CrysTBox

Last updated
CrysTBox
Developer(s) Miloslav Klinger
Initial release9 December 2014;9 years ago (2014-12-09)
Written in MATLAB
Operating system Microsoft Windows
Available inEnglish
Type Scientific
License Free for non-commercial use
Website crystbox.fzu.cz

CrysTBox (Crystallographic Tool Box) is a suite of computer tools designed to accelerate material research based on transmission electron microscope images via highly accurate automated analysis and interactive visualization. Relying on artificial intelligence and computer vision, CrysTBox makes routine crystallographic analyses simpler, faster and more accurate compared to human evaluators. The high level of automation together with sub-pixel precision [1] and interactive visualization makes the quantitative crystallographic analysis accessible even for non-crystallographers allowing for an interdisciplinary research. Simultaneously, experienced material scientists can take advantage of advanced functionalities for comprehensive analyses.

Contents

CrysTBox is being developed in the Laboratory of electron microscopy at the Institute of Physics of the Czech Academy of Sciences. For academic purposes, it is available for free. As of 2022, the suite has been deployed at research and educational facilities in more than 90 countries [2] supporting research of ETH Zurich, [3] Lawrence Berkeley National Laboratory, [4] Max Planck Institutes, [5] Chinese Academy of Sciences, [6] Fraunhofer Institutes [7] or Oxford University. [8]

Suite

As a scientific tool, CrysTBox suite is freely available for academic purposes, it supports file formats widely used in the community and offers interconnection with other scientific software.

Availability

CrysTBox is freely available on demand for non-commercial use by non-commercial subjects. The only safe way to download CrysTBox installers is via a request form on the official website. [note 1] Commercial use is not allowed due to the license of MATLAB used for CrysTBox compilation. [2]

Notable research and users

Besides education, CrysTBox is mainly used in research with fields of application spanning from nuclear research [9] to archaeology and paleontology. [10] Among others, the suite was employed in development of additive manufacturing (including 3D printed biodegradable alloys, [7] metallic glass [11] or high-entropy alloys [12] ), resistant coatings, [13] laser shock peening, [14] water cleaning technologies [15] or characterization of 50 million years old flint. [10]

Institutions whose research was supported by CrysTBox include educational facilities such as ETH Zurich, [3] University of California, [16] Uppsala University, [13] Oxford University, [8] University of Waterloo, [15] Indian Institute of Technology, [17] Nanyang Technological University [12] or University of Tokyo [18] as well as research institutes like Max Planck Institutes, [12] Chinese Academy of Sciences, [6] Fraunhofer Institutes [7] or US national laboratories (NL) such as Oak Ridge NL, [9] Lawrence Berkeley NL, [4] Idaho NL [9] and Lawrence Livermoore NL. [14]

Limitations and disadvantages

CrysTBox is compiled to a stand-alone installers using MATLAB Compiler. Therefore, 1-2 GB of MATLAB libraries are installed together with the toolbox.

The diffraction simulation used in cellViewer is based on kinematic diffraction theory. This allows for a real-time response to user interaction, but it does not cover advanced diffraction features like double diffraction covered by dynamical diffraction theory, even though some phenomena caused by multiple electron-matter interactions are visualized by CrysTBox - for instance Kikuchi lines.

The analytical tools provide correction for scale calibration imperfections, but does not provide adjustment for image distortions such as elliptical distortion. If high-accuracy measurement is needed or if the distortion exceeds standard levels, appropriate tools [19] should be applied prior to the analysis.

Crystallographic visualization tools

In order to visualize functional relations and provide better understanding of experimental data, the graphical interface emphasize user interactivity and functional interconnection. There are two visualization tools in the suite: one depicting single material while another being focused on intergrowths of two different materials.

cellViewer - single crystal visualization

User interface of cellViewer. CellViewer.png
User interface of cellViewer.

CellViewer allows to visualize the sample material in four modes widely used in material research:

Graphical user interface provides user with two interactive views side by side. These views can display arbitrary combination of the four aforementioned visualization modes allowing to perceive their mutual relations. For instance, rotation of the atomic structure in direct space leads (if set so) to an instant update of the simulated diffraction pattern. If any diffraction spot is selected, corresponding crystallographic planes are shown in the unit cell etc. Such interconnections are implemented for each pair of the four available visualization modes. The electronic visualization allows to simplify understanding of widely used, yet less intuitive representations such as the inverse pole figure. For instance by drawing the coloured triangle of the inverse pole figure into the stereographic projection or to the more intuitive 3D atomic structure. [1]

ifaceViewer - intergrowth visualization

User interface of ifaceViewer. IfaceViewer.png
User interface of ifaceViewer.

