Re: Reject filled hole partially surrounded by open circle

Posted by jmcginnity on Nov 01, 2013; 2:54am
URL: http://imagej.273.s1.nabble.com/Reject-filled-hole-partially-surrounded-by-open-circle-tp5005398p5005413.html

Hi,
My initial request was confusing so here is better explanation.

Using Analyse Particles I would like to measure the diameters of bubbles in a stack of images.  These are images of bubbles that have been processed to yield filled holes.  The processing that has been done to get the images was Image Edge - Deriche / Threshold / Fill Holes.  The next steps I generally do are: Erode (to remove lines), watershed (to separate any adjoining particles) and then I run Analyse Particles to get the bubble diameters.
However, in my measurements, I do not want to include filled holes that are partially surrounded by a broken circle, because these are not bubbles but images of light that passes directly through the centre of the bubbles.
   I was wondering if there is any routine that I could use prior to Erode that would identify filled holes that have a concave line as a nearest neighbour.  If so, I could then reject these. Is this possible in ImageJ ?  

In the image below there are 11 filled holes.  Of these, 5 are partially enclosed by broken circles or concave lines.  I wish to exclude these 5 filled holes from being analysed by Analyse Particles.
Thanks,
Justin