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Advanced operations of Digital Micrograph, the TEM photo processing software



Transmission Electron Microscope (TEM) is often used in scientific research experiments in order to investigate the surface morphology of objects, especially for the observation of fine structures (sub-microscopic structures or ultrastructures) smaller than 0.2 microns. However, the processing of TEM test results, commonly known as ".dm3" format files, often leaves many researchers at a loss. In fact, as one of the most professional software for TEM image analysis and processing, Digital Micrograph (DM) is not as difficult to operate as one might think. Some of the basic operations of the software have been introduced previously, and the following author will combine his own research experience and choose relevant scientific research examples to explain the advanced operation of DM software.

2.Measurement of crystal plane spacing

Calculation of the lattice spacing of this material phase based on high-resolution TEM image measurements is a fundamental operation for mastering DM. Based on the measured lattice spacing, combined with X-ray diffraction (XRD) results, the material composition can be further verified and the corresponding crystalline surfaces of the material phase can be analysed. The specific operation steps are as follows:

2.1 Zooming and moving pictures

Open a high magnification TEM photo in ".dm3" format, zoom in and select the area to be measured.

Usually, imported high magnification TEM images show clear lattice fringes. However, there are some images where the lattice fringes look slightly blurred due to various reasons such as signal-to-noise ratio. For such images, we first need to use the zoom function (right side of the red box in Fig. 1), and then use the chiral tool (left side of the red box in Fig. 1) to move the area to be measured to the centre of the interface.

Figure 1: Zooming and moving pictures

2.2 Rough measurements of lattice spacing

Determine the lattice fringe area to be measured, in the "Standard Tools" under the selection of linear tools, drag the mouse to draw a straight line in the figure. Note that the drawn line should be as perpendicular to the lattice stripes to ensure accuracy. As shown in Figure 3, you can see in the "Control" tool will appear under the length of the line, in order to facilitate the calculation, the general selection of the line length of 10 lattice spacing, so you can roughly estimate the lattice spacing of about 0.3014 nm.

Figure 2: Rough measurements of lattice spacing

2.3 Accurate measurement of lattice spacing

In practical scientific analyses, there are high demands on the accuracy of data, especially for lattice spacing measurements, where small errors can lead to large deviations. In order to measure the lattice spacing more accurately, researchers usually use the following process. Firstly, after zooming in and selecting the area of the picture, select the "Standard Tools" under the line tool (Figure 3 red box) to draw a straight line on the picture, the software interface will appear in an additional "Profile" box, but the "Profile" box in the picture will not be displayed. However, the lattice stripes in the "Profile" box are not clear (blue box in Figure 3).

Figure 3:Accurate measurement of lattice spacing

In order to make the selected lattice stripes as clear as possible and the measurements as accurate as possible, you can double-click on the drawn line and set the line width to 20, as shown in Figure 4.

Figure 4:Setting the line width

At this time, you can see that the lattice stripes in the "Profile" box become clear and three-dimensional, the closer the height of each column, the more accurate the results. As shown in Figure 5, with the left mouse button in the "Profile" box drag the dotted line box, then will display the length of the box line, the length of the box line is the total length of the selected lattice stripes, the figure was selected for the lattice spacing of 10 cycles, about 2.998 nm, which can be calculated that the lattice stripe spacing of 0.2998 nm.

Figure 5:Precise calculation of lattice spacing

3.Selected electron diffraction analyses

A set of fully analysed TEM images must be missing the selection of electron diffraction (SAED) images, which can further achieve the identification of the crystal structure and crystal phase composition of the sample to be tested, thus improving the accuracy and reliability of the sample analysis. As shown in Fig. 7, firstly, open a common SAED image according to the above steps and determine the position of the centre of the circle. Using the "Standard Tools" under the centre of the circle calibration function (Figure 6, left red box), select the two more obvious points of symmetry over the centre of the circle in the picture, the left mouse button were clicked (green box in the picture), and then appeared in the centre of the circle shown in Figure 6.

Figure 6: Diffractogram circle centre determination

On the basis of determining the centre of the circle, the diffraction spots on the SAED diagram need to be further calibrated to determine the crystal plane spacing. Select the tool shown in Figure 7 (in the red box), and then use the left mouse button to click on the diffraction map one by one on the relatively clear and obvious diffraction spots, in order to the accuracy of the results, the diffraction spots should be calibrated should be at least greater than 3, zoom in to see the map after the click of the diffraction spots are marked by numbers (Figure 7, right).

Figure 7: Calibration of diffraction spots

After calibration, select "Show Results Window" under "Window" in the menu bar to open "Results" to view the results. The results include distance "d", error "R" and angle "Degree". The distances of all diffraction points from the centre of the circle as well as the diffraction angle with respect to the first diffraction spot can be clearly seen in the graph (Fig. 8).