The ifaceViewer allows for visualization of two misoriented materials and their interface such as crystal twins or grain boundaries. The user interface provides three views: two smaller views, each depicting one unit cell of selected material and orientation, and a larger view depicting an appropriate interface of the two structures. The interface can be visualized in four modes:

All three views in the user interface are functionally interconnected. If the content of one view is rotated by the user, the other views follow. If a crystallographic plane or direction is selected in one view, it is shown in other views and corresponding crystallographic indices are stated. The tool also allows to highlight coincident site lattice or calculate the list of planes and directions which are parallel or nearly parallel in the two misoriented materials. [1]

Automated analysis of TEM images

CrysTBox offers tools for automated processing of diffraction patterns and high-resolution transmission electron microscope images. Since the tools employ algorithms of artificial intelligence and computer vision, they are designed to require minimal operator effort providing higher accuracy compared to manual evaluation. Four analytical tools can be used to index diffraction patterns, measure lattice constants (distances and angles), sample thickness etc. Despite the high level of automation, the user is able to control the whole process and perform individual steps manually if needed.

diffractGUI - HRTEM and diffraction processing

User interface of diffractGUI. DiffractGUI.png
User interface of diffractGUI.

DiffractGUI allows for an automated analysis of diffraction patterns and high-resolution images of single crystal or limited number of crystallites. It is able to determine crystal orientation, index individual diffraction spots and measure interplanar angles and distances in picometric precision. [20] The input image may depict:

The input image is processed in the following steps:

  1. Preprocessing with accordance to the settings and image nature (resolution and noise reduction, Fourier transform for direct space images etc.).
  2. Detection of diffraction reflections at various scales [21] (difference of Gaussians typically used for spot detection, Hough transform [22] [23] for CBED disk detection [24] ).
  3. The strongest detections are selected across the scale space.
  4. A regular lattice is fit to the set of the strongest detections using RANSAC [25] algorithm.
  5. Lengths and angles of the lattice basis vectors are measured.
  6. Crystal lattice orientation is determined and diffraction reflections are identified using theoretical parameters of the sample material. [26] [27]

Compared to human evaluation, diffractGUI considers tens or even hundreds of diffraction spots at once and, therefore, can localize the pattern with sub-pixel precision. [20]

ringGUI - ring diffraction analysis

User interface of ringGUI. RingGUI.png
User interface of ringGUI.

RingGUI allows for an automated processing of ring diffraction images of polycrystalline or powder samples. It can be used to identify the diffraction rings, quantify the interplanar distances and thus characterize or identify the sample material. With known material, it can assist in microscope calibration. The input image is processed as follows:

  1. beam-stopper detection,
  2. localization of the ring center,
  3. quantification of the diffraction profile and estimation of its background intensity,
  4. identification of the rings [27] in the image (peaks in the profile).

The results can be further processed and visualized in two interactive, functionally interconnected graphical elements:

Both, the diffraction image as well as diffraction profile can be used to select diffraction rings with a mouse click. The corresponding ring is then highlighted in both graphical representations and details are listed. [1]

twoBeamGUI - sample thickness estimation

User interface of twoBeamGUI. TwoBeam.png
User interface of twoBeamGUI.

Sample thickness can be estimated using twoBeamGUI from a convergent beam electron diffraction pattern (CBED) in two beam approximation. [26] [28] The procedure is based on an automated extraction of the intensity profile across the diffracted disk in the following steps:

  1. diffraction disk radius is determined using multi-scale Hough transform, [24]
  2. the transmitted and diffracted disks are localized and the reflection is indexed, [26] [27]
  3. the disks are horizontally aligned, cropped out and profiles are measured across the disks,
  4. the profile across the diffracted disk is matched with a series of profiles automatically simulated [26] for given material, reflection and specified thickness range.

