Fluorescence intensity in dendritic spines

I would like to measure fluorescence intensity in dendritic spines. I have been looking for plugins or open source software to do it but I could not find anything that can fit my analysis.
I found this paper that did a line to analysis the intensity profile along the spine http://www.jneurosci.org/content/33/5/1846/tab-figures-data (But since I have a lot of images and very heterogenous spines I would like to find something that I can avoid manual measures)
I would like to do something similar of the paper above with 2 fluorophores or 3 different proteins staining on the dendritic spine ( Please, see attached the tiff figure with 2 of my fluorescent proteins of interest)
So far I have found software that analyses the morphology of the spine and classified by type but not fluoresncence intensity. (e.g. neurostudio, SynPan)
Furthermore, I would like to measure the localization of these proteins at the membrane of the dendritic spine.
Any guide or help, I would really appreciate it.
Thanks in advance.

22 div spine.tif (625.5 KB)