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DNA MicroArray Image Processing Case Study

4.9 | 14 ratings Rate this file 18 Downloads (last 30 days) File Size: 4.24 MB File ID: #2573 Version:
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DNA MicroArray Image Processing Case Study


Robert Bemis (view profile)


22 Oct 2002 (Updated )

Case study used in Biomedical and Image Processing seminars (highlights algorithm development).

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In one type of gene expression analysis, fluorescently tagged messenger RNA from different cells are hybridized to a microscopic array of thousands of complimentary DNA spots that correspond to different genes. Illuminated spots emit different color light, indicating which genes are expressed (e.g., green=control, red=sample, yellow=both).
In this case study, MATLAB, the Image Processing and Signal Processing toolboxes were used to determine the green intensities from a small portion of a microarray image containing 4,800 spots. A 10x10 pattern of spots was detected by averaging rows and columns to produce horizontal and vertical profiles. Periodicity was determined automatically by autocorrelation and used to form an optimal length filter for morphological background removal. A rectangular grid of bounding boxes was defined. Each spot was individually addressed and segmented by thresholding to form a mask. The mask was used to isolate each spot from surrounding background. Individual spot intensity was determined by integrating pixel intensities. Finally, integrated intensities were tabulated and saved to a data file for subsequent statistical analysis to determine which genes matter most.

With the MATLAB code and example image in this package you can follow the steps used for this application.


This file inspired Fuzzy K Means Clustering.

Required Products Image Processing Toolbox
Signal Processing Toolbox
MATLAB release MATLAB 7 (R14)
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Comments and Ratings (20)

can we make a pharmacophore by using this data?

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24 May 2014 nastaran


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29 Aug 2013 mona

mona (view profile)

thanks, this file is very helpful , but i need to know the data set you have been used to import this image from it

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06 Jan 2012 Helen Chen

21 Feb 2011 B.K. Mishra

hi every body can any body tell me how we use support vector clustering for classify DNA microarray

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29 Dec 2010 Esteban A. Vidal

Thank you so much! Nice work, very useful for my thesis

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26 May 2009 Leo T

Leo T (view profile)

thanks ! this file help me do my project for ICA and microarray ^^!

07 Oct 2007 Saeed Arshad


29 Mar 2007 Danie John

This is a wonderful example

04 Jun 2006 M Mehta



19 Nov 2005 Luigi Rosa

Research work

15 Jul 2005 Hadi Hosseinzadegan

Thank you, The file helped my project

16 May 2005 ali haider


02 May 2005 Haig Djambazian

The fucntion strel is missing from the downloaded files.

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11 Mar 2005 anvesh reddy

18 Feb 2005 Vibhor Maheshwari

Can we have some more Bio Image processing examples

01 Dec 2004 maheswar gunampally

it is excellent.very ingormatine

22 Apr 2004 howard li

26 Mar 2004 amol ingole

i got good information from this file.i am doing project in microarray image processing.

19 Aug 2010 1.1


01 Sep 2016

Updated license

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