Re: fill holes based on size filter

Posted by Krs5 on May 21, 2015; 3:41pm
URL: http://imagej.273.s1.nabble.com/fill-holes-based-on-size-filter-tp5012897p5012899.html

Dear Matt,

I would select the larger holes that you want to reject via Analyze Particles and set the Size + Add to Manager. Highlight all the ROIs found in the manager and select More>> OR (Combine). Add this selection to the manager. Select this ROI and Edit > Selection > Make Inverse. Now you have selected everything except the larger holes and you can do your measurements.

But maybe somebody else knows a more elegant way to do this?

Best wishes

Kees


Dr Ir K.R. Straatman
Senior Experimental Officer
Advanced Imaging Facility
Centre for Core Biotechnology Services
University of Leicester
http://www2.le.ac.uk/colleges/medbiopsych/facilities-and-services/cbs/lite/aif



-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of PEARSON Matthew
Sent: 21 May 2015 14:32
To: [hidden email]
Subject: fill holes based on size filter

Hi all,

I just wanted to clarify something in imageJ.  I'm using both "include holes" in analyse particles and "limit to threshold" in set measurements.  If there is an area within my thresholded object that is not included in the threshold yet is completely encapsulated by the threshold, what will be measured?  Limit to threshold suggests, this non-thresholded area would not be measured but include holes suggests it would be measured?

Which leads me on to the real problem at hand, i'd like to be able to filter the holes i am including based on size.  Smaller holes, enclosed by the threshold i'd include up to a certain size and holes any bigger i want to reject.  Is there a simple way to do this?

Thanks for the help,

Matt




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