This paper describes a realization of Bootloader for microcontrollers AVR and investigates a design for its implementation into the Sci-Trace device. Electronics in Sci-Trace consists of control board, patch board and secondary modules. Patch board only function is to connect the control board and secondary modules. Secondary modules have several functions, such as lighting regulation, step motors control, etc. Information display is connected to control board and it is used to show the temperature inside the device, supply voltage and bus utilization. Electronical parts are located in standard rack system. Special firmware was designed for control board and secondary modules microcontrollers. Also software for simple firmware upgrade into ...