How to calculate area of a particle that contains abundant irregular inclusions

Posted by crystal_analysis on Apr 08, 2011; 2:57pm
URL: http://imagej.273.s1.nabble.com/How-to-calculate-area-of-a-particle-that-contains-abundant-irregular-inclusions-tp3684892.html

Hello,
          I have a series of images from mineral crystals. The images show the element content of the various mineral phases. I want to calculate the proportion of area covered by a certain intensity. For instance, in the example below I want to calculated the area covered by the mineral with the orange level of intensity.

So, I transformed the image in an 8-bit format.



Then, using the threshold function I merged the blue intensity with the background. Finally I turned the image into a binary image. But, from there I have not been able to calculate the area of only the white intensity pixels. I want to exclude the area of inclusion within the large crystals. I think that the fact there are many small irregular inclusions prevents Image J from doing a proper calculation. When I try the analyze particles function and check the outlines box, Image J calculate an area from a bunch of the small inclusions, but does not calculate the large crystals.... If you have any suggestion for a proper procedure please let me know. Thanks a lot

Cheers