Figure 8: SAED diffraction spot calibration results

Combined with the XRD test results, through the "d" value of the comparison (in this case, the PDF card is randomly selected), you can determine the crystal surface index. As shown in Figure 9, according to the "Results" results, "d" value of 0.31355 nm, which corresponds to the figure (1 1 1) crystal surface, accordingly determined the diffraction spot crystal surface.

Figure 9: Sample PDF Standard Card

For polycrystalline materials, the obtained results were imported into a graphing software such as PPT or PS and processed to obtain the SAED pattern of the diffracted circles (Fig. 10).

Figure 10: SAED mapping of polycrystalline materials

4.Dislocation analysis

In addition to the above functions, DM also has another function that cannot be ignored, which is the identification and analysis of lattice dislocations. Of course, even for TEM photographs with fewer lattice dislocations, the use of this analysis means that the lattice picture can be made clearer. Below, the author will explain it in detail.

4.1 Fourier transform

First of all, open a high magnification TEM image, select the "ROI Tools" area of the rectangular box selection tool (Figure 11, red box), in the figure to select the operation area. Note that, in order to make the selected area is square, you need to box while holding down the "Alt" key on the keyboard, as shown in Figure 12.

Figure 11: Selection of work area

After selecting the work area, you can carry out the Fourier transform of the region, click on the menu bar of the "Process", in the drop-down menu, select "FFT", pop-up the region of the Fourier transform map (Figure 12).

Figure 11: Fourier transform transform (math.)

4.2 Inverse Fourier Transform

As in Figure 13, for the Fourier transformed region, select "Masking Tools" in the toolbar on the left side of the DM, click on the Periodic Mask tool (red box in Figure 13) and click on the periodic points in the figure.

Figure 13: Mask Tool Processing

As in Figure 14, select "Process" in the menu bar, select "Apply Mask" in the drop-down menu, and then click "OK", you can get the inverse Fourier transform preprocessing picture.

Figure 14: Inverse Fourier transform preprocessing

Finally, to get the working area of the picture for the "Inverse FFT" operation can be obtained Figure 15, the right side of the red box inverse Fourier transform picture.

Figure 15: Inverse Fourier transform results

From the figure, we can see that the lattice has obvious interlacing, which is because there are a certain amount of dislocations in the region chosen by the author. Of course, if the selected region has fewer or no dislocations, the lattice stripes in the final inverse Fourier transformed image will be clearer compared to the original image (regarding the selection of the region, readers can try to figure it out by themselves).

5.Examples of applications

With the popularity of TEM technology, its related applications, especially in the field of scientific research, have become more and more widespread, and DM-processed TEM images are also commonly found in scientific research papers in various fields. Magnesium thermal reduction is defined as the reduction of various metal oxides (e.g. SiO2, ZrO2, TiO2 and GeO2) by the following reactions of magnesium vaporised or liquefied at high temperatures. Magnetothermal reduction of various types of silica/carbon (SiO2/C) composites is often used to synthesise silica/carbon (Si/C) composites and silicon carbide (SiC) materials, which are very important in the field of non-metallic oxide ceramics research.Jihoon et al [1] have shown that this method can be used to reduce the carbon in the composite by controlling the synthesis parameters such as the contact area between the silica and the carbon of the parent material, the reaction temperature, the heating rate and the amount of reaction mixture used to control the resulting crystalline ratio between Si and SiC. As shown in Fig. 16, the crystalline streaks of the SiC (111) crystallites on the surface of the carbon nanospheres after the reaction can be clearly observed by TEM analysis, combined with XRD results.

Fig. 16 TEM and XRD analyses of SiC In addition, TEM analyses are often applied in the field of electrochemical energy storage devices. shen et al [2] prepared a novel Fe3C-doped asymmetric porous carbon film electrode material using a simple phase transformation method, which demonstrated excellent electrochemical properties. Figure 17 shows the TEM image, HR-TEM image and SEAD pattern of the composite. From them, the lattice striations of Fe3C can be clearly seen, and its crystallographic spacing is 0.201 nm, which matches well with the (0 3 1) crystallographic plane of Fe3C.The SAED plots mark the diffraction rings of the (0 2 0), (0 3 1) and (4 0 1) crystallographic planes of Fe3C, respectively. Fig. 18 TEM analysis of Fe3C


[1] Jihoon Ahn, Hee Soo Kim, Jung Pyo, Jin-Kyu Lee, Won Cheol Yoo, Variation in Crystalline Phases: Controlling the Selectivity between Silicon and Silicon Carbide via Magnesiothermic Reduction using Silica/Carbon Composites. Chemical Material, 2016, 28, 1526−1536/

[2] Weiming Shen, Wei Kou, Yang Liu, Yan Dai, Wenji Zheng, Gaohong He, Shuting Wang, Yue Zhang, Xuemei Wu, Shuai Fan, Xiangcun Li, Fe3C-doped asymmetric porous carbon membrane binder-free integrated materials as high performance anodes of lithium-ion batteries. Chemical Engineering Journal, 2019, 368, 310-320.