Re: Batch process images with specific ROis

Posted by gnelson on
URL: http://imagej.273.s1.nabble.com/Batch-process-images-with-specific-ROis-tp5021442p5021451.html

HiFranco,

I think what you want is a loop to got through each ROI individually once
you have added them all to the ROI manager.  Is that correct?  I have done
something similar where I counted local maxima inside each ROI using the
code below:

for(j=0; j<roiManager("count"); j++) {
                        roiManager("select", j);
                        run("Find Maxima...", "noise="+tolerance+" output=[Count]");
// run("Find Maxima...", "noise="+tolerance+" output=[Point Selection]");
                        run("Add Selection...");
                        }
                saveAs("Results",
dir2+File.separator+originalImage+"_nuc_coloc_and_h2ax.xls"); //This is
savign as it goes along in case it crashes

                selectWindow(originalImage);

I then saved an image with the overlays burned on so I had a history of what
I did.  Plus, a separate csv file is saved for each image.
Obviously, you can alter to only measure whatever you are interested in.
Does that help?

Glyn.



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