MAGIC Tool: MicroArray Genome Imaging & Clustering Tool
MATLAB Central File Exchange - DNA MicroArray Image Processing Case Study
Cluster 3.0: The open source clustering software available here implement the most commonly used clustering methods for gene expression data analysis.
PAM: Prediction Analysis for Microarrays
MIAME: Minimum Information About a Microarray Experiment that is needed to enable the interpretation of the results of the experiment unambiguously and potentially to reproduce the experiment