Web-based Electron Microscopy Application Software: Web-EMAPS
J.M. Zuo1,3 and J. C. Mabon2,3
1 Department of Materials Science and Engineering
2 Center for Microanalysis of Materials
3 Frederick Seitz Materials Research Laboratory, University of Illinois at Urbana-Champaign, IL 61801
We have developed web-based electron microscopy application software (Web-EMAPS) that is designed for both microscopy research and teaching. The software can be accessed via a web browser from anywhere and anytime. The philosophy is to take the advantage of web accessibility and the control afforded by centralized computing to make sophisticated simulation tools available to both experienced researchers and beginners to advance quantitative electron microscopy. The site can be accessed via http://emaps.mrl.uiuc.edu/.
The program simulates realistic electron diffraction patterns and images for crystals through a web-browser user interface [fig. 1]. The simulations are powered by well-tested software developed over several years in JMZ’s research, for example, in quantitative CBED. Initial functions include: 1) crystal structure definition and rendering [fig. 2], 2) kinematic diffraction including Kikuchi and HOLZ lines [fig. 3], 3) Convergent beam electron diffraction by the Bloch wave method [fig. 4], 4) HREM image simulation by the Bloch wave method [fig. 5], 5) electron probe propagation and channeling, 6) structure factor and d-spacing calculations, and 7) Coherent electron diffraction.
The site has a database of common crystals in modern materials science. Provision is also made for users or students to define their own crystals or upload a CIF (crystallographic information file) file to define a crystal. A crystal is simply defined by the unit cell, atomic positions, and symmetry. Symmetry is defined by the space group number with the origin setting following the convention defined in the international table for crystallography. On the same menu, a crystal drawing function is provided using the open source Java applet, Jmol.
Kinematic electron diffraction pattern is simulated based on the diffraction geometry and kinematic intensities. The example shown in Fig. 3 was simulated from GaAs along  zone axis at 200 kV. Two diffraction modes are provided, one for selected area electron diffraction and the other for CBED.
Dynamic electron diffraction pattern is simulated using the Bloch wave theory . Beams included in the simulation are selected based on the criteria described in ref . The scattering factors are calculated using the Doyle and Turner atomic scattering factors for x-ray listed in the international table for crystallography. The electron adsorption effect is included by calculating adsorption potential using the Einstein model . The simulated diffraction pattern is mapped onto a square pixel area. The mapping is specified by the length of x-axis in number of pixels and the angle relative to the horizontal line. The image is viewed using the NIH ImageJ Java applet or downloaded as a 16-bit image file in TIFF format. An example of a CBED simulation for GaAs is shown in fig.4.
Functions for HREM image simulation, coherent CBED and electron probe and probe propagation are also based on the Bloch wave method. An example of HREM image simulation is given in fig. 5. The electron probe simulations will be useful in STEM analysis. The site will be continually developed to add functionality. We welcome the community’s suggestions and error reports.
This Work was supported by DOE under contracts DEFG02-01ER45923 and DEFG02-91ER45439.
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 D. Bird and Q. A. King : Acta Cryst. A46, 202 (1990)
Fig. 1 The web browser user interface of WebEMAPS
Fig. 2 Rendered 3x3 GaAs cubic cells. Crystal drawing uses the open source Java application , Jmol
Fig. 3 Simulated kinematical electron diffraction pattern for GaAs along  at 200 kV, camera length of 2000 mm
Fig. 4 Simulated GaAs  CBED pattern at 200 kV and thickness of 300 nm. The disk size is 0.45 of the x-axis, (002).
Fig. 5 Simulated tableau of HREM images of GaAs along , 200 kV, t0=50, dt =50 Å, f0=0, dt=20 nm and Cs = 1mm.