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 |
相關次數: | 點閱:372 下載:0 |
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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.
[1] 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.
[2] S. Dutta, C. Rivetti, N. R. Gassman, C. G. Young, B. T. Jones, K. Scarpinato, and M. Guthold, “Analysis of single, cisplatin induced dna bends by atomic force mi- croscopy and simulations,” Journal of Molecular Recognition, 2018.
[3] “https://en.wikipedia.org/wiki/dna,” 2018.
[4] K. Drlica et al., “Understanding dna and gene cloning: a guide for the curious.,”
Understanding DNA and Gene Cloning: a Guide for the Curious., no. ed. 2, 1992.
[5] J. Bednar, P. Furrer, V. Katritch, A. Stasiak, J. Dubochet, and A. Stasiak, “Deter- mination of dna persistence length by cryoelectron 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.
[6] 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.
[7] H. Wang and J. N. Milstein, “Simulation assisted analysis of the intrinsic stiffness for short dna molecules imaged with scanning atomic force microscopy,” PloS one, vol. 10, no. 11, p. e0142277, 2015.
[8] H. Freeman, “On the encoding of arbitrary geometric configurations,” IRE Transac- tions on Electronic Computers, no. 2, pp. 260–268, 1961.
[9] H. Freeman, “Computer processing of line-drawing images,” ACM Computing Sur- veys (CSUR), vol. 6, no. 1, pp. 57–97, 1974.
106
[10] T. Spisz, Y. Fang, R. Reeves, C. Seymour, I. Bankman, and J. Hoh, “Automated sizing of dna fragments in atomic force microscope images,” Medical and Biological Engineering and Computing, vol. 36, no. 6, pp. 667–672, 1998.
[11] C. Rivetti, “A simple and optimized length estimator for digitized dna contours,” Cytometry Part A, vol. 75, no. 10, pp. 854–861, 2009.
[12] Z. Kulpa, “Area and perimeter measurement of blobs in discrete binary pictures,” Computer Graphics and Image Processing, vol. 6, no. 5, pp. 434–451, 1977.
[13] 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.
[14] M.-C. Hsaio, “Dna contour length estimator utilizing shape number from afm imag- ing,” National Taiwan Universiry of science and technology, 2016.
[15] E. Ficarra, D. Masotti, E. Macii, L. Benini, G. Zuccheri, and B. Samorì, “Auto- matic intrinsic dna curvature computation from afm images,” IEEE Transactions on Biomedical Engineering, vol. 52, no. 12, pp. 2074–2086, 2005.
[16] Z.-X.Dai,“Accurateestimationfordigitalcurvetangentvectorofbiologicalsamples from afm systems,” National Taiwan Universiry of science and technology, 2018.
[17] A. Sundstrom, S. Cirrone, S. Paxia, C. Hsueh, R. Kjolby, J. K. Gimzewski, J. Reed, and B. Mishra, “Image analysis and length estimation of biomolecules using afm,” IEEE Transactions on Information Technology in Biomedicine, vol. 16, no. 6, pp. 1200–1207, 2012.
[18] P.-I. Chang and M.-C. Hsaio, “Resolution-free accurate dna contour length estima- tion from atomic force microscopy images,” Scanning, 2019.
[19] C. Rivetti, C. Walker, and C. Bustamante, “Polymer chain statistics and conforma- tional analysis of dna molecules with bends or sections of different flexibility,” Jour- nal of molecular biology, vol. 280, no. 1, pp. 41–59, 1998.
107
[20] S. B. Gray, “Local properties of binary images in two dimensions,” IEEE Transac- tions on Computers, vol. 100, no. 5, pp. 551–561, 1971.
[21] W. K. Pratt, “Digital image processing: Piks scientific inside/william k. pratt.–ny,” 2007.
[22] K. Pearson, “The problem of the random walk,” Nature, vol. 72, no. 1867, p. 342, 1905.
[23] A. Papoulis, “Probability, random variables, and stochastic processes,” 1965.
[24] “https://www.mathworks.com/matlabcentral/fileexchange/13351-fast-and-robust- self-intersections.”
[25] R. C. Gonzalez, R. E. Woods, and S. L. Eddins, Digital Image Processing Using MATLAB®. Gatesmark Publishing, 2009.
[26] 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.
[27] H.-J. Lu, “Automatic self-crossing intersection tracing for string-like biopolymer afmimages,” National Taiwan Universiry of science and technology, 2018.
[28] E.BribiescaandA.Guzman,“Howtodescribepureformandhowtomeasurediffer- ences in shapes using shape numbers.,” Pattern Recognition, vol. 12, no. 2, pp. 101– 112, 1980.
[29] Z.Han,W.X.Feng,L.Z.Hui,L.DaHai,andL.Y.Chou,“Anewimageencryption algorithm based on chaos system,” in Robotics, intelligent systems and signal pro- cessing, 2003. Proceedings. 2003 IEEE international conference on, vol. 2, pp. 778– 782, IEEE, 2003.
[30] L. Neumann and J. Matas, “Text localization in real world images using efficiently pruned exhaustive search,” in Document Analysis and Recognition (ICDAR), 2011 International Conference on, pp. 687–691, IEEE, 2011.