Once the procedure is completed, the measured profile and the most similar simulated profile are displayed with the diffracted disk on the background. This allows the user to verify correctness of the automated estimate and easily check the similarity of other intensity profiles within the specified thickness range. [1]

gpaGUI - geometric phase analysis

User interface of gpaGUI. GpaGUI.png
User interface of gpaGUI.

The tool called gpaGUI provides an interactive interface for geometric phase analysis. It allows to generate 2D maps of various crystallographic quantities using high-resolution images. [29] [30]

Since the geometric phase analysis is performed in frequency domain, the high-resolution image needs to be transformed into frequential representation using Fourier transform. Mathematically, the frequential image is a complex matrix with the size equal to the original image. Crystallographically, it can be seen as an artificial diffraction pattern of the original image depicting intensity peaks corresponding to the crystallographic planes present in the original image. After performing desired calculations, the frequential representation can be transformed back to the original spatial domain using inverse Fourier transform.

Various crystallographic analyses can be performed using the frequential image. If it is filtered so that only the information from a region close to a particular diffraction spot is used (the rest is set to zero), a filtered direct image obtained by inverse Fourier transform then depicts only the planes corresponding to the selected diffraction spot. Moreover, due to its complex nature, the frequential image can be used to calculate amplitude and phase. Together with a vector of one crystallographic plane depicted in the image, they can be used to generate a 2D map interplanar distance of given plane. [29] If two vectors of non-parallel planes are known, the method can be used to generate maps of strain and displacement. [30]

Graphical user interface of gpaGUI is vertically divided into two halves, each of which contains:

Since each half of the interface allows to specify one crystallographic plane, gpaGUI allows to calculate all the aforementioned crystallographic quantities including those which require two vectors. Precision and repeatability of the whole analysis relies on accuracy of the diffraction peak localization. To overcome inaccuracy of manual peak localization (with a mouse click), gpaGUI provides a possibility to process the input image with diffractGUI in order to accurately localize and index the peaks. [1]

See also

Notes

  1. ↑ CrysTBox is not distributed by any website aggregating various software installers or uninstallers. Installers downloaded from these sources can contain malware. Similarly, no additional software is required to uninstall CrysTBox. Any software pretending to do so has no connection to CrysTBox developer.

Related Research Articles

<span class="mw-page-title-main">Crystallography</span> Scientific study of crystal structures

Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics. The word crystallography is derived from the Ancient Greek word κρύσταλλος, with its meaning extending to all solids with some degree of transparency, and γράφειν. In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography.

<span class="mw-page-title-main">X-ray crystallography</span> Technique used for determining crystal structures and identifying mineral compounds

X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the positions of the atoms in the crystal can be determined, as well as their chemical bonds, crystallographic disorder, and various other information.

Solid-state chemistry, also sometimes referred as materials chemistry, is the study of the synthesis, structure, and properties of solid phase materials. It therefore has a strong overlap with solid-state physics, mineralogy, crystallography, ceramics, metallurgy, thermodynamics, materials science and electronics with a focus on the synthesis of novel materials and their characterization. A diverse range of synthetic techniques, such as the ceramic method and chemical vapour depostion, make solid-state materials. Solids can be classified as crystalline or amorphous on basis of the nature of order present in the arrangement of their constituent particles. Their elemental compositions, microstructures, and physical properties can be characterized through a variety of analytical methods.

<span class="mw-page-title-main">Transmission electron microscopy</span> Imaging and diffraction using electrons that pass through samples

Transmission electron microscopy (TEM) is a microscopy technique in which a beam of electrons is transmitted through a specimen to form an image. The specimen is most often an ultrathin section less than 100 nm thick or a suspension on a grid. An image is formed from the interaction of the electrons with the sample as the beam is transmitted through the specimen. The image is then magnified and focused onto an imaging device, such as a fluorescent screen, a layer of photographic film, or a detector such as a scintillator attached to a charge-coupled device or a direct electron detector.

<span class="mw-page-title-main">Electron diffraction</span> Bending of electron beams due to electrostatic interactions with matter

Electron diffraction is a generic term for phenomena associated with changes in the direction of electron beams due to elastic interactions with atoms. It occurs due to elastic scattering, when there is no change in the energy of the electrons. The negatively charged electrons are scattered due to Coulomb forces when they interact with both the positively charged atomic core and the negatively charged electrons around the atoms. The resulting map of the directions of the electrons far from the sample is called a diffraction pattern, see for instance Figure 1. Beyond patterns showing the directions of electrons, electron diffraction also plays a major role in the contrast of images in electron microscopes.

