BioImageXD
It says: BioImageXD - free open source software for analysis, processing and 3D rendering of multi dimensional, multi data channel, time series image data from microscopy and other sources.
License: Freeware, Source code available
http://sourceforge.net/projects/bioimagexd/
CoLocalizer Pro
It says: CoLocalizer Pro is a quantitative colocalization analysis software. It calculates specialized coefficients to characterize colocalization of fluorescence markers objectively.
License: Commercial, free Trial
http://www.colocalizer.com/pro.html
ImageJ
Wikipedia: ImageJ is a public domain, Java-based image processing program developed at the National Institutes of Health.
License: Freeware, but based on Java
Macnification
For capturing, organizing, editing and analyzing microscopic images of different file formats.
License: Commercial, free Trial
http://www.orbicule.com/macnification/
OMA
It says: The OMA program was developed by researchers as a way to investigate and post-process photometric images from CCD detectors used for laser-based imaging of reacting and nonreacting flows as well as some spectroscopic applications.
License: Freeware, Source code available
http://oma-x.org/omaWebPage/index.html