Image processing software packages

Free

Fiji: Free image processing software based on Java
ImageJ: Original ImageJ software before Fiji was released
Icy: Open community platform for bioimage informatics
Cell profiler Image analysis software: Creation of modular image analysis pipelines
Imaris Viewer: Software for 3D rendering and visualization
Zeiss Zen Blue: Free Lite version of Zeiss Zen software for Image processing (Registration is required)
IMOD: Tomographic Reconstruction
Huygens Suite: Partial version
Metamorph: Automation and Image Analysis

Amira: Visualization and manipulation of data (Free trial)
Autoquant Deconvolution: Advanced Image Deconvolution and 3D Visualization Software (Free 30-Day Demo)
Volocity: Demo 3D imaging software

Biii: Community portal to help "choose the right knife" for BioImage processing & analysis