ImageJ Software (Open Source)

Reference:

1. Image processing with ImageJ by Dr. Michael D. Abramoff.

Web Resources:

1. ImageJ Home - ImageJ and most of its plug-ins and macros are available for download. 
2. ImageJ manual by Tony Collins
3. Biomedical Imaging plug-ins (VolumeJ)
4. The Medientechnik und design group tutorial on writing plug-ins.
5. NeuronJ