PMID: 15376953Sep 21, 2004Paper

Gridline: automatic grid alignment in DNA microarray scans

IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society
Peter Bajcsy

Abstract

We present a new automatic grid alignment algorithm for detecting two-dimensional (2-D) arrays of spots in DNA microarray images. Our motivation for this work is the lack of automation in high-throughput microarray data analysis that leads to a) spatial inaccuracy of located spots and hence inaccuracy of extracted information from a spot and b) inconsistency of extracted features due to manual selection of grid alignment parameters. The proposed grid alignment algorithm is novel in the sense that 1) it can detect irregularly row- and column-spaced spots in a 2-D array, 2) it is independent of spot color and size, 3) it is general to localize a grid of other primitive shapes than the spot shapes, 4) it can perform grid alignment on any number of input channels, 5) it reduces the number of free parameters to minimum by data driven optimization of most algorithmic parameters, and 6) it has a built-in speed versus accuracy tradeoff mechanism to accommodate user's requirements on performance time and accuracy of the results. The developed algorithm also automatically identifies multiple blocks of 2-D arrays, as it is the case in microarray images, and compensates for grid rotations in addition to grid translations.

References

Jul 13, 2001·Bioinformatics·M SteinfathJ O'Brien
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Feb 6, 2002·Genome Research·Ajay N JainDaniel Pinkel
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Citations

Aug 29, 2006·Medical & Biological Engineering & Computing·Mingjun ZhangTzyh-Jong Tarn
Mar 1, 2008·Expert Opinion on Medical Diagnostics·Klaus KayserGian Kayser
Mar 20, 2012·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Bogdan BeleanRomulus Terebes
Dec 3, 2008·Computerized Medical Imaging and Graphics : the Official Journal of the Computerized Medical Imaging Society·Nikolaos Giannakeas, Dimitrios I Fotiadis
Oct 7, 2006·IEEE Transactions on Image Processing : a Publication of the IEEE Signal Processing Society·Michele Ceccarelli, Giuliano Antoniol
Jun 11, 2008·IEEE Transactions on Medical Imaging·Eleni Zacharia, Dimitris Maroulis
Jan 6, 2005·IEEE Transactions on Nanobioscience·Rastislav LukacAnastasios N Venetsanopoulos
Jul 14, 2005·IEEE Transactions on Medical Imaging·K BlekasI E Lagaris
May 15, 2013·Computer Methods and Programs in Biomedicine·Zidong WangXiaohui Liu
Oct 30, 2014·Medical & Biological Engineering & Computing·Bogdan BeleanAdrian Bot
May 27, 2015·IEEE Journal of Biomedical and Health Informatics·Abhik DattaKin-Choong Yow

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