Re: basic ImageJ question

Posted by Michael Doube-2 on Sep 25, 2007; 6:30pm
URL: http://imagej.273.s1.nabble.com/basic-ImageJ-question-tp3698326p3698327.html

Hi Phillip

You should be able to write a quick macro that can threshold the red and
green parts of the image and count thresholded pixels: try Gabriel
Landini's Threshold_Colour:

http://www.dentistry.bham.ac.uk/landinig/software/software.html

Or alternatively you could split the channels into R, G and B stacks and
apply something like this to each channel:

http://doube.org/macros.html#vfb

Mike

Phillip Fujiyoshi wrote:

> Sorry to be so ignorant -- we're trying to figure out if ImageJ is the
> right software for our purposes.  We have confocal image stacks of
> roots colonized by fungus.  The fungal structures fluoresce green from
> the stain we use and are recognized at a separate channel than the
> plant tissue, which appears red.  Can ImageJ automatically distinguish
> the amount of space occupied by the two different colors?
>
> Phillip Fujiyoshi
> USDA-ARS
> Plant Pathology
> UC Davis

--
Michael Doube  BPhil BVSc MRCVS
PhD Student
Dental Institute
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