<span class="mw-page-title-main">Synchrotron light source</span> Particle accelerator designed to produce intense x-ray beams

A synchrotron light source is a source of electromagnetic radiation (EM) usually produced by a storage ring, for scientific and technical purposes. First observed in synchrotrons, synchrotron light is now produced by storage rings and other specialized particle accelerators, typically accelerating electrons. Once the high-energy electron beam has been generated, it is directed into auxiliary components such as bending magnets and insertion devices in storage rings and free electron lasers. These supply the strong magnetic fields perpendicular to the beam that are needed to stimulate the high energy electrons to emit photons.

Reflection high-energy electron diffraction (RHEED) is a technique used to characterize the surface of crystalline materials. RHEED systems gather information only from the surface layer of the sample, which distinguishes RHEED from other materials characterization methods that also rely on diffraction of high-energy electrons. Transmission electron microscopy, another common electron diffraction method samples mainly the bulk of the sample due to the geometry of the system, although in special cases it can provide surface information. Low-energy electron diffraction (LEED) is also surface sensitive, but LEED achieves surface sensitivity through the use of low energy electrons.

<span class="mw-page-title-main">Electron backscatter diffraction</span> Scanning electron microscopy technique

Electron backscatter diffraction (EBSD) is a scanning electron microscopy (SEM) technique used to study the crystallographic structure of materials. EBSD is carried out in a scanning electron microscope equipped with an EBSD detector comprising at least a phosphorescent screen, a compact lens and a low-light camera. In the microscope an incident beam of electrons hits a tilted sample. As backscattered electrons leave the sample, they interact with the atoms and are both elastically diffracted and lose energy, leaving the sample at various scattering angles before reaching the phosphor screen forming Kikuchi patterns (EBSPs). The EBSD spatial resolution depends on many factors, including the nature of the material under study and the sample preparation. They can be indexed to provide information about the material's grain structure, grain orientation, and phase at the micro-scale. EBSD is used for impurities and defect studies, plastic deformation, and statistical analysis for average misorientation, grain size, and crystallographic texture. EBSD can also be combined with energy-dispersive X-ray spectroscopy (EDS), cathodoluminescence (CL), and wavelength-dispersive X-ray spectroscopy (WDS) for advanced phase identification and materials discovery.

Electron crystallography is a method to determine the arrangement of atoms in solids using a transmission electron microscope (TEM). It can involve the use of high-resolution transmission electron microscopy images, electron diffraction patterns including convergent-beam electron diffraction or combinations of these. It has been successful in determining some bulk structures, and also surface structures. Two related methods are low-energy electron diffraction which has solved the structure of many surfaces, and reflection high-energy electron diffraction which is used to monitor surfaces often during growth.

<span class="mw-page-title-main">Scanning transmission electron microscopy</span> Scanning microscopy using thin samples and transmitted electrons

A scanning transmission electron microscope (STEM) is a type of transmission electron microscope (TEM). Pronunciation is [stɛm] or [ɛsti:i:ɛm]. As with a conventional transmission electron microscope (CTEM), images are formed by electrons passing through a sufficiently thin specimen. However, unlike CTEM, in STEM the electron beam is focused to a fine spot which is then scanned over the sample in a raster illumination system constructed so that the sample is illuminated at each point with the beam parallel to the optical axis. The rastering of the beam across the sample makes STEM suitable for analytical techniques such as Z-contrast annular dark-field imaging, and spectroscopic mapping by energy dispersive X-ray (EDX) spectroscopy, or electron energy loss spectroscopy (EELS). These signals can be obtained simultaneously, allowing direct correlation of images and spectroscopic data.

<span class="mw-page-title-main">Selected area diffraction</span>

Selected area (electron) diffraction is a crystallographic experimental technique typically performed using a transmission electron microscope (TEM). It is a specific case of electron diffraction used primarily in material science and solid state physics as one of the most common experimental techniques. Especially with appropriate analytical software, SAD patterns (SADP) can be used to determine crystal orientation, measure lattice constants or examine its defects.

