Posted by
Krs5 on
Dec 15, 2012; 1:52pm
URL: http://imagej.273.s1.nabble.com/object-oriented-segmentation-tp5001110p5001177.html
Hi Michiel,
It looks like the plugin Watershed makes the pixels at the boarder white with as result that the cells are not recognized as edge anymore. If you add
makeRectangle(2, 1, 1341, 1021);
before you run Analyse Particles it should go OK.
Best wishes
Kees
________________________________________
From: ImageJ Interest Group [
[hidden email]] On Behalf Of Michiel van Dommelen [
[hidden email]]
Sent: 14 December 2012 11:51
To:
[hidden email]
Subject: Re: object-oriented segmentation
Hey Kees,
I got it working! I used the plugin from Daniel Saga (
http://bigwww.epfl.ch/sage/soft/watershed/<
http://bigwww.epfl.ch/sage/soft/watershed/> ). The only thing I do not
understand is why the "exclude on edge" functionality is not working in this
code. Would you have any idea? Of course I have to tweak some settings to
make it robust enough for higher throughput. For the rest it is working like
a charm.
I got it working with the code below:
selectWindow("Cytoplasm_Raw.jpg");
run("Duplicate...", "title=[Cytoplasm_Raw_temp.jpg]");
run("Median...", "radius=5");
run("Auto Threshold", "method=Triangle white");
run("Divide...", "value=2"); //this makes the cytoplasm grey in dual color
overlay
selectWindow("Nuclei_Raw.jpg");
run("Duplicate...", "title=[Nuclei_Raw_temp.jpg]");
run("Median...", "radius=5");
run("Auto Threshold", "method=Triangle white");
run("Watershed");
imageCalculator("Add", "Nuclei_Raw_temp.jpg","Cytoplasm_Raw_temp.jpg");
//this makes dual color overlay
rename("2ColorOverlay");
selectWindow("Cytoplasm_Raw_temp.jpg");
close();
selectWindow("2ColorOverlay");
run("Watershed ", "blurring='0' watershed='1 1 0 100 0 0' display='0'
"); //this is the plugin I installed
selectWindow("Binary watershed lines");
run("Invert LUT");
run("Set Scale...", "distance=1 known=0.617 pixel=1 unit=um global");
//These 2 lines adjust the settings specific to my images
run("Analyze Particles...", "size=350-Infinity circularity=0.00-1.00
show=Nothing exclude clear include add");//These 2 lines adjust the settings
specific to my images
selectWindow("Nuclei_Raw.jpg");
roiManager("Show All with labels");
roiManager("Show All");
selectWindow("Cytoplasm_Raw.jpg");
roiManager("Show All with labels");
roiManager("Show All");
Thanks for all your help!
Warm regards,
Michiel
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