Overview
In order to automate the image processing, we need to know the layout of the spots as they were defined in the original GAL file. The instructions below illustrate the steps needed to extract this information.
Processing the GAL File
Reading the Gene Array Layout (GAL) File
In order to automate the image analysis, the location of each treatment spot on a filter needs to be known. At MBARI, we use a custom text format to describe the application of spots by the piezzo electric printer. Each printer run prints a number of ESP filters on a single filter sheet. Each individual filter is subsequently cut from the filter sheet. A complete GAL file can be read using:
import java.io.File import java.net.URL import org.mbari.esp.ia.services.GeneArrayAnalysisService import org.mbari.esp.ia.services.ToolBox // READ GAL FILE val geneArrayIOService = ToolBox.geneArrayIOService val allGalPoints = geneArrayIOService.read(new URL("file:/test07/110220hab5wcomp_2011-03-07_150545_Run.txt")) // CREATE IMAGE val bufferedImage1 = GeneArrayAnalysisService.toBufferedImage(allGalPoints, true, 100, 2) val imageIOService = ToolBox.imageIOService imageIOService.write(bufferedImage1, new File("110220hab5wcomp_2011-03-07_150545_Run.png"))
This produces the following image:
Subsetting the GAL Points
For our analysis, we only want the points that represent a single filter. In order to exclude the others we just subset the GAL points using:
// SUBSET - 12500 is a square in microns from the upper left corner of the GAL image val galPoints = GeneArrayAnalysisService.filterSingleSpot(allGalPoints, 12500) // CREATE IMAGE val bufferedImage2 = GeneArrayAnalysisService.toBufferedImage(galPoints, true, 20, 10) imageIOService.write(bufferedImage2, new File("110220hab5wcomp_2011-03-07_150545_Run-single.png"))
