This document is the operation manual for JEOL 2500SE (S)TEM, which includes the description of various parts of the microscope, overall schematic, side entry specimen holder, control panels, and graphic user interface. It also provides procedures for sample loading, column alignment, condenser alignment, eucentric height adjustment, stigmation adjustment, tilt balance, axis align, image focus, finding the zone axis, objective astigmatism correction, image capture, camera setup, image search and capture, HRTEM image capture, STEM mode, EELS, and sample unloading.