Diffraction topography is a imaging technique based on Bragg diffraction. Diffraction topographic images ("topographies") record the intensity profile of a beam of X-rays diffracted by a crystal. A topography thus represents a two-dimensional spatial intensity mapping of reflected X-rays, i.e. the spatial fine structure of a Laue reflection. This intensity mapping reflects the distribution of scattering power inside the crystal; topographs therefore reveal the irregularities in a non-ideal crystal lattice. X-ray diffraction topography is one variant of X-ray imaging, making use of diffraction contrast rather than absorption contrast which is usually used in radiography and computed tomography (CT). Topography is exploited to a lesser extends with neutrons, and has similarities to dark field imaging in the electron microscope community.

<span class="mw-page-title-main">Low-energy electron microscopy</span>

Low-energy electron microscopy, or LEEM, is an analytical surface science technique used to image atomically clean surfaces, atom-surface interactions, and thin (crystalline) films. In LEEM, high-energy electrons are emitted from an electron gun, focused using a set of condenser optics, and sent through a magnetic beam deflector. The “fast” electrons travel through an objective lens and begin decelerating to low energies near the sample surface because the sample is held at a potential near that of the gun. The low-energy electrons are now termed “surface-sensitive” and the near-surface sampling depth can be varied by tuning the energy of the incident electrons. The low-energy elastically backscattered electrons travel back through the objective lens, reaccelerate to the gun voltage, and pass through the beam separator again. However, now the electrons travel away from the condenser optics and into the projector lenses. Imaging of the back focal plane of the objective lens into the object plane of the projector lens produces a diffraction pattern at the imaging plane and recorded in a number of different ways. The intensity distribution of the diffraction pattern will depend on the periodicity at the sample surface and is a direct result of the wave nature of the electrons. One can produce individual images of the diffraction pattern spot intensities by turning off the intermediate lens and inserting a contrast aperture in the back focal plane of the objective lens, thus allowing for real-time observations of dynamic processes at surfaces. Such phenomena include : tomography, phase transitions, adsorption, reaction, segregation, thin film growth, etching, strain relief, sublimation, and magnetic microstructure. These investigations are only possible because of the accessibility of the sample; allowing for a wide variety of in situ studies over a wide temperature range. LEEM was invented by Ernst Bauer in 1962; however, not fully developed until 1985.

A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal.

Lattice light-sheet microscopy is a modified version of light sheet fluorescence microscopy that increases image acquisition speed while decreasing damage to cells caused by phototoxicity. This is achieved by using a structured light sheet to excite fluorescence in successive planes of a specimen, generating a time series of 3D images which can provide information about dynamic biological processes.

<span class="mw-page-title-main">Geometric phase analysis</span> Method of digital signal processing

Geometric phase analysis is a method of digital signal processing used to determine crystallographic quantities such as d-spacing or strain from high-resolution transmission electron microscope images. The analysis needs to be performed using specialized computer program.

<span class="mw-page-title-main">Convergent beam electron diffraction</span> Convergent beam electron diffraction technique

Convergent beam electron diffraction (CBED) is an electron diffraction technique where a convergent or divergent beam of electrons is used to study materials.

4D scanning transmission electron microscopy is a subset of scanning transmission electron microscopy (STEM) which utilizes a pixelated electron detector to capture a convergent beam electron diffraction (CBED) pattern at each scan location. This technique captures a 2 dimensional reciprocal space image associated with each scan point as the beam rasters across a 2 dimensional region in real space, hence the name 4D STEM. Its development was enabled by evolution in STEM detectors and improvements computational power. The technique has applications in visual diffraction imaging, phase orientation and strain mapping, phase contrast analysis, among others.

Transmission Kikuchi Diffraction (TKD), also sometimes called transmission-electron backscatter diffraction (t-EBSD), is a method for orientation mapping at the nanoscale. It’s used for analysing the microstructures of thin transmission electron microscopy (TEM) specimens in the scanning electron microscope (SEM). This technique has been widely utilised in the characterization of nano-crystalline materials, including oxides, superconductors, and metallic alloys.

Dark-field X-ray microscopy is an imaging technique used for multiscale structural characterisation. It is capable of mapping deeply embedded structural elements with nm-resolution using synchrotron X-ray diffraction-based imaging. The technique works by using scattered X-rays to create a high degree of contrast, and by measuring the intensity and spatial distribution of the diffracted beams, it is possible to obtain a three-dimensional map of the sample's structure, orientation, and local strain.

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