##First batch run. Saves files that are grayscale with even illumination
#Convert each image to grayscale
run("8-bit");
#Apply an already prepared image to account for uneven illumination. Use Gaussian blur with radius of 200. Blurred image must be open in ImageJ before running the Batch function
currentTitle = getTitle();
referenceTitle = "gauss200blur.jpg"
imageCalculator("Subtract create 32-bit", currentTitle, referenceTitle);
saveAs("Jpeg", ("Result of " + currentTitle));

##Second batch run
#Enhance contrast
//run("Brightness/Contrast...");
run("Enhance Contrast", "saturated=0.35");
run("Enhance Contrast...", "saturated=1 normalize");
#Threshold the image, making only the animals of interest black and the rest of the pixels white
run("Auto Threshold", "method=Yen");
#Measure pixels in each image from several ROIs. First define ROIs and save them as RoiSet
//roiManager("Open", "../RoiSet.zip");
roiManager("multi-measure measure_all one append");