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Bioinformatics Advance Access originally published online on November 8, 2006
Bioinformatics 2007 23(2):247-248; doi:10.1093/bioinformatics/btl564
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© The Author 2006. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

AGScan: a pluggable microarray image quantification software based on the ImageJ library

R. Cathelin , F. Lopez 1 and Ch. Klopp *

INRA, Sigenae UR875 Biométrie et Intelligence Artificielle/Génétique Cellulaire, BP 52627, 31326 Castanet-Tolosan Cedex, France
1 TAGC, INSERM-ERM 206 Parc Scientifique de Luminy, 13288 Marseille, France

*To whom correspondence should be addressed.


  Abstract

Summary: Many different programs are available to analyze microarray images. Most programs are commercial packages, some are free. In the latter group only few propose automatic grid alignment and batch mode. More often than not a program implements only one quantification algorithm. AGScan is an open source program that works on all major platforms. It is based on the ImageJ library [Rasband (1997–2006)] and offers a plug-in extension system to add new functions to manipulate images, align grid and quantify spots. It is appropriate for daily laboratory use and also as a framework for new algorithms.

Availability: The program is freely distributed under X11 Licence. The install instructions can be found in the user manual. The software can be downloaded from http://mulcyber.toulouse.inra.fr/projects/agscan/. The questions and plug-ins can be sent to the contact listed below.

Contact: christophe.klopp{at}toulouse.inra.fr

Associate Editor: Trey Ideker

Received on August 25, 2006; revised on October 10, 2006; accepted on November 3, 2006

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