http://imagej.273.s1.nabble.com/Calculate-area-on-a-per-object-basis-tp5014278p5014279.html
If I understand you correctly, you have large red objects which may contain more than one green objects within them. If this is the case, after you segment the red objects, you can use them as an overlay on the green channel.
Then, you can iterate over the red objects, use adjust, threshold for each ROI separately, and then you'll be able to keep track: which green objects are within which red object.
I hope I understood your problem correctly.
> On Sep 9, 2015, at 6:35 AM, Danielle Harmon <
[hidden email]> wrote:
>
> Dear List,
>
> I have images with two channels (red and green). I'd like to first segment the red objects and then calculate the amount (area) of green signal per red object, on an object by object basis.
>
> I can easily calculate the area of green contained within the red with the script below, but I can't figure out how to get the area of green per red object. Is it possible? Any and all advice is very welcome!!
>
> Thanks tons!
>
> Danielle
>
> p.s. I hope to automate/batch this analysis.
>
> imgName=getTitle();
> run("Split Channels");
> selectWindow(imgName + " (blue)");
> close();
> selectWindow(imgName + " (red)");
> setAutoThreshold("Default");
> //run("Threshold...");
> setThreshold(40, 255);
> setOption("BlackBackground", false);
> run("Convert to Mask");
> run("Analyze Particles...", "size=50-Infinity show=Outlines summarize");
> selectWindow(imgName + " (red)");
> selectWindow("Drawing of " + imgName + " (red)");
> close();
> selectWindow(imgName + " (red)");
> //run("Threshold...");
> setThreshold(0, 243);
> run("Convert to Mask");
> imageCalculator("Subtract create", imgName + " (green)", imgName + " (red)");
> selectWindow("Result of " + imgName + " (green)");
> setAutoThreshold("Default");
> //run("Threshold...");
> setThreshold(75, 255);
> run("Convert to Mask");
> run("Analyze Particles...", "size=0-Infinity show=Outlines summarize");
>
>
>
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