Image analysis and simulation software in transmission electron microscopy

It is surprising that manufacturers of TEM and STEM microscopes do not provide suitable user-friendly software packages for the analysis and simulation of diffraction patterns, two-and many-beams conventional TEM images, high resolution micrographs, etc. Nothing close to the software tools available for example in X-Ray crystallography has yet been developed. This presentation describes my personal attempt to setup such a general software package for TEM/STEM use. The present development has been started in 1999 using java as the unique programming language. Java is an object oriented language that has been long considered as a low performing computer language not adapted to scientific calculations. This is no more the case as the execution speed of well written Java code is comparable to that of “C”. At present major scientific software, for example Mathematica, are either written in Java language or offer a link to Java written code. The software system here described is a complete rewrite of EMS developed during the period 1980-1987 and organized in separated executables that in general did not provide a graphical user interface (GUI). As a benefit of this approach, batch execution was possible as well as scripting. On the contrary, jems is fully object based and makes use of the numerous Java swing widgets to build its GUI. This radically different approach is very efficient to develop modular code for image analysis and simulation in transmission electron microscopy. The primary jems window is shown in figure 1. A list of the atoms of the structure being used for image analysis or simulation and a projection of the structure is displayed. There is no limit on the number of atoms except that sets by the available RAM (here (Cd, Zn) Se particle with 256 atoms). The