// FIJI practical 3: Simple macros
// Task 0: Test Batch processing
// Copy the code to Batch process tool

selectWindow("NucleiDAPIconfocal.png");

// Make a copy to keep the original for measurements in the end
run("Duplicate...", "title=NucleiDAPIconfocal_dubl.png");

run("Gaussian Blur...", "sigma=2");
setAutoThreshold("Otsu dark");
run("Convert to Mask");
run("Fill Holes");
run("Watershed");
run("Analyze Particles...", "size=500-Infinity clear add");

selectWindow("NucleiDAPIconfocal.png");
roiManager("Show All with labels");
roiManager("Measure");