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CrysTBox diffractGUI - spot/disk diffraction analysis


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General information

The main purpose of this tool is to automatically determine the zone axis from a diffraction pattern, assign crystallographic indices to the diffraction spots and to measure the interplanar distances. The input image can be a spot pattern (SAED), disk pattern (CBED, nanodiffraction) or HRTEM image. Except of the automatic zone axis determination, diffractGUI can be helpful for manual analyses (it measures d-spacings and interplanar angles) or during camera length calibration.
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Input image > diffractGUI > Zone axis (1 0 -1)

Input

Image

  • diffraction image (SAED, CBED, nanodiffraction) or HRTEM image
  • may depict more patterns at time (twins, multiple grains,...)
  • supported file formats: DM3 (prefered as it contains scaling information) and all common image formats (JPG, PNG, TIF,...)
Sample material
  • defined by unit cell
  • supported file formats: .CIF, .CELL
  • some materials are predefined, but user can specify arbitrary material (details...)

Examples

If you are interested how diffractGUI copes with various input images, see examples.

Window description

diffractGUI window

The application window consists of one figure and several panels. The figure allows the user to see the input image and grahical visualization of the resuts. Surrounding panels provide control of the analysis, allow settings of the most important parameters and list the results.

A detailed description of the graphical user interface follows.

Input image panel
Input image panel

This panel contains basic information about the input image such as the image name, resolution and sample material corresponding to the depicted pattern.

Resolution
The image resolution can be set manually here.
Material
Material can be chosen from this pop-up menu. You can pick one from listed materials or you can select a file describing your own material (file specification). Material does not need to be chosen prior to the analysis, it can be chaged during the procedure.
Show
Shows the input image.

Procedure panel
Procedure panel

This panel allows you to launch the analysis procedure and to control its individual steps if needed. The analysis can be launched by single click on the button Launch all or it can be performed step by step by clicking on buttons bellow corresponding to individual analysis steps. Partial results of the individual steps can be displayed using corresponding Show buttons.

Launch all
This button launches all the steps of the analysis at once. Prior to launching the analysis, some basic settings can be done using Speed and Spot size pop-up menus
Speed
This pop-up menu allows you to speed-up the beam detection and lattice fitting, which are normally the most timeconsuming steps. Fast mode, however, is recommended for the less tricky images. This settings applies on the blob detection only. It does not apply on disk detection using the Hough transform.
Spot size
Here you can give the tool a hint whether to focus on smaller spots, larger spots or disks. In case of diffraction pattern consisting of textured disks (such as CBED) value Disks (CBED) shall be set.
Detect ITEM scale
Detection of a scalebar burnt into the image by ITEM acquisition software is launched by this button. The result can be found next to the button. If the detection is successfull, bar length should be stated together with the length stated in the scalebar - for example "Label: "10 1/nm", Length: 158 px".
Detect beams
This button starts the detection of diffraction spots or disks in the image.
Method
Method used for the detection of diffraction spots or disks can be set here. The spots can be detected using blob detection methods (all entries containing "Gaussian" or "Hessian"), while the disks should be detected using Hough transform.
Detected disk sizes
Sizes of the spots to detect can be specified here for the blob detection methods.
Get N candidates
Picks N strongest detections for further processing. Number of the selected candidates can be changed using Num. of candidates.
Num. of candidates
This filed states number of the strongest detected spots/disks, which should serve for fitting a regular recirpocal lattice using RANSAC algorithm. Number of finally accepted candidates does not need to be equal to the number specified by the user. It can be lower (if there is isufficient number of detections) or higher (if there is more than one candidate with detection score equal to the score of the N-th candidate).
Analysed spot size
The algorithm can analyse only a specific subset of the detected disks (Detected disk sizes). Here you can specify sizes of the spots from which the N strongest candidates are chosen.
Ransac - fit lattice
RANSAC algorithm fits a regular reciprocal lattice to the set of strongest detected spots or disks.
Num. of iterations
Number of RANSAC iterations.
Choose vectors
Several "basic" vectors are localized in the regular lattice found by RANSAC algorithm. The details about the vectors can be seen in D-sapcing panel. If the vectors are not centered correctly on the transmitted beam, you can center them manually using menu Image / Set primary beam. If there is more than one lattice found by RANSAC, the vectors are localized in the lattice specified using Lattice pop-up menu.
Lattice
If there are multiple lattices in the image and RANSAC is set to detect them (Settings / RANSAC / RANSAC Multimodel settings), you can select the lattice to be processed.
Find zone axis
After this button is pressed, the algorithm tries to map the theoretical d-spacings and interplanar angles to the experimental ones measured in the image. If it succeeds, the results are shown in the Zone axis panel.
Max. plane index
This field sets a maximal plane index (in Miller indices) of the theoretical planes, whose d-spacings and interplanar angles are compared to the experimental values in order to identify the "basic" vectors (see Choose vectors) and determine the zone axis.

