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tarokiritani/Preprocess_Stack_for_Cell_Counting.ijm

Created April 28, 2017 09:23
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imagej macro that preprocesses confocal image stack for cell counting
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Preprocess_Stack_for_Cell_Counting.ijm
run("Bandpass Filter...", "filter_large=100 filter_small=5.1 suppress=None tolerance=5 autoscale process");
for(i=1;i<nSlices + 1;i++){
setSlice(i);
getStatistics(area, mean, min, max, std, histogram);
setThreshold(mean + 2 * std, 255);
run("Make Binary", "slice");
}
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