ImageJ is my favorite software tool for image processing and image analysis. ImageJ is written in Java and should run instantely on Windows, Linux and Mac OS X.

The most important application in our department is the evaluation of microcomputed tomography images. The images are rather large (1 - 2 GB). To avoid memory conflicts the complex evaluations are performed on Ubuntu 64-bit machines with plenty of RAM (up to 12 GB). The preprocessing, however, can be done with an average notebook.

Other programs which we use:

• MeshLab (conversion of 3D data formats)
• Paraview (visualization)
• ITK/VTK (for custom made evaluation programs)