Imaris from Bitplane allows the visualization of data stacks in a real-time interactive manner. Its segmentation algorithms let you separate objects and visualize them in 3D volume rendering. It includes analysis tools for measurements and tracking of cell movements over time. Data can be further displayed as animations. Another available functionality is the calculation of colocalization coefficients.
Autoquant deconvolution program removes out-of-focus or fluorescent signal from single images and image stacks.
Adobe Creative Suite
Fiji is the latest version of ImageJ, bundling many plugins in the original version and continuously updating as well as adding new ones.
Neurolucida 3D reconstruction and analysis of tubular, strand-like structures such as blood vessels.