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Microscopy 101


b. Click on the SAED pattern without the beam block, and then click on the SAED pattern with the (000) spot located. Tis will put the two images in the correct order for the next DiffTools step. If the sequence of capturing the two patterns is 1) with the beam block in place and then 2) without the beam block in place, the images are already in the required order.


c. Run the DiffTools menu item, DiffTools – Transpose Centre to produce the result shown in Figure 4B. Te resultant image retains the calibration tags, and DiffTools also adds the location of the center of the pattern in the image tag that can be used with some of its other tools. Te image must be saved to retain the center location tag for future work.


3) Te third method uses a slightly more complicated script, but it does not require much user intervention. It also gen- erates two additional


images that are image processed.


Since the user aligns the transmitted beam with the center of the image with the aid of the crossed lines, the trans- mitted beam is always contained within a square array of pixels centered about the point where the lines cross. Te following is an outline of the algorithm that can be used to write a similar script. Te results from applying it to the SAED patterns in Figure 3 are shown in Figure 5. a. Determine which of the two images has the transmitted beam. One simple and sure way to do this is to subtract the sum of intensities of a center ROI from the sum of intensities of the whole image and compare results for the two images. Te pattern with the larger value is the one without the beam block.


b. Create a new image that is a clone of the image with the beam block. Tis preserves the tag information and gives the basis of the new filename.


c. Replace the data in the square ROI of the image with the beam block with the data from the same ROI in the image without the beam block.


d. Name the new image the same as the image with the beam block and add the suffix “+” to denote that it is the modified file and save it. Te resultant image is shown in Figure 5A. Figure 5B shows the image of Figure 5A processed within DM using the gamma control set with a value of 0.62. Tis image was not processed using a script, but is included here to compare with the other images.


e. Create a “Reveal Weak Reflections” image. Tis is eas- ily done by using DiffTools and then incorporating the DM script command, ChooseMenuItem(“DiffTools”, “”, “Reveal Weak Reflections”) into your script. Tis result is shown in Figure 5C.


f. Create a gamma-processed image. You can incorporate Dave Mitchell’s “Invert Image Contrast.s” script [4] into this script to invert the Reveal Weak Reflection image and produce a gamma-processed image as shown in Figure 5D.


Figure 5: “Double-exposure” SAED patterns. A) Center replaced with transmitted beam from image without the beam block. B) Image (A) manually processed in DM with gamma of 0.62. C) “Reveal Weak Reflections” processed image of (A). D) “Inverted Image Contrast” processed image of (C).


58 Aſter following the procedures presented in Parts 1 and 2


of this series, a researcher will have a well-calibrated and cen- tered digital SAED pattern with good intensities in multiple reflections and with its center position marked and known.


www.microscopy-today.com • 2020 May


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