processing using matlab,” Institute of Geodesy and Photogrammetry, ETH Zurich, vol. 63, 1967.
    [25] L. Lam, S.-W. Lee, and C. Y. Suen, “Thinning methodologies-a comprehensive sur- vey,” IEEE Transactions on pattern analysis and machine intelligence, vol. 14, no. 9, pp. 869–885, 1992.
    [26] J. Matas, Z. Shao, and J. Kittler, “Estimation of curvature and tangent direction by median filtered differencing,” in Image Analysis and Processing, pp. 83–88, Springer, 1995.
    [27] H. Freeman, “On the encoding of arbitrary geometric configurations,” IRE Transac- tions on Electronic Computer, vol. no. 2, pp. 260–268, 1961.
    [28] E. Bribiesca and A. Guzman, “How to describe pure form and how to measure differences in shapes using shape numbers,” Pattern Recognition, vol. 12, no. 21, pp. 101–112, 1980.

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