User Manual for QEDtest
Contents
1. per point 0 56 seconds otal acquisition time 90 87 seconds e222 Timing report for Camera MSC LMFS48S5A binning 2 Size of image 1024 x 1024 pixels otal time per point 5 38 seconds Exposure time per point 0 01 seconds Total overhead time per point 5 37 seconds Avg CCD read out time 4 86 seconds Other overhead time per point 0 51 seconds otal acquisition time 258 10 seconds Figure 6 Screenshot of the results window after acquiring test data stacks on two different cameras with two different binnings Reset tilt and tilt de scan In the case that an unexpected error occurs during the acquisition of the test data stack e g the tilt or shift limits set by the microscope manufacturer have been exceeded the illumination tilt and diffraction shift may not be reset automatically In this case pressing the Reset tilt and de scan button will ensure that the illumination tilt and the diffraction shift are set again to the values they were at before the test script was started2. QEDtest User Manual v1 3 User Manual for QEDtest HREM Research Inc Introduction The QEDtest Plug In for DigitalMicrograph DM serves the purpose of testing whether a TEM is capable of acquiring large angle rocking beam electron diffraction LARBED or precession electron diffraction PED patterns or diffraction maps using the QED plugin This plug in allows the user to perform three tasks 1 Calibrate the tilt scan and tilt de scan 2 Acquire a test data stack which consists of an on axis diffraction pattern as well as 8 PED patterns at precession angles 1 8 2 8 3 8 4 8 5 8 6 8 7 8 and 8 8 times the maximum tilt angle specified Each of the PED patterns 1s comprised of the sum of 6 patterns acquired for different tilts around the circle of the specified tilt magnitude 3 Reset the illumination tilt and diffraction shift This Plug In requires an online installation of DM and the capability of DM to control the illumination deflection coils as well as the diffraction shift This functionality is commonly provided if the EMControl plug in is installed and DM can control the TEM at all e g adjust the defocus of the objective lens Installation The QEDtest Plug In is easily installed by copying the files QEDtest gt2 and QEDlib gt1 to the DigitalMicrograph PlugIns folder Please re start DM after copying these files Usage After successful installation the menu QED will appear in the DM menu bar This menu ha
3. e exposure time to 0 01 seconds and converge your illumination This will spread the intensity of your central beam You can then increase the exposure time according to the dynamic range of your CCD camera The camera length can be chosen as you would in a real experiment e g about 300 mm to capture also high order reflections On some installations of DM it may be necessary to make sure that DM has properly read the current microscope settings To do this first pressing Start View in DM s own Camera View floating tool box and then pressing Stop View to stop the view mode Please make sure that the view mode is stopped before proceeding any QEDtest or QED command Seles Please make sure that the selection includes a recognizeable feature You may either use image shift or move the selection Press Continue to proceed with the calibration or Cancel to abort Continue Cancel QED Test Dialog l Exp time sec 00 Binning fi Calibrate Tit and De scan Acquire Test Data Stack Reset Tit and De Scan 10 1 nm Available memory 1310 MB Figure 2 Screenshot demonstrating how the diffraction pattern should be set up for running the automated calibration routine z QEDtest User Manual v1 3 Pressing the Calibrate Tilt and Descan button will launch the fully automated calibration procedure This procedure will first produce a continually updating image of the diffraction pattern The user is th
4. en asked to move the central spot of the diffraction pattern well inside the region of interest ROI defined in the image Alternatively one may also move the ROI However one should not move the ROI too far from the image center because otherwise the calibration routine may shift the diffraction pattern outside the area captured by the CCD Once the user has brought the central beam within the ROI the actual calibration may be started by pressing the Continue button which should finish with the message Calibration successful as shown in Fig 3 lt 5 Ey Image shift 0 251 JOY EZ mutual correlation DigitalMicrograph Figure 3 Screenshot of the 3 images shown during calibration The image on the left is the reference image the image in the center shows the tilted or shifted diffraction pattern and the one on the far right shows a special correlation function used to measure the relative shift between the two images You may want to perform calibration at another camera length say at one half of the first calibration and check the results If your camera lengths are properly calibrated amplitudes of the tilt calibration should not change much with the camera length If your diffraction pattern rotates with camera length then the directions but not the amplitudes of the tilt vectors should change If the two calibrations are almost identical your calibration is most likely correct The diffraction shift may
