Nov 27, 2017 - section. Figure 1 shows the main interface of QSAED3. It includes (i) a frame with a drop-down/graphical menu and a panel; (ii) the processing ...
Quantification and Processing of SAED Pattern
(QSAED3d)
User’s manual
X.Z. LI, Ph. D
(November 27, 2017)
Copyright 2011-2017 LANDYNE © All Right Reserved
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Contents 1. Introduction................................................................................................................................. 3 1.1 Version history .......................................................................................................................... 3 1.2 Design features ......................................................................................................................... 3 1.3 Purposes .................................................................................................................................... 3 2. Image processing of SAED pattern ............................................................................................. 4 2.1 Digital viewer............................................................................................................................ 4 2.2 Resize/Rotation/Center/Invert/Square ...................................................................................... 4 2.3 Preparation of SAED patterns for publication ......................................................................... 4 3. Analysis and quantification of SAED pattern ............................................................................. 5 3.1 Calibration using scaling bar ................................................................................................... 5 3.2 1D line profile ........................................................................................................................... 5 3.3 Measurement of basic vectors ................................................................................................... 5 3.4 Intensity retrieve in 2D pattern ................................................................................................ 5 3.5 Preparation of (hkl) intensity list .............................................................................................. 5 3.6 Improvement in the SAED pattern ........................................................................................... 5 4. Usage of QSAED3....................................................................................................................... 6 4.1 Step by step ............................................................................................................................... 6 4.2 Save the data of the retrieved intensities .................................................................................. 9 4.3 Save the SAED pattern with the retrieved intensities ............................................................... 9 5. Installation of QSAED3 ............................................................................................................ 14 5.1 JRE and JAI ............................................................................................................................ 14 5.2 Installation .............................................................................................................................. 14 5.3 Run QSAED3 as stand-alone software ................................................................................... 14 5.4 Run QSAED3 in the Landyne suite ......................................................................................... 14 5.5 Get the license ......................................................................................................................... 14 6. References ................................................................................................................................. 14
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1. Introduction Selected area electron diffraction analysis has been extensively used in materials science for phase identification, interpretation of twins and coexisted multiple phases and so forth. Electron diffraction patterns from a single crystal grain and from a polycrystalline sample are common in essence but different in many aspects, so we treat the two cases separately for quantification and processing of electron diffraction patterns. ProJECT/QPCED has been developed for selected-area electron diffraction patterns of polycrystalline samples [1,2]. ProJECT/QSAED has been developed for selected-area electron diffraction patterns of single crystal samples [3,4]. 1.1 Version history The first version of QSAED was developed during 2003~2006, which was included in the JECP package [3]. Improvements were made in the second version during 2014~2015, which was published in Microscopy & Microanalysis meeting in Hartford, CT (August 3-7, 2014) [4]. Current version is QSAED3d, in which many new functions were added for practical usage and a new window style has been used in design. 1.2 Design features QSAED3 has been written in Java SE8. Further code optimization (including obfuscation) is carried out for the compiled class files. Java Runtime Environment (JRE) and Java Advanced Imaging (JAI) are required to run QSAED3. The installation of JRE and JAI is given in the latter section. Figure 1 shows the main interface of QSAED3. It includes (i) a frame with a drop-down/graphical menu and a panel; (ii) the processing operation and parameters input are carried out in corresponding dialog windows; (iii) an input SAED pattern can be easily loaded using the dragdrop-box or the normal window file system; (iv) Both of the processed data and images can be saved to files. 1.3 Purposes An experimental SAED pattern is usually needed to go through resize/rotate/invert/square processing before it is used in the manuscript for publication. QSAED3 simplifies the process to get the images of the SAED pattern you need. The basic reciprocal lattice spacing can be precisely measured in QSAED3. The spacing is measured in pixel and can be converted to nm after the scaling bar is measured. The accurate is better than 1 pixel. The SAED pattern can be analyzed as 1D intensity profile along a line defined by user. The SAED pattern can be quantified and processed as 2D intensity distribution. The background intensity distribution is searched first and then the intensities of all diffraction spots are retrieved. The intensities of (h,k,l) and (-h,-k,-l) reflections can be averaged according to the assigned symmetry or replaced by the maximum one. The measured intensities can be displayed on the SAED pattern as circles with different radiuses. The measured intensities can be used in structurerelated analysis, especially in electron crystallography. 3
Figure 1. Main GUI of QSAED3.
2. Image processing of SAED pattern 1.1 Digital viewer The Digital Viewer can be used to view the digital data in a popup window when a mouse pointer is moving in the loaded SAED image. It is a useful tool, e.g., to check if a peak is saturated in the center part; to select the location of a diffraction spot. 2.2 Resize/Rotation/Center/Invert/Square The loaded image of SAED pattern will appear in square shape even the original image is in rectangular shape. The pattern can be adjusted by resize/rotation/center/invert (gray contrast) operation. The guide lines and circles can be displayed for rotation and alignment. 2.3 Preparation of SAED patterns for publication The region of interest (roi) size and pixel per inch (ppi) of the output image can be customized. The image, the retrieved intensity, or the combination of them can be saved in the output file.
