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Microarray / Macroarray Image Processing Tools

  • GPC VisualGrid
Visual Grid is a free scaled down sample version of BioChip Explorer developed at GPC Biotech AG. It allows both automatic, semi-automatic, and manual adjustment for the grid position overlayed on the microarray/macroarray images. Forground and background internsities are estimated and can be exported in a spreadsheet. We found there are two useful features in VisualGrid that we can't find in other image processing tools. One is that a correlation graph can be generated if there are replicate spots on the membrane, so that we can identify which genes do not generate reproducible data. The other useful feature is that spots can be sorted based on their estimated intensity values. Since the spot image is displayed alongside its intensity value, it's very easy for users to identify which cell is not spotted right or the grid over it is not positioned right.


  • TIGR SpotFinder
TIGR Spotfinder reads paired 16-bit TIFF image files generated by most microarray scanners. It's a good choice for processing 2-dye cDNA array images.


  • ScanAlyze
ScanAlyze processes 2-dye fluorescent images of microarrays. However, the spots on the array cannot be too dense or screwed too much. Otherwise, the performance of Spotfinder is not very satisfatory..


  • Clusfavor
Gene Expression Cluster and Factor Analysis Using Varimax Orthogonal Rotation. It is based on clustering and principal components analyses of oligonucleotide and cDNA microarray gene expression; CLUSFAVOR Windows-based computer program for unsupervised hierarchical cluster and principal component analyses of DNA microarray transcriptional profiles.