An improved microarray image analysis architecture using mathematical morphology

DNA microarrays are now widely used to measure gene expression levels of healthy and cancerous cells. To allow further experiment for drug development to treat cancer, colour intensity from images of microarray spots need to be extracted as accurate as possible. The intensity extraction requires pre...

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Main Author:	Samsudin, Nurnabilah
Format:	Thesis
Language:	English English English
Published:	2015
Subjects:	QH301 Biology
Online Access:	http://eprints.uthm.edu.my/1410/2/NURNABILAH%20SAMSUDIN%20COPYRIGHT%20DECLARATION.pdf http://eprints.uthm.edu.my/1410/1/24p%20NURNABILAH%20SAMSUDIN.pdf http://eprints.uthm.edu.my/1410/3/NURNABILAH%20SAMSUDIN%20WATERMARK.pdf
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spelling	my-uthm-ep.14102021-10-03T06:46:08Z An improved microarray image analysis architecture using mathematical morphology 2015-09 Samsudin, Nurnabilah QH301 Biology DNA microarrays are now widely used to measure gene expression levels of healthy and cancerous cells. To allow further experiment for drug development to treat cancer, colour intensity from images of microarray spots need to be extracted as accurate as possible. The intensity extraction requires pre-requisite analysis stages including noise removal, and followed by location gridding. However, it remains as a challenging task for microarray analysis due to the variation of noise that infested the images. In this study, microarray analysis architecture using mathematical morphology was proposed, namely Mathematical Morphology Microarray Image Analysis (MaMIA).Firstly, in denoising stage, noise identification is conducted to identify and reverse the noise. Next, combinations of mathematical morphology were applied to the microarray and its pixel derivatives during the gridding stage. Raw microarrays used by MaMIA are available at Stanford Microarray Database (SMD), Gene Expression Omnibus (GEO) and from a dilution experiment (DILN). From comparisons with previous existing architectures, Optimal Multilevel Thresholding (OMTG) and Automated Robust MicroArray Data Analysis (ARMADA), MaMIA have proven to efficiently remove noise with highest value, 81.6657dB for Peak Signal to Noise Ratio (PSNR) and success identification of spots in cases of noises; with highest gridding accuracy level of 98.34%.Overall processing time, MaMIA architecture can perform gridding in less than 22 seconds, fastest as compared to its contender. This research have revealed the potential of analysing microarray by mainly using mathematical morphology operation, either applied on microarray or its pixel derivative. 2015-09 Thesis http://eprints.uthm.edu.my/1410/ http://eprints.uthm.edu.my/1410/2/NURNABILAH%20SAMSUDIN%20COPYRIGHT%20DECLARATION.pdf text en staffonly http://eprints.uthm.edu.my/1410/1/24p%20NURNABILAH%20SAMSUDIN.pdf text en public http://eprints.uthm.edu.my/1410/3/NURNABILAH%20SAMSUDIN%20WATERMARK.pdf text en validuser mphil masters Universiti Tun Hussein Onn Malaysia Faculty of Science Computer and Information Technology
institution	Universiti Tun Hussein Onn Malaysia
collection	UTHM Institutional Repository
language	English English English
topic	QH301 Biology
spellingShingle	QH301 Biology Samsudin, Nurnabilah An improved microarray image analysis architecture using mathematical morphology
description	DNA microarrays are now widely used to measure gene expression levels of healthy and cancerous cells. To allow further experiment for drug development to treat cancer, colour intensity from images of microarray spots need to be extracted as accurate as possible. The intensity extraction requires pre-requisite analysis stages including noise removal, and followed by location gridding. However, it remains as a challenging task for microarray analysis due to the variation of noise that infested the images. In this study, microarray analysis architecture using mathematical morphology was proposed, namely Mathematical Morphology Microarray Image Analysis (MaMIA).Firstly, in denoising stage, noise identification is conducted to identify and reverse the noise. Next, combinations of mathematical morphology were applied to the microarray and its pixel derivatives during the gridding stage. Raw microarrays used by MaMIA are available at Stanford Microarray Database (SMD), Gene Expression Omnibus (GEO) and from a dilution experiment (DILN). From comparisons with previous existing architectures, Optimal Multilevel Thresholding (OMTG) and Automated Robust MicroArray Data Analysis (ARMADA), MaMIA have proven to efficiently remove noise with highest value, 81.6657dB for Peak Signal to Noise Ratio (PSNR) and success identification of spots in cases of noises; with highest gridding accuracy level of 98.34%.Overall processing time, MaMIA architecture can perform gridding in less than 22 seconds, fastest as compared to its contender. This research have revealed the potential of analysing microarray by mainly using mathematical morphology operation, either applied on microarray or its pixel derivative.
format	Thesis
qualification_name	Master of Philosophy (M.Phil.)
qualification_level	Master's degree
author	Samsudin, Nurnabilah
author_facet	Samsudin, Nurnabilah
author_sort	Samsudin, Nurnabilah
title	An improved microarray image analysis architecture using mathematical morphology
title_short	An improved microarray image analysis architecture using mathematical morphology
title_full	An improved microarray image analysis architecture using mathematical morphology
title_fullStr	An improved microarray image analysis architecture using mathematical morphology
title_full_unstemmed	An improved microarray image analysis architecture using mathematical morphology
title_sort	improved microarray image analysis architecture using mathematical morphology
granting_institution	Universiti Tun Hussein Onn Malaysia
granting_department	Faculty of Science Computer and Information Technology
publishDate	2015
url	http://eprints.uthm.edu.my/1410/2/NURNABILAH%20SAMSUDIN%20COPYRIGHT%20DECLARATION.pdf http://eprints.uthm.edu.my/1410/1/24p%20NURNABILAH%20SAMSUDIN.pdf http://eprints.uthm.edu.my/1410/3/NURNABILAH%20SAMSUDIN%20WATERMARK.pdf
_version_	1747830783210422272

An improved microarray image analysis architecture using mathematical morphology

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