Threading problem? Montage with Overlay?

Posted by Nathaniel Ryckman on May 31, 2011; 9:46pm
URL: http://imagej.273.s1.nabble.com/Threading-problem-Montage-with-Overlay-tp3684401.html

Here are the goals that I have:

1) I have many stained cells that I would like to cut out and then montage. I have the cells' Rois.
2) After I have a montage, I would like to create an overlay using the Rois from step 1.

Any ideas would be appreciated.

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I used the following to obtain square images of the cells to montage:

IJ.makeRectangle();
IJ.run("Duplicate...", "title");
IJ.run("Canvas Size...", "width= height= position=");

// Select window
iw = WindowManager.getImage("title").getWindow();
WindowManager.setCurrentWindow(iw);


The problem that I am having is that there seems to be some threading going on that I am not fully aware of or am not handling correctly when I call the IJ commands.....

I suspect that there is a threading problem because, when I run the program normally, I end up with cells that have been duplicated several times (total squares duplicated stays the same though), but, when I run the program in debug mode, I do not get this error.

Thanks again!