Automatic+Array+Alignment

Basic Idea A program that would automatically align the id grid of spots with the visual spots on the peptide arrays in CIM would be very beneficial. I am fairly confident of a method that could align these spots. All of the spots on the array would be found using DBSCAN. Next for each spot the program would go through each DBSCAN spot and ask "Is this spot the spot with an id of y?" An SVM would be used to answer this question. The SVM would be trained with pre-aligned slides so that the DBSCAN data and the aligned gal file would be given to it. Spot y would have a feature set that included the position of the all the spots on the array and all of the gal spot positions. If all of this data turns out to be too computationally intensive, then certain spots could be chosen such as 100 spots surround spot y as well as the 100 spots in the four corners of the array. If a spot is recognized to have an id of y by the SVM, then it is given this id. After all of the spots have been checked, the program would go through and use regression SVM to figure out where the id spots should be placed since they weren't assigned to any recognized DBSCAN spot. When everything is all done a gal file and gpr file could be produced that had everything lined up. One additional feature that could be added on later is a module of the program that would look for uneven splotches in the image and mark all of the spots within this splotch as "bad". At the end of the day, there would be a complete automatic alignment program.

Example Images of the Automatic Array Alignment Program Nate and I worked on "S:\Research\Cancer_Eradication\Users\kwhittem\kwhittem\kwhittem\Array Analysis Project\Java code\AutomaticSlideAlignment4 Nate's Work\MicroarrayAnalyzer5 Nates Work\AutomaticSlideAlignmentEclipse2-26-10\output.html" This program tried to align with a red reflect image of which a copy is found here "C:\kurt\storage\CIM Research Folder\kwhittem\Array Analysis Project\Java code\AutomaticSlideAlignment3 where I left Program to Nate\zbig_red_reflect_one_block_cropped2.jpg" Note that this html file shows that the correlation coefficient with human is 0.92, but as I remember the program was not updated this number in the html file. I remember clearly that when things were aligned as well as they are in this image that the correlation coefficient was 0.94. Also see automatic array alignment program diagram here "C:\kurt\storage\CIM Research Folder\DR\2012\12-12-12\Automatic Array Alignment program diagram\Automatic Array Alignment Program Diagram 12-12-12.svg"

Literature Automatic DNA microarray gridding based on Support Vector Machines http://www.researchgate.net/publication/224355444_Automatic_DNA_microarray_gridding_based_on_Support_Vector_Machines Unsupervised SVM-based gridding for DNA microarray images. http://www.researchgate.net/publication/38057390_Unsupervised_SVM-based_gridding_for_DNA_microarray_images

Kevin did some work to automatically align the array, but he said that he did not get that far. Nevertheless, his stuff can be found here:

S:\Administration\software\custom software\Slide Align and here C:\kurt\storage\CIM Research Folder\DR\2012\11-28-12\Kevin Slide Alignment\SlideAlign