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Holes within particles

Posted by Bill Mohler on Dec 02, 2010; 9:59pm
URL: http://imagej.273.s1.nabble.com/Holes-within-particles-tp3686310.html

After considerable time puzzling it over, I'm concluding that Analyze
Particles with the Include Holes option unchecked actually *does not*
properly identify particles within particles (as portrayed in the wiki
lesson
http://imagejdocu.tudor.lu/doku.php?id=gui:analyze:analyze_particles).  
To be more specific and correct, it *can* find particles that reside
within holes inside of a larger particle.  However, it does not define
the boundary of the hole as an inner edge of the larger particle that
contains it.  In other words, a particle with a hole in it is not
portrayed as a hollow ROI, but rather as a solid ROI with no hint of the
inner hole.

Is this a known and unavoidable feature?  Is there a setting that I
haven't found yet that solves this problem?

I'm attaching a jpeg to demonstrate the problem.  ROI edges are in
cyan.  Look very closely at the Large ROIs that contain holes, and you
will notice that there is no cyan outline around the outer edge of a
hole: for example, look at the black region surrounding ROIs 9-11; it is
actually a hole withing the huge ROI 2, but the outer edges of the black
are not rimmed in cyan, because it has not been recognized.  But any
particles within a hole ( like 9-11, which are above my 300pix size
cutoff) are properly outlined.

I really need to work out a fix for this problem, because these
arrangements are very common in my images.

Thanks for any help,
Bill


--

William A. Mohler

Associate Professor
Dept. of Genetics and Developmental Biology
University of Connecticut Health Center

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skype: wmohler
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Phi_Av_7_DarkBkgd_Mask_300-Inf_Rois.jpg (669K) Download Attachment