basic ImageJ question

[Phillip Fujiyoshi]

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-2]

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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