Re: Counting spots within nuclei

Posted by Gabriel Landini on Aug 07, 2011; 3:32pm
URL: http://imagej.273.s1.nabble.com/Counting-spots-within-nuclei-tp3683546p3683552.html

On Sunday 07 Aug 2011, David Knecht charter wrote:
> Hi Fabrice- I got the binary ROI's of the nuclei added to the manager, but
> I am not sure how to now analyze those ROI's in the protein channel to
> count the spots/nucleus.  Do you have a sample batch macro I can look at
> to modify?  Thanks- Dave

If you have the nuclear binary profiles and the binarised spots in another
channel, you can subtract the spots from the nuclei so each nucleus will have
as many holes as spots. Then you can use the "ParticleHoleNumber.txt" macro
from the morphology collection available at:
http://www.dentistry.bham.ac.uk/landinig/software/software.html
to count how many holes there are in each nucleus.
That macro generates a table where the column GrIntDen is the number of holes
in the particle.

Please be aware that most of the macros in there expect white particles on
black background.

Cheers
Gabriel