I know this method published in PLoS ONE but do not whether I will be able to use it as I do not have matlab. I will try to use ImageJ or FIJI...
Kozlowski C, Weimer RM (2012) An Automated Method to Quantify Microglia Morphology and Application to Monitor Activation State Longitudinally In Vivo. PLoS ONE 7(2): e31814. doi:10.1371/journal.pone.0031814
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0031814
Thanks in advance for your help.