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Bioinformatics Advance Access published online on November 8, 2006
Bioinformatics, 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
Received August 25, 2006
Revised October 10, 2006
Accepted November 3, 2006

Applications note

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

R. Cathelin 1, F. Lopez 2, and Ch. Klopp 1 *

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

* To whom correspondence should be addressed.
Ch. Klopp, E-mail: christophe.klopp{at}toulouse.inra.fr


  Abstract

Summary: Many different programs are available to analyse 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 [1] 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.

Associate Editor: Trey Ideker
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