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imageJ-macro-findZombies.ijm
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imageJ-macro-findZombies.ijm
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//Runs script in batch mode if not commented out
// setBatchMode(true);
args = split(getArgument(),','); // optional arguments for "input" and "output" directories
// arg = getArgument();
// if (lengthOf(args) == 0) {
// // Run script by choosing the source directories
// dir_raw = getDirectory("Choose Directory of Raw Images");
// } else {
// // the user gave some directories
dir_raw = args[0];
// dir_raw = arg;
// }
filenames = getFileList(dir_raw);
num_images = filenames.length;
// num_pairs = filenames.length / 2;
filenames = dir_raw + File.separator + filenames[0];
// filenames_B = dir_raw + File.separator + filenames[1];
// name_new_A = "A__SubtractBackground-Contrast-Convert__";
// name_new_B = "B__SubtractBackground-Contrast-Convert__";
// run on the base image pair (A)
run("Image Sequence...", "open=[filenames] number=num_images starting=1 increment=1 file=tif sort");
// dumIm=getImageID();
// run("Z Project...", "projection=[Average Intensity]");
// imageCalculator("Subtract create stack", "raw","AVG_raw");
// run("Enhance Contrast", "saturated=0.35");
// run("Apply LUT", "stack");
// run("8-bit");
// run("Image Sequence... ", "format=TIFF name=" + name_new_A + " save=" + file_new_A);
// // close all the "A" images
// run("Close All");
// // run on the cross image pair (B)
// run("Image Sequence...", "open=[filenames_B] number=num_images starting=2 increment=2 file=tif sort");
// run("Z Project...", "projection=[Average Intensity]");
// imageCalculator("Subtract create stack", "raw","AVG_raw");
// run("Enhance Contrast", "saturated=0.35");
// run("Apply LUT", "stack");
// run("8-bit");
// run("Image Sequence... ", "format=TIFF name=" + name_new_B + " save=" + file_new_B);
// // close all the "B" images
// run("Close All");
// // close imageJ
// run("Quit");