微衛星核酸遺傳態品多型條帶的自動物件分割與解譯絕對長度

Genotyping Polymorphic Bands of Microsatellite DNA with Automatic Object-Segmentation and Translated Absolute Size

沈昌志(Chang-Chih Shen)

指導教授 ： 陳朝欽

國立清華大學/電機資訊學院/資訊系統與應用研究所/碩士(2007年)

https://doi.org/10.6843/NTHU.2007.00034

摘要

微衛星DNA的遺傳態品多型條帶上的自動影像資料分析(Aida)，包含自動化的影像分割以及轉換資料為絕對長度。計算的自動化分析在實驗的重製性以及人為的檢驗方面顯得格外重要。為了能在影像上切割出灰階值高低不一的物件，在作物件分割之前，本論文使用兩種不同的方法，分別是peak method以及 window　method來做物件的定位，以達到影像分析的自動化。接下來使用Otsu演算法來作物件分割。切割出來的物件我們稱為條帶，我們從分割後的影像上開始計算每個條帶的統計量，比如條帶的大小，灰階值等等。另外，基於選擇特定的DNA長度標準來計算樣本條帶的長度，會得到浮點數的結果，造成在資料整合上的損失。本論文使用文化大學張春梵老師實驗室自製的DNA長度標準，稱為MarkQoff，即可計算出每個樣本條帶的絕對長度。

關鍵字

自動影像資料分析 ； 物件分割 ； 絕對長度 ； 條帶 ； 跑道 ； 長度標準

並列摘要

Automatic image data analysis (Aida) on the genotyping polymorphic bands of microsatellite DNA requires routinely automatic image segmentation and especially translated absolute data. Computerized automatic analysis is crucial in reproducibility and artifact-proof despite of the available commercial software which is highly interactive and hence gravely time-consuming. Albeit, the genotyping data of microsatellite DNA fragment that is represented as relative mobility sizes with floating points based on selected DNA size standards may lead to great loss in data integration. The implemented Aida system with general-Aida-modules (GAM) of object segmentation and specific-Aida-modules (SAM) of data translation intends to provide efficient solutions in its semi-automatic format. In an experiment of twenty images, the Aida system demonstrated 85~95% accuracy in automatic band segmentation. Moreover, the Aida system along with in-house DNA size standards of MarkQoff (Marker-Quarter-Off) successfully translated absolute size data of DNA fragments with zero standard deviation while analyzing triplicate genotyping images of three running distances. In contrast to Aida system’s superior performance, the results of commercial software based on fifteen DNA size standards in triplicate genotyping images delivered the DNA fragment size data up to 2.19 base pair of standard deviation along with the discrepancies of data floating points and missing bands.

並列關鍵字

Automatic Image Data Analysis ； Object Segmentation ； Absolute Size ； Band ； Lane ； Size Standard

參考文獻

[Tsa05] Tsai MY, Chang CF, Chu HT, Chan CH, Chang KJ, Kao CY and Chen CC, “Microarray Images Pre-Analysis for Critical Gene Expression Computation with Implemented Algorithmic Kernel.” Hwa Kang Journal of Agriculture, 16: 43 - 50, 2005.

[Adi01] Adiga PSU et al., “Automatic analysis of agarose gel images,” Bioinformatics, 17(11): 1084 - 1090, 2001.

[Akb04] Akbari A and Albregtsen F, “Automatic Segmentation of DNA Bands in One Dimensional Gel Images Produced by Hybridizing Techniques,” Proceedings of the 26th Annual International Conference of the IEEE EMBS(26): 2852 - 2855, 2004.

[App97] Appel RD, Vargas JR, Palagi PM, Walther D, and Hochstrasser DF, “Melanie II - a third-generation software package for analysis of two-dimensional electrophoresis images: II. Algorithms.” Electrophoresis, 18: 2735 - 2748, 1997.

[Bet96] Bettens E, Scheunders P, Sijbers J, Van DD, and Moens L, “Automatic segmentation and modeling of two-dimensional electrophoresis gels.” International Conference on Image Processing, 2: 665 - 668, 1996.