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CrysTBox - gpaGUI step by step


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gpaGUI step by step

In contrast to the other analytical tools, there is no strict workflow in gpaGUI (see GUI below). Still, some hint of how the tool can be cotrnolled, can be found below.

If you are not familiar with GPA, you might like the paper Geometric phase analysis of high resolution electron microscope images by M.J. Hÿtch. which can be found here. In this brilliant work, all the necessary equations are explained and illustrated with examples. The reference can be obtained any time in gpaGUI main menu in Help / About GPA (see aside).

1 - Open input image

In order to demonstrate how gpaGUI operates, a sample image is provided and loaded by default. Your own micrographs can be loaded using the Browse button in the Image panel or via the menu File / Open image. Either way leads to a dialog box (see aside).

(2 - Optional: Set image resolution)

If the image contains metadata with the image resolution, it is loaded and can be seen in the Image panel. Otherwise, you have to specify the resolution manually.

You can let gpaGUI to parse scalebars burnt into the image via Tools / Detect scalebar. If the scalebar is read successfully, the resolution is calculated and after you check it, it can be applied. If there is a conflict between the scalebar resolution and the value stated previously in the GUI, you will be notified and given a choice of whether to use one or another.

3 - Select sample material

The sample material can be changed at any time during the analysis. Details about material database and selection can be found here.

4 - Select diffraction spot

Only a small portion of the frequential information (FFT or artificial diffractogram in other words) is used in GPA. Typically, it is a small circular region around a diffraction reflection, which carries the information we are after. For some quantities (e.g. d-spacing map) only one diffraction spot is needed while for another (e.g. strain or misplacement) two different reflections must be selected at a time. Therefore there are two sets of similar controls in gpaGUI window - the left half of the window allows for analysis of one reflection, the right half for analysis of another.

The reflection of interest can be selected by clicking into the small FFT image in the Reflection panel (see aside). Zooming in and out using a mouse wheel may help you to improve the selection accuracy. To keep only the necessary information, the reflection is masked using a circular mask outlined with two concentric circles - inner (solid) and outer (dashed). The mask is defined using two circles because is not binary. Instead of a sharp edge, there is a gradual fade-out between the inner and outer circle. The circles' size and other parameters can be specified in Diffraction mask tab in the upper left corner of the window.

Accuracy and repeatability of GPA results depends on how precisely the reflection is localized. Therefore it might be helpful to take the full advantage of another CrysTBox tool - diffractGUI, which offers an accurate localization and identification of the depicted reflections. To perform this analysis, click the button Analyze using diffractGUI in the Input panel. Then a dialog appears telling you what happens next:

  1. A new instance of diffractGUI is opened with an appropriate input image loaded and sample material set.
  2. You go through the diffractGUI analysis procedure. The only action needed to obtain correct results on default gpaGUI image is pressing Launch all.
  3. As soon as you are happy with the results, just close diffractGUI window and the results are automatically passed back to gpaGUI.

After completing the analysis, a number of blue crosses apears in the FFT image. Each cross corresponds to an identified reflection. After clicking at one, the mask is accurately centered to the reflection position, the cross turns green and the plane indices are shown below the image (see aside).

5 - Show results

After picking one or two reflections, use the pop-up menu to select the quantity to be show in the view below (see aside). If no reflection is selected, only HRTEM is available. One reflection allows you to calculate and show quantities including Filtered HRTEM (showing only the fringes corresponding to the selected reflection) or a d-spacing map (length, X and Y component). Finally, selecting two non-colinear reflections provide further options like strain or displacement map.

For many quantities (such as d-spacing or strain maps), the analyst is often interested in a rather limited range of values. On the other hand, the difference between the lowest and highest depicted values is much higher than the range of interest (often caused by artifacts). By default, thousands of colour shades representing the data are spread covering all the displayed values all the way from the lowest to the highest. This may result in the range of interest being only covered by a few similar shades making the important information lost in useless artifacts. To deal with this problem, the user can set the range of interest manually in the Righ/Left view tab in top-right corner. An example can be seen below.

HRTEM image d-spacing map (default colour range) d-spacing map (colour range reduced to 0.255 - 0.285 nm)
6 - Inspect results

There are several features in gpaGUI, which might help the user with data analysis and interpretation. Similarly to other CrysTBox tools, gpaGUI allows for zooming in and out via the mouse wheel. Since two different quantities can be visualized simultaneously in the left and right view, it may be beneficious to synchronize the view limits so that zooming in one view is instantly relfected in another. To enable this feature, tick the Synchronize view limits checkbox in the View/Selection tab.

Cursor panels provide a quantitative insight into data visualized in two main views. After clicking into a view, the selected pixel and its neighbours together with their numeric values are shown In the Cursor panel above (see aside). For many purposes, this information can be too detailed and local. Therefore, wider regions can be inspected using a Region of Interest (ROI). To define a polygon outlining an ROI, press the button Select ROI. Then, individual vertices defining the polygon can be selected clicking into the image or map. Once the polygon is completed and confirmed by a double-click, various characteristics are listed in the Cursor panel - they include ROI area, mean value, median, standard deviation etc. (see aside).

Cursors are defined separately for each view, allowing the user to inspect one position in one view and a different position or even an ROI in another. Cursors in both views can be, however, synchronized in a way similar to the limits synchronization (described above). This synchronization can be enabled ticking the Synchronize cursor/ROI checkbox in the View/Selection tab.

7 - Export

Contents of both views can be exported in three ways (depicted below):

  1. Image only. The image size can be specified in CrysTBox Server Export settings.
  2. Image with colourbar and labeled axes. The image size, font size, colour etc. can be specified in CrysTBox Server Export settings. Unfortunately, the broad white margin is unavoidable.
  3. Data. The data is exported in TIF format supporting integers and single-precision floating point values. Therefore, even a d-spacing map depicting d-spacing estimates in nm can be exported. The image size corresponds to the size of the image being processed.

Preview not available for TIF
The file can be downloaded here.

Image only Image with colourbar Data

Author contact

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