Skip to main content

Constructing the Histogram Representation for Automatic Gridding of cDNA Microarray Images

  • Conference paper
Medical Biometrics (ICMB 2008)

Part of the book series: Lecture Notes in Computer Science ((LNIP,volume 4901))

Included in the following conference series:

  • 1138 Accesses

Abstract

This paper proposes an novel approach for automatic gridding of cDNA microarray images based on histogram representation. The approach constructs histogram representation to characterize microarray images and use it, instead of raw signal intensities used in previous gridding methods, to identify spots. The histogram representation can efficiently reduce noise and the influence from low raw signal intensities and local contaminations. The proposed approach is successfully tested on different types of microarray images and is compared with several previous algorithms.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 39.99
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 54.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

Preview

Unable to display preview. Download preview PDF.

Unable to display preview. Download preview PDF.

References

  1. Schena, M., Shalon, D., Davis, R.W., Brown, P.O.: Quantitative monitoring of gene expression patterns with a complementary microarray. Science 270, 467–470 (1995)

    Article  Google Scholar 

  2. Baldi, P., Hatfield, G.W.: DNA microarrays and gene expression. Cambridge University Press, Cambridge (2002)

    Book  Google Scholar 

  3. Schena, M.: Microarray analysis. John Wiley & sons, Inc., New York, USA (2003)

    Google Scholar 

  4. Antoniol, G., Ceccarelli, M.A.: Markov Random Field Approach to Microarray Image Gridding. In: Proc. 17th Int’l Conf. Pattern Recognition, pp. 550–553 (2004)

    Google Scholar 

  5. Bassett, D.E., Eisen, M.B., Boguski, M.S.: Gene expression informatics-it’s all in your mine. Nat. Genet. 21(Suppl.), 51–55 (1999)

    Article  Google Scholar 

  6. Antoniol, G., Ceccarelli, M.: Microarray image gridding with stochastic search based approaches. Image and Vision Computing 25, 155–163 (2007)

    Article  Google Scholar 

  7. Yang, Y., Buckley, M., Dudoit, S., Speed, T.: Comparison of Methods for Image Analysis on cDNA Microarray Data. J. Computational and Graphical Statistics 11, 108–136 (2002)

    Article  MathSciNet  Google Scholar 

  8. Rueda, L., Vidyadharan, V.: A Hill-Climbing Approach for Automatic Gridding of cDNA Microarray Images. IEEE/ACM Transactions on Computational Biology and Bioinformatics 3, 72–83 (2006)

    Article  Google Scholar 

  9. Axon Instruments, IncGenePix Pro 4.0, Documentation (2002), http://www.axon.com/

  10. Eisen, M.B.: ScanAlyze, Software and Documentation (1999), http://rana.lbl.gov/EisenSoftware.htm

  11. Buhler, J., Ideker, T., Haynor, D.: Dapple: Improved Techniques for Finding Spots on DNA Microarrays, UW CSE Technical Report UWTR, 12 (2000)

    Google Scholar 

  12. Jain, A., Tokuyasu, T., Snijders, A., Segraves, R., Albertson, D., Pinkel, D.: Fully Automatic Quantification of Microarray Data. Genome Research 12, 324–335 (2002)

    Article  Google Scholar 

  13. Angulo, J., Serra, J.: Automatic analysis of DNA microarray images using mathematical morphology Bioinformatics.  19, 553–562 (2003)

    Google Scholar 

  14. Hartelius, K., Carstensen, J.M.: Bayesian grid matching. IEEE Transactions Pattern Analysis and Machine Intelligence 25, 162–173 (2003)

    Article  Google Scholar 

  15. Steinfath, M., Wruck, W., Seidel, H.: Automated Image Analysis for Array Hybridization Experiments. Bioinformatics 17, 634–641 (2001)

    Article  Google Scholar 

  16. Katzer, M., Kummer, F., Sagerer, G.: A Markov Random Field Model of Microarray Gridding. In: Proc. 2003 ACM Symp. Applied Computing (2003)

    Google Scholar 

  17. Katzer, M., Kummer, F., Sagerer, G.: Methods for automatic microarray image segmentation. IEEE Trans. Nanobioscience 2, 202–214 (2003)

    Article  Google Scholar 

  18. Webb, A.R., Ltd, Q., Malvern, U.: Statistical pattern recognition. John Wiley & Sons, LTD., Chichester (2002)

    Book  Google Scholar 

  19. Snijders, A.M., Nowak, N., Segraves, R., Blackwood, S., Brown, N., Conroy, J., Hamilton, G., Hindle, A.H., Huey, B., Kimura, K.: Assembly of microarrays for genome-wide measurement of DNA copy number by CGH. Nat. Genet. 29, 263–264 (2001)

    Article  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2007 Springer-Verlag Berlin Heidelberg

About this paper

Cite this paper

Wang, HQ., Wong, HS., Zhu, H. (2007). Constructing the Histogram Representation for Automatic Gridding of cDNA Microarray Images. In: Zhang, D. (eds) Medical Biometrics. ICMB 2008. Lecture Notes in Computer Science, vol 4901. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-540-77413-6_32

Download citation

  • DOI: https://doi.org/10.1007/978-3-540-77413-6_32

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-540-77410-5

  • Online ISBN: 978-3-540-77413-6

  • eBook Packages: Computer ScienceComputer Science (R0)

Publish with us

Policies and ethics