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CrysTBox - Crystallographic Toolbox

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What is CrysTBox

CrysTBox (Crystallographic Toolbox) is a free set of automated tools intended to help crystallographers and electron microscopists with their everydays work. Six tools are available - three instruments for an automated analysis of electron diffraction patterns and micrographs (diffractGUI, ringGUI and twoBeamGUI), two visualization tools (cellViewer and ifaceViewer) and one GPA implementation (gpaGUI). Plugin for Gatan DigitalMicrograph included. Here you can learn how to get the installers.

News

2018-06-22 CrysTBox has spread to 70 countries
2017-10-09 Workshop: Three-day workshop on how to squeeze maximum out of CrysTBox, The University of Johannesburg, Johannesburg, South Africa.
2017-07-07 New version - CrysTBox Server 1.10 (build 0064)
  • new tool ifaceViewer: interface visualization tool
  • new tool twoBeamGUI: tool for estimation of TEM sample thickness
  • new tool gpaGUI: implementation of Geometric Phase Analysis
  • several features added
The full information >>
2017-07-07 New paper - M. Klinger. More features, more tools, more CrysTBox. Journal of Applied Crystallography, 50(4), 2017. doi:10.1107/S1600576717006793.
The full text >>
More ...

CrysTBox Tools

A brief description of the individual tools and their functionalities can be found below. Generally, the supported image formats are .DM3, .DM4, .TIFF, .JPG, .PNG etc. while the sample material can be specified using .CIF and .CELL files. The use of CIF/CELL files is very simple and flexible in the lates release.

cellViewer - visualization tool

  • two interactive views can show:
    • direct space (e.g. unit cell)
    • reciprocal space (spot diffraction)
    • stereographic projection
    • inverse pole figure (IPF)
  • can be used for visualization of diffractGUI results
  • can calculate TEM holder tilts needed to achieve desired zone axis
  • offers crystallographic calculator

Details >>
Short video >>

diffractGUI - spot/disk diffraction analysis

  • can process SAED, CBED, nanodiffraction, HRTEM
  • automatically determines sample orientation (zone axis)
  • identifies individual diffraction spots
  • interplanar angles and distances measured with precision of up to a few picometers (details in [2] and [3])
  • results can be visualized by cellViwer
  • fast, precise and effortless

Details >>
Examples >>
Short video >>
Step-by-step guide >>

ringGUI - ring diffraction analysis

  • automatically identifies depicted rings using Miller indices
  • determines sample material from list of candidate materials given by user
  • image enhancement for more representative and readable results
  • fast, precise and effortless
  • helpful in camera calibration

Details >>
Examples >>
Short video >>
Step-by-step guide >>

ifaceViewer - interface visualization (NEW)

  • visualization of two misoriented phases and their interface
  • misorientation can be given by angle & axis, Euler angles, CSL, rotation matrix etc.
  • coincident-site lattice is highlighted
  • values of sigma can be calculated
  • visualization and conversion of crystallographic planes and directions between two phases

Short video >>
Step-by-step guide >>

gpaGUI - implementation of GPA (NEW)

  • implementation of Geometric Phase Analysis
  • can be used for mapping dislocations, strain, displacement etc. in the image
  • offers user friendly inspection of the results
  • diffraction reflections in FFT can be accurately localized by diffractGUI
  • resulting data and images can be exported

Short video >>
Step-by-step guide >>

twoBeamGUI - TEM sample thickness estimation (NEW)

  • sample thicnkess estimation based on CBED in two-beam approximation
  • fast, precise and effortless (details in [1])
  • allows for visual inspection of measured and theoretical intensity profile of diffracted disc

Short video >>
Step-by-step guide >>

Video Tutorials

Video tutorials showing how to work with the toolbox are available here. You can see one-minute illustrative videos as well as an 18-minute tutorial covering basic controls and abilities of diffractGUI, ringGUI and cellViewer.

Quick-start videos >>
Tutorial >>

How to get CrysTBox

If you are new to CrysTBox, please fill in the application form.
If you have an old CrysTBox version you would like to update, please fill in your e-mail in the update form.
CrysTBox is implemented in MATLAB and is freely available for non-commercial purposes in form of a standalone application installer. Since our institute has educational license for MATLAB, the toolbox can not be used for commercial purposes. Complete license statement can be found here.

System Requirements

The installers are normally built for Windows platform in 32-bit and 64-bit version. As the software relies on MATLAB Compiler Runtime, the hardware requirements are generally expected to match the requirements of MATALB R2014b: 1GB RAM, 2GB of a disk space, no specific requirements on graphic card. A GPU with 1GB memory supporting OpenGL 3.3 is recommended, however CrysTBox can use a software emulation.

Installation and troubleshooting

The installation procedure should be quite simple and intuitive. Still, If you happened to face any troubles during the installation or afterwards, you may find some useful tips here.
CrysTBox Installation >>
Installation of DM plug-in >>
Troubleshooting >>

Publications

Here you can find some publications about CrysTBox. References and BiBTex entries can be generated in the application main menu (Help / Citations). If you find the software useful for your research, please cite it.
Thank you.


  • M. Klinger. More features, more tools, more CrysTBox. Journal of Applied Crystallography, 50(4), 2017. doi:10.1107/S1600576717006793.
    The full text >>
  • M. Klinger, L. Polívka, A. Jager and M. Tyunina. Quantitative analysis of structural inhomogeneity in nanomaterials using transmission electron microscopy. Journal of Applied Crystallography, 49(3), 2016. doi:10.1107/S1600576716003800.
  • M. Klinger and A. Jäger. Crystallographic Tool Box (CrysTBox): automated tools for transmission electron microscopists and crystallographers. Journal of Applied Crystallography, 48(6), 2015. doi:10.1107/S1600576715017252.
  • M. Klinger. CrysTBox - Crystallographic Toolbox. Institute of Physics of the Czech Academy of Sciences, 2015. URL: http://www.fzu.cz/~klinger/crystbox.pdf. (ISBN 978-80-905962-3-8)
  • M. Klinger, M. Němec, L. Polívka, V. Gärtnerová and A. Jäger. Automated CBED processing: Sample thickness estimation based on analysis of zone-axis CBED pattern. Ultramicroscopy, 150(0):88-95, 2015. doi:10.1016/j.ultramic.2014.12.006.

Acknowledgements

Development of this software would not have been possible without many people providing feedback, funding, support and fruitful discussion. I would like to thank to Aleš Jäger, Alexandr Dejneka, Bernhard Schaffer, Christian Gspan, Eric Leroy, Hongwei Liu, Jan Duchoň, Jun Wu, Konstantinos Goulas, Lukáš Palatinus, Maciej Zubko, Marina Tyunina, Martin Němec, Pavel Lejček, Robin Schäublin, Viera Gärtnerová, Walter Guy.

Author contact

If you have any questions, offers or comments, please feel free to contact me:
Miloslav Klinger
e-mail: klingeratpost [dot] cz