Re: simple thresholding problem

Posted by Martin Höhne on Jan 29, 2016; 9:18am
URL: http://imagej.273.s1.nabble.com/simple-thresholding-problem-tp5015481p5015482.html

Thomas,

the macro posted below might be a starting point. For the macro you need to these two filters/plugins installed:
http://rsb.info.nih.gov/ij/plugins/mexican-hat/index.html
http://rsb.info.nih.gov/ij/plugins/mean-shift.html

Best,
Martin
----------------------------------------------------------
run("Mexican Hat Filter", "radius=4");
run("Mean Shift", "spatial=2 color=100");
setAutoThreshold("Li dark");
setOption("BlackBackground", true);
run("Convert to Mask");
run("Fill Holes");
run("Watershed");

Playing with the filter settings might improve the outcome