5. inated by the beam The insets show an enlarged view of the center of the diffraction pattern On this microscope the linear tilt de scan calibration begins to become inaccurate at tilt amplitudes above 60 mrad but see Fig 5 The first frame of the data stack the untilted pattern is not shown The calibration of the tilt and tilt de scan is linear 1 e it is assumed that the deflection produced by the combination of commands sent to the X tilt and Y tilt deflectors as well as the X diffraction shift and Y diffraction shift deflectors is strictly proportional to the values submitted with the command At large tilt angles however it is very likely that this linear relationship breaks down This break down of the linearity of the deflectors can be seen in Fig 4 at tilt angles above 60 mrad The QED Plug In therefore includes a feature for correcting such alignment distortions Fig 5 gives an example of two PED patterns with a tilt amplitude of 120 mrad recorded without and with the Alignment Correction QEDtest User Manual v1 3 tilt amplitude 120 mrad tilt amplitude 120 mrad 10 1 nm 10 1 nm Figure 5 PED patterns recorded by the QED Plug In on a Zeiss EM912 with a tilt amplitude of 120 mrad demonstrating the effect of the QED alignment correction The left PED pattern has been recorded without alignment correction and the one on the right with the Alignment Correction flag turned on During the acquisition of the test data stac
6. k this routine also measures the time required for different parts of the exposure and prints a report in the results window Figure 6 shows an example output for a microscope equipped with two CCD cameras an Orius 200W camera installed in the wide angle port as well as a bottom mounted MultiScan camera This report splits the time required for each exposure into different contributions The main components to the acquisition time of each frame are the read out time and for long exposures the exposure time Additional overhead time named Other overhead time per point in Fig 6 is attributed to the time required to deflect the electron beam Fig 6 shows very clearly that the read out time for the MultiScan CCD is much longer than for the Orius camera QEDtest User Manual v1 3 wa Results 222 Timing report for Camera Orius SC200w binning 1 ize of image 2048 x 2048 pixels otal time per point 2 98 seconds Exposure time per point 0 01 seconds Total overhead time per point 2 97 seconds Avg CCD read out time 2 21 seconds Other overhead time per point 76 seconds weerrrerreeereereerereeereeerreeerereerreeereeerereeerereeereeees otal acquisition time 142 87 seconds e222 Timing report for Camera Orius SC200W binning 2 Size of image 1024 x 1024 pixels otal time per point 1 89 seconds Exposure time per point 0 01 seconds Total overhead time per point 1 88 seconds Avg CCD read out time 1 33 seconds Other overhead time
7. or may not depend on the camera length depending on which type of microscope you have You may confirm the calibration of both illumination tilt and diffraction shift if you can get the data stack as shown in Figure 4 by using the Acquire Test Data Stack button Acquisition of the test data stack and measuring acquisition time Once the deflection coils have been calibrated the test data stack may be acquired This procedure is fully automated and requires no user intervention This function produces a data stack of nine diffraction patterns the first one being an untilted diffraction pattern and subsequent ones being PED patterns with increasing tilt amplitude up to the maximum tilt angle you specify set to 80 mrad by default Each individual PED pattern is the sum of 6 diffraction patterns in which the beam 1s positioned at 6 different positions on the circle with 3 QEDtest User Manual v1 3 constant beam tilt amplitude This means that a total of 1 8 6 49 individual diffraction patterns will be acquired producing a data stack containing 9 patterns An example data stack is shown in Fig 4 This data set has been recorded with the sample removed from the beam This test Plug In does not implement the aberration compensation featured by the QED Plug In 10 mrad 20 mrad 30 mrad 50 mrad 60 mrad Figure 4 Example data set only frames 1 8 recorded by the QEDtest plugin on a Zeiss EM912 without the sample being illum
8. s only single item QED Test Clicking on this item will open the following graphical user interface GUI TA QED T fm QED Test Dialog Exp time sec ltt Binning ia Max Tit mrad 80 Calibrate Tilt and De scan Acquire Test Data Stack Reset Tilt and De Scan Available memory 2050 MB Figure 1 QED test GUI with buttons for calibration and acquisition of a test data stack l QEDtest User Manual v1 3 This GUI allows the user to define the acquisition time for diffraction patterns and the desired binning as well as the automated calibration of the tilt scan and tilt de scan and the acquisition of the test data set Acquisition of the test data stack only works if the calibration has been performed for this camera length Otherwise an error message reminding the user of the missing calibration will appear Calibration The Calibration requires that diffraction patterns acquired by DM are calibrated in the units 1 um 1 nm or 1 A Only then can the software calibrate the illumination tilt produced by the commands that are sent to the microscope It is suggested to have the TEM set up in diffraction mode but with the sample removed from the beam so that only the central spot is visible It is important to select the exposure time and binning such that the CCD will not be damaged If you are not sure how much intensity you have in your central beam we suggest to set th
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