Electron Microscope Simulator

By Natalia Penar, Diana Coroiu and Michał Sadowski


Electron microscopy (EM) is a fundamental technique which can be used to  investigate the ultrastructure of cells, microstructure of inorganic crystals, and the structures of proteins. It has become an essential investigative approach in almost all scientific disciplines, yet it is hard for the curious student to get easy access to such a facility that would complement their scientific education. In this article, this issue is addressed and a feasible solution described by bringing to life an online simulator that can be an essential tool in the students’ learning. This simulator aims to mimic a real scanning electron microscope (SEM), walking the user through a tutorial that explains every essential function of the instrument.


Electron microscopy (EM) is  an essential technique used in fields of biology, chemistry, physics etc. Both high school and university students often need to get acquainted with it and are frequently tested on their knowledge regarding EM. However, it is not until the later stages of higher education that a select group of students actually get to use an electron microscope. Hence, the aim of this project was to create an electron microscope simulator, which would be available to students at all levels of their education free of charge, to help facilitate their understanding of EM.


The simulator is a web-based application. A standard set of web technologies was used for the user interface (HTML, CSS, JS with Bootstrap and additional external libraries). On the back-end it is a Flask application served from a Linux VPS. Other technologies used in our project were Adobe Xd for creating prototypes. The images used in the simulator  were taken with the Carl Zeiss SIGMA HD VP Field Emission SEM.

Simulator description

Users have a choice of exploring the functionality of the simulator on their own or they can take advantage of a walk-through tutorial. The tutorial demonstrates how to use the application and explains how a real microscope works, while clarifying the main differences between the simulator and a real device. The step-by-step instructions are presented in the form of an interactive tutorial, even allowing some freedom in the direction and order the various settings are made, such that the user can occasionally make their own decision as to what to do next. 

The aim of the tutorial is to obtain a clear image of a pollen grain placed on the eye of a fly. Just like with an operational SEM, the first image of the slide is that of the whole fly. The image is out of focus, and not centred around the area of interest. Using the focus knob and the joystick, the user is first asked to find the part of interest and bring it into focus. Once the task is completed, the user can proceed to zoomin, and adjust the contrast and brightness to improve the quality of the image. After zooming in once again, the specimen becomes a little out of focus, so the focus has to be adjusted again. The user also gets the chance to change the scanning speed of the EM up or down, to see how the quality of the picture changes with it. Zooming in again will bring the user to a second opportunity to adjust contrast and brightness, focus, and the scanning speed. A final zoom will be required to obtain the final image.

Figures 1 and 2 depict a screenshot of a simulator and images that can be obtained from it, respectively.

Figure 1. A screenshot of the electron microscope simulator.

Figure 2. Sample screenshots of images obtained in the simulator after zooming in and adjusting the electron microscope settings. 


The SEM simulator will allow students on different levels of education to get acquainted with the technique essential in multiple areas of science.


The authors would like to give special thanks to Dr Nicola Cayzer, the Project Supervisor.

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