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研究生:黃正瑋
研究生(外文):Cheng-Wei Huang
論文名稱:基因晶片影像自動切割方法之研究
論文名稱(外文):An Automated Segmentation Approach for DNA Microarray Image
指導教授:王元凱王元凱引用關係
指導教授(外文):Yuan-Kai Wang
學位類別:碩士
校院名稱:輔仁大學
系所名稱:電子工程學系
學門:工程學門
學類:電資工程學類
論文出版年:2004
畢業學年度:92
語文別:中文
論文頁數:81
中文關鍵詞:生物晶片影像分析切割實驗點主動式輪廓模型以小波轉換為基礎之晶格系統剖面圖分析
外文關鍵詞:microarray image analysisspot segmentationactive contour modelwavelet_based griddingprofile analysis
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生物晶片(Biochip, Microarray, DNA chip)是一個可以平行篩檢大量生物資訊的工具,它讓我們實現了基因序列分析、功能解讀、疾病治療等夢想。相對的,產生的生物資訊也非常的多,因此,發展自動且精確的晶片影像分析工具是刻不容緩的。我們提出一個影像分析的方法,來解決基因晶片影像中,晶格系統建立(Gridding)以及尋找實驗點(Spot)輪廓的問題。所提出的方法,以主動式輪廓法(Active Contour Model)為主。首先,我們先將彩色影像轉成灰階,利用邊緣偵測(Edge Detection)來強化實驗點(Spot)的邊,然後利用小波轉換分析行總和(Column-sum)以及列總和(Row-sum)剖面圖(profile)來建立晶格系統,以取得每個實驗點的初始輪廓(Initial Contour)。接著再將控制點往質心方向內縮進行能量函數(Energy Function)的最佳化搜尋,以得到較佳的實驗點輪廓。我們所提出的方法,已應用在Stanford Microarray Database的晶片影像中,且得到很好的結果。我們所提出的方法有以下幾個優點:(1) 對於影像傾斜的問題,我們可以自動的校正,不需要人工的調整。(2) 能偵測不規則的行間距與列間距。(3) 不會受到顏色以及實驗點大小的影響。(4) 允許輸入不同數目的頻帶。此外,我們所提出的方法不但可以處理晶片影像中的多個實驗點,並且找到更精確的實驗點輪廓。

DNA microarray is a new tool used to examine expression levels for thousands of genes simultaneously. However, large amounts of bioinformation will be produced in DNA microarray experiments. It’s extremely urgent to develop automatic and precise tools for the analysis of DNA microarray. Image analysis is the first important step for the automatic processing of microarray experiments. In this paper, a novel approach for accurate spot finding in DNA microarray images using active contour model is proposed. In our approach, a microarray image is first transformed into a gray-level one. Wavelet-based profile analysis is then performed for building orthogonal grid system of the image. Each spot is enclosed within a grid after the wavelet-based profile analysis. The boundary of the grid is specified as initial contour of the spot. By shrinking the initial contour through energy conservation, more precise contour of the spot will be located. The approach is tested on microarray images obtained from Stanford Microarray Database. Comprehensive experiments show highly encouraging results. Major contributions of the proposed approach include the followings: (1) We solve the problem of image rotation without manual adjustment. (2) The detection is robust with irregular spot gaps. (3) Our approach is not affected by variations of color and size of spots. (4) Our approach performs well on different number of input channels. Besides, the proposed approach can not only handle multiple spots in microarray images, but also find more precise contours of spots.

中文摘要
英文摘要
誌謝
目 錄
圖目錄
第一章 導論
1.1 研究動機
1.2 研究目的
1.3 前言
第二章 論文架構
2.1 彩色模型轉換
2.2 旋轉校正
2.3 晶格系統之建立
2.4 背景校正與實驗點的排
2.5 以主動式輪廓模型切割實驗點
第三章 旋轉校正
3.1 行總和與列總和剖面圖
3.2 旋轉校正結果
第四章 建立晶格系統
4.1 剖面圖之小波轉換
4.2 尋找晶格點
4.3 各種情形之結果
第五章 實驗點切割演算法
5.1控制點
5.2能量函數
5.3 搜尋方向
5.4能量的正規化
5.5 主動式輪廓模型執行步驟
第六章 實驗結果
第七章 結論
參考文獻

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