Confocal images(detection and quantification)

I have made stacks of multi channel confocal Z- serial section images
of immunohistochemical localization of a specific type of protein found
on the intima of the thoracic aorta of rats. I have also merge the
images obtained by each channel into a single image. There are a bunch
of stuff that I need to do, and I have decided to use imagej to conduct
them. Firstly, I need to be able to detect the outline of the intima
since it is very thin compared to the media and adventitia, they all
make up the wall of the aorta. I have been looking at a technique
called segmentation using snakes but I am not sure fully how that
works. Secondly, I need to quantify the fluorescent intensity of each Z
section of the stack taking into consideration that the three
dimensional fluorescent staining of the protein is not symmetric about
the z -axis. Since I am dealing in effect with hundreds of images, I
need to have this process (detection and quantification) as automated
as possible.

Jimmy