D-spacing panel
D-spacing panel Chosen 'basic' vectors

This panel shows the details about the lattice vectors measured in the image using Choose vectors button. Exact vector lengths, length ratios and d-spacings are stated. A diagram identifying the vectors in the image and showing the interplanar angles (see bottom left image) can be shown by the Show button next to the button Choose vectors.

Zone-axis panel
Zone-axis panel

The final results of the analysis are shown here. If there exist some valid assignment of the measured d-spacings to the theoretical ones, the details of such assignment are stated here. On the left hand side, there is a visualization of the assignment. The blue vertical lines on the bottom of the plot represent the theoretical d-spacings specific fo the material chosen using Material pop-up menu. The vertical blue lines on the top of the plot stand for the d-spacings measured in the experimental image and listed in the D-spacing panel. Light-blue lines between the theoretical and experimental d-spacings represent the assignment - each measured d-spacing is paired with the theoretical one. Only those assignments which fulfill certain physical and crystallographical constraints (see Lattice check and Consistency check) are taken into account. Each assignment is scored. The score is based on a comparison of the experimental and theoretical d-spacing, interplanar angles and it optionally reflects the structure factor. Only certain number of the best-scored assignments (and corresponding zone axes) is listed in the Zone ax. popup menu. There are also some quality measures reflecting how chosen assignment comply with the theory (see Total angular dist. and d-spacing STDEV).

Zone ax.
Typically, there are many possible assignments and therefore many possible zone axes, because the measured d-spacing may correspond to many crystallographically equivalent planes. Sometimes, it may also happen, that the experimental d-spacing can be paired with more than one theoretical d-spacing. Possible assignments (and corresponding zone axes) are listed in this pop-up menu. Only several best-scored zone axes are available here. Maximum number of enlisted zone axes can be set using Settings / Max. number of resulting solutions.
Cal. coef.
This value allows for an adjustment of camera calibration inaccuracies. Measured d-spacing values are multiplied by this coefficient prior to the comparison with the theoretical d-spacings.
Found planes
This table states the details of the chosen assignment - the plane indices corresponding to the experimentaly measured vectors found using Choose vectors button.
Zone axis
Chosen zone axis.
Consistency check
Checks, whether all pairs of four "basic" vectors agree on resulting zone axis. If the chosen assignment fufills this constraint, "OK" appears.
Lattice check
Checks, whether vector additions of all pairs of four "basic" vectors agree with Miller indices of corresponding spots. If the chosen assignment fufills this constraint, "OK" appears.
Total angular dist.
Sum of squares of angular distances between the four measured "basic" vectors and their theoretical counterparts. The lower number, the better. Values may differ from image to image, from material to material, however numbers higher than ten usually indicate a problem.
d-spacing STDEV
This number equals to the standard deviation of differences between the measured and theoretical d-spacing values. The lower numbers the better. Values may differ from material to material, from zone axis to zone axis, however reasonable values are thousnadths or hunderedths.

Author contact

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