How to permanently add selections to images

Posted by PEARSON Matthew on Nov 02, 2016; 9:33am
URL: http://imagej.273.s1.nabble.com/How-to-permanently-add-selections-to-images-tp5017523.html

Hi all,

I'm having some issues making selections permanent on images.  The idea is that the macro makes various selections, then at the end an image should be produced that has those selections "flattened" on.  This image is purely to show the user where the selections are and what has been measured, it doesn't have to be the raw image its merely representative.

I have tried using the run("Draw") option but the lines are quite thick & blocky and don't seem to be able to make them thinner.  I have also tried roiManager("deselect") which is equivalent to selecting all ROI's in the manager then using run("Flatten"); i get a flattened image but the ROI's are not present on it.  This is what i tried:

roiManager("show all without labels");
roiManager("deselect");
run("From ROI Manager");
run("Flatten");

Is there an alternative?  It would be nice if you could simply show all ROI's and then if there was a function to create an image as it is currently displayed-like a screenshot.  I assumed this is what run("Flatten") does?

Thanks for the help,

Matt


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Matt Pearson
Microscopy Facility
MRC Human Genetics Unit
Institute of Genetics and Molecular Medicine (IGMM)
University of Edinburgh
Crewe Road
EH4 2XU





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