http://imagej.273.s1.nabble.com/object-oriented-segmentation-tp5001110p5001186.html
2012/12/15 Straatman, Kees R. (Dr.) <
> 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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