This user manual focuses on Fiji (Fiji Is Just ImageJ), a processing tool based on the ImageJ program but largest and with best-known distribution than ImageJ. Its main purpose is the dissemination of an ImageJ with Java, Java 3D, more plugins integrated and organized in a menu with a consistent structure to facilitate image processing in the scientific community, scripting languages and extensive tutorials and documentation. It is easier to install than ImageJ, because it organizes all required components into a self-contained package that will run on any computer platform and contains an automatic update function. In addition, it also allows the programming of macros.