how to define a ROI with selection and thresholding

Posted by pang on Mar 21, 2013; 3:23pm
URL: http://imagej.273.s1.nabble.com/how-to-define-a-ROI-with-selection-and-thresholding-tp5002332.html

Dear ImageJ colleagues,

I would like to use makeRectangle to identify a specific area I would like to work on, and then set a threshold using the OTSU method.  Next I want to make a selection with thresholded pixels within  the Rectangle.

makeRectangle(512, 512, 512, 512);
setAutoThreshold("Otsu dark");
run("Create Selection");
roiManager("Add");

I found that ImageJ created selection on the whole image with the thresholded value determined by the Rectangele. I really want to create selection only within the rectangle. How could I do that?


Thanks!

Zhengyu

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