In the Detector/Microprot project we have (in cooperation with colleagues at Campus Wels) developed an image analysis framework called Spotty - now version 1.0.2182 is released!
This framework offers multiple image analyses especially suited for fluorescence microscopy images. It can, e.g., be used to gain information about the interaction of proteins, the recovery rate, and the mobility factor of cell regions; the analyses relevant in these cases are intensity analysis, µPatterning image analysis, and FRAP.