Fiji - Fiji is just imageJ (batteries included). An easily self updatable, and installable distrubution of imageJ with built in scripting, plugins and other cool stuff. A lot of analysis can be done using Fiji/ImageJ, i.e. Colocalization.
Manuals about how to use Fiji/ImageJ are available on various websites. Please check the links.
- Fiji website
Fiji is just ImageJ (batteries incuded) - download, wiki, manuals