CellDetection2.ijm 931 Bytes
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open("/Users/tischi/Dropbox/Presentations_Courses/2015--Tischi--Kopenhagen/0000--PracticalImagej/data/autophagosomes/autophagosomes_raw.tif");
run("Gaussian Blur...", "sigma=10");
rename("blurredImage");
run("Find Maxima...", "noise=100 output=[Segmented Particles]");
rename("cells");
selectWindow("blurredImage");
setThreshold(230, 714);
setOption("BlackBackground", false);
run("Convert to Mask");
rename("foreground");
imageCalculator("AND create", "foreground","cells");
run("Analyze Particles...", "size=100-Infinity exclude add");
open("/Users/tischi/Dropbox/Presentations_Courses/2015--Tischi--Kopenhagen/0000--PracticalImagej/data/autophagosomes/autophagosomes_raw.tif");
rename("raw");
run("Duplicate...", "title=median_bg");
run("Median...", "radius=5");
imageCalculator("Subtract create", "raw","median_bg");
run("Find Maxima...", "noise=100 output=[Single Points]");
run("Divide...", "value=255");
rename("spots.tif")