Stomatal density

[Aristophanes]

Hi,
I'm researching the density of stomata for a certain plant. Stomata are holes bordered by two cells, which can be viewed under a microscope. I have a digital camera attached to my microscope which allows me to take pictures of stomata. So far, I have been identifying them with my own eyes. Not only do I imagine they would be difficult for software to detect due to the texture of these photographs, but they are present in different focal depths, so I have to take several pictures at different focal depths to see all of the stomata for a single area of the slide. Below is an image of what this looks like.
I was wondering if anyone has any suggestions or recommendations as to how to detect them using imageJ.
Any help would be greatly appreciated!

[Marcel]

Hello,

i would try to identify the stomata with template matching.
See e.g. this plugin (allows multi matching of a template!):

https://sites.google.com/site/qingzongtseng/template-matching-ij-plugin

At least in the inner parts of you sample image you should get some useful results (you can use the results of multiple measurements for an statistical trend of the density).