About elmiX

One major drawback in teaching processing and analysis of electron microscopy (EM) data is the limited accessibility to EM software for students and lecturers outside an electron microscopy laboratory. Commonly used EM software is usually commercial and the available demo versions of these programs often lack important program features. Another disadvantage is the limitation that prominent EM software packages are usually bound to a certain operating system. In order to bridge this gap we have compiled the GNU/Linux live system elmiX which is based on the Debian GNU/Linux distribution [1, 2, 3] and runs on PCs with Intel compatible CPUs (Pentium II and later) equipped with at least 256 MB RAM. All programs are available for immediate use with manuals and internet links to the web pages of the respective authors after boot from the live system.

The current version of elmiX contains the following electron microscopy software:

• CASINO (by D. Drouin) [4]
  monte CArlo SImulation of electroN trajectory in sOlids
• CM Alignment Help (by M. T. Otten) [5]
  program for step-by-step alignment of Philips CM microscopes (good help function with basics on electron optics)
• Crystal (by M. T. Otten) [5]
  program for performing simple crystallographic calculations
• CTF Explorer (by M.V. Sidorov) [6]
  allows to calculate the Phase Contrast Transfer Function of a TEM
• Digital Micrograph (by Gatan) [7]
  advanced program for image and EELS analysis
• EELS Model (by J. Verbeeck) [8]
  software to quantify EEL spectra by using model fitting
• Electron Direct Methods (by L. Marks & R. Kilaas) [9]
  set of programs to combine various aspects of image processing and manipulation of HRTEM images and diffraction patterns as well as direct methods
• GRIP (Groningen image processing) (by W. Keegstra) [20]
  2D image analysis of 2D protein crystals and single particle analysis
• CRYSCON (by Shape Software) [21]
  general crystallographic conversion utility
• ImageJ (by W. Rasband) [10]
  open source image processing and analysis
• Java Electron Crystallography Package (by X.Z. Li) [11]
  stereographic projection, simulation and analysis of electron diffraction patterns
• JEMS Student Edition (by P. Stadelmann) [12]
  the swiss army knife for simulation of HRTEM images and diffraction patterns
• Monte Carlo Simulations of electron-solid interactions (by D. Joy) [13]
  introduction to Monte Carlo simulation of electron transport in solids
• NCEMSS (by R. Kilaas) [9]
  HRTEM image and diffraction pattern simulation on the basis of the multi-slice algorithm
• Off-line CBED Thickness (by M. T. Otten) [5]
  program for calculating specimen thickness from convergent beam electron diffraction patterns
• Powder Cell (by W. Kraus, G. Nolze) [14]
  displays crystal structures and calculates (xray) powder diagrams and d-spacings
• Process Diffraction (by J. Labar) [15]
  allows to obtain quantitative structural information from selected area electron diffraction patterns
• Space Group Explorer (by Calidris) [16]
  gives equivalent positions in real and reciprocal space, the symmetry of the diffraction pattern, and information about systematic absences and enhancements. It also gives phase relationships of the Fourier terms, and seminvariant vectors
• VESTA (by K. Momma, F. Izumi) [17]
  program for displaying crystal structures with co-ordination polyhedra etc. (excellent graphics!)
• XVis (by O. Yefanov) [18]
  an educational open-source program for demonstration of reciprocal-space construction and diffraction principles

For use in teaching and for home exercises the elmiX software collection comes with a number of office (including PDF writing capability and printer support) and scientific plotting programs, utilities, a browser to access the various given web resources, a free and open source multimedia and flash player and the unit converter tool NumericalChameleon [19].

These programs are complemented with (still only a few) tutorials, lectures, scientific papers and sample files that were provided by members of the elmiX and EM community.

The always latest version of the elmiX live system can be obtained as ISO image from here.

References

1. R. Stallman and GNU team (1984). GNU project, http://www.gnu.org
2. L. Torvalds and Kernel team (1991). http://www.kernel.org
3. I. Murdock and Debian team (1993). http://www.debian.org
4. http://www.gel.usherbrooke.ca/casino/index.html
5. M. T. Otten, private communication
6. http://clik.to/ctfexplorer
7. http://www.gatan.com/
8. http://webh01.ua.ac.be/eelsmod/eelsmodel.htm
9. http://www.numis.northwestern.edu/edm/
10. http://rsb.info.nih.gov/ij/
11. http://www.unl.edu/CMRAcfem/XZLI/programs.htm
12. http://cimewww.epfl.ch/people/stadelmann/jemsSE/jemsSEv3_2710u2008.htm
13. http://web.utk.edu/~srcutk/htm/simulati.htm
14. http://www.bam.de/de/service/publikationen/powder_cell_a.htm
15. http://www.mfa.kfki.hu/~labar/ProcDif.htm
16. http://www.calidris-em.com/archive.html
17. http://www.geocities.jp/kmo_mma/crystal/en/vesta.html
18. http://x-ray.net.ua/xvis.html
19. http://www.jonelo.de/java/nc/
20. http://www.rug.nl/gbb/research/researchgroups/electronmicroscopy/projects/image
21. http://www.shapesoftware.com/

Acknowledgements

We thank all authors and contributors for the kind permission to include their programs. Special thanks to Achim Herwartz for the photographic artwork, to Jakob and Samuel Weirich for providing the LEGO microscope, and to Alexander Schwedt for the EBSD pattern of ferrite that is shipped as default background since elmiX 2010.0.

The current elmiX version was mastered with the help of the Debian Live build scripts available at http://packages.debian.org.