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Figure 2. Digital viewer. 3. Analysis and quantification of SAED pattern 3.1 Calibration using scaling bar The scaling bar on the SAED pattern can be measured and saved for the later use, e.g., the basic reciprocal vectors are measure in pixel and then changed to in 1/nm. 3.2 1D line profile The line profile tool provides a quick and rough way to estimate the diffraction intensity profile by drawing the line on the SAED pattern. This is especially useful for SAED patterns from aperiodic structure or from the second phase. 3.3 Measurement of basic vectors After the refinement of the basic vectors against the large amounts of selected diffraction spots, the lengths of the basic vectors and the angle between them can be precisely measured down to 0.1 pixel. With the data of the scaling bar measured before, the basic vectors can be accurately determined. 3.4 Intensity retrieve in 2D pattern The intensities of the background intensity can be determined and checked as a profile of intensity vs. the radius. After removing the background intensity for each pixel, the intensity of the diffraction spot can be measured by using direct integration/sum or by using the Gaussian bell function. The second method is useful for the diffraction spot with saturated pixels. 3.5 Improvement in the SAED pattern QSAED3 provides two methods to improve the SAED pattern. In case that there is a beam stopper in an SAED pattern, the diffraction spot (h,k,l) under the shadow of the beam stopper can be replaced by the opposite spot (-h,-k,-l), so a complete pattern can be displayed.
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In case the SAED pattern was taken in a slight away the true zone axis, the averaged intensities of can be used according to symmetry, so an SAED pattern similar to the true zone axis can be restored. 3.6 Preparation of (hkl) intensity list The SAED pattern was firstly analyzed by using two basic vectors, which is assigned as (1,0) and (0,1). When the zone axis of the SAED pattern under study is known, the two basic vectors can be labelled as the Bravais indices, thus the transformation from (H,K) to (h,k,l) can be done. 4. Usage of QSAED3 4.1 Step by step The usage of QSAED3 is easy and straightforward. A step by step guide is presented here. Without a valid license, QSAED3 runs in demo mode and only the demo_qsaed.tif is allowed to be loaded.
Figure 3. Image of the demo_qsaed.tif. 1. Experimental SAED pattern in .tif or .jpg format can be loaded in two methods. Drag-anddrop method: mouse point on the SAED pattern, hold left mouse button and drag the image to the drag-drop box on the graphic menu bar and release the mouse button. Window file system: click the drag-drop box, find the SAED pattern file and the load the SAED pattern. 2. Turn on the digital viewer. 3. Work on the SAED pattern using the operations in the Process drop-down menu.
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Figure 4. Resize, rotate, center, invert operations on the SAED pattern
Figure 5. Edge grayscale dialog, resize and rotate dialog and shift and center dialog. 7
Figure 6. SAED pattern is prepared for publication. 4. Calibrate the scaling bar: turn on the shift¢er, hold mouse left button to drag the image and release. Measure the scaling bar and click Done button. 5. Define the size and resolution of the image, which define the view image and the output image.
Figure 7. Scaling factor 6. Quantification of 2D pattern: it is suggested to use the original image in .tif format for quantification. If necessary define the beam blocker area. Click three spots on the SAED pattern to define the basic vectors. With the help of the digital viewer, the positions can be roughly located. Refine a few times until the basic vectors are acceptable. Define the 8
resolution range and then prepare/check the background, change the loop and step if needed. Select the intensity extracting option and get the intensities. If the index (h,k,l) to (H,K) is defined, make the transformation for all diffraction spots. 7.
Figure 8. Measure the scale bar 8. After step 6, click Basic vectors in drop-down menu to get the info of basic vectors. 9. Analysis of 1D profile: draw a line by defining the beginning point and the end point. Select the gridlines step. The profile is movable by holding the mouse left button. 10. The retrieved 2D pattern can be improved and display in a selected color and options in Preference. 11. To get serial number (SN), click Help/current driver. 4.2 Save the data of the retrieved intensities The retrieved intensities with indices can be saved in File drop-down menu. 4.3 Save the SAED pattern with the retrieved intensities The SAED pattern with/without the retrieved intensities can be saved in File drop-down menu. 9
Figure 9. Lattice refinement
Figure 10. Basic vectors.
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Figure 11. Background intensity
Figure 12. The SAED pattern with extracted intensities. 11
Figure 13. Adjustment of the retrieved intensities and the preference dialogs.
Figure 14. (a) Retrieved intensities and (b) adjusted intensities.
Figure 15. Profile style.
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Figure 16. Selection of a line for intensity profile.
Figure 17. The intensity profile.
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5. Installation of QSAED3 5.1 JRE and JAI Download and install the most recent JRE from Java official site. Download and install the JAI, which is also available in http://www.unl.edu/ncmn-cfem/xzli/download. 5.2 Installation Create a dedicated fold for LANDYNE software suit. Copy and decompress the package. If you have a license file, copy the license to the same fold with the program (qsaed3.jar or qsaed3.exe). 5.3 Run QSAED3c as a stand-alone software To run QSAED3, double click the icon of QSAED3.exe or type: java -jar (-Xmx512m) QSAED3.jar in command line. -Xmx512m is an option to locate the memory of Java virtual machine up to 512 MB. 5.4 Run QSAED3c in the Landyne suite` Click the QSAED3 in Landyne launcher to start the software. 5.5 Get the license A license file is needed to unlock the program (qsaed3.jar) for loading SAED pattern. Without the license file the program is locked up in demo mode, which works with demo-qsaed.tif. License can be purchased from LANDYNE computer software. 6. References [1] X.Z. Li, Processing and Quantification of Polycrystalline Electron Diffraction Patterns, Microsc. Microanal. 17: Suppl. S02 (2011) p. 1096. [2] X.Z. Li, QPCED2.0: a computer program for the processing and quantification of polycrystalline electron diffraction patterns, J. Appl. Cryst. 45 (2012) p. 862. [3] X.Z. Li, JECP—a Java Electron Crystallography Project, Microscopy Today 14:5, 2006, 32. [4] X.Z. LI, JECP/QSAED, a Computer Program for Quantification of SAED Patterns, Microsc. Microanal. 20 (Suppl 3), 2014, 1486. [5] http://www.unl.edu/ncmn-cfem/xzli/computer-programs and http://landyne.ueuo.com.
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