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DNA MicroArray Image Processing Case Study

version 1.1.0.1 (4.24 MB) by

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.

Comments and Ratings (20)

can we make a pharmacophore by using this data?

nastaran

tnx

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

Helen Chen

B.K. Mishra

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

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

Leo T

Leo T (view profile)

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

Saeed Arshad

Best

Danie John

This is a wonderful example

M Mehta

ABHISHEK TRIPATHI

SUPERBEB VERY HELPING IN MY PROJECT

Luigi Rosa

Research work

Hadi Hosseinzadegan

Thank you, The file helped my project

ali haider

thanks

Haig Djambazian

The fucntion strel is missing from the downloaded files.

anvesh reddy

Vibhor Maheshwari

Can we have some more Bio Image processing examples

maheswar gunampally

it is excellent.very ingormatine

howard li

amol ingole

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

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MATLAB Release
MATLAB 7 (R14)
Acknowledgements

Inspired: fuzzy k means clustering

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