AIM can currently handle only differential microarray experiments where you are interested in spot intensity / gene expression ratios between two differently labelled samples. Contact the author for workarounds / new software in case you want to do something else.
You need two scanned TIFF images of each of your slides. An ASCII file which lists all of your slides and images allows simple import into AIM. The file must contain at least three tab-separated columns: The first column contains a unique name for each slide. The name must be a legal file name. The second and third column must contain the green and red image to get the green over red ratio in the output.
AIM uses XML formatted files internally. The quantitation and gridding output can be exported in the GenePixResults (GPR) format defined by Axon. We plan to implement a (configurable) database export feature that would use an external SQL client program to store the columns of the GPR output in user defined columns of database tables. A bit of it can be seen in the 'Output options' dialog of the GUI