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imageJ-macro-runstack-continuous.ijm
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imageJ-macro-runstack-continuous.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
if (lengthOf(args) == 0) {
// Run script by choosing the source/destination directories
dir_raw = getDirectory("Choose Directory of Raw Images");
dir_new = getDirectory("Choose Directory of Processed Images");
} else {
// the user gave some directories
dir_raw = args[0];
dir_new = args[1];
}
filenames = getFileList(dir_raw);
num_images = filenames.length;
num_pairs = filenames.length - 1;
filenames_A = dir_raw + File.separator + filenames[0];
name_new_A = "SubtractBackground-Contrast-Convert__";
file_new_A = dir_new + File.separator + name_new_A + "00000.tif";
print('A: ' + filenames_A);
// run on the base image pair (A)
run("Image Sequence...", "open=[filenames_A] 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("8-bit");
//run("Apply LUT", "stack");
run("Image Sequence... ", "format=TIFF name=" + name_new_A + " save=" + file_new_A);
// close all the "A" images
run("Close All");
// close imageJ
run("Quit");