Beam Shift matrix calibration » History » Version 17
Anchi Cheng, 07/29/2015 01:19 AM
1 | 10 | Anchi Cheng | h1. Beam Shift matrix calibration (Optional) |
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2 | 1 | Amber Herold | |
3 | 16 | Anchi Cheng | h1. DO NOT GO THROUGH THIS CALIBRATION ON JEOL SCOPES. DO [[Image Beam Compensation calibration]] instead. |
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5 | 15 | Anchi Cheng | h2. This calibration requires concentrating the beam on a small area of the sensor. Do not attempt this on radiation-damage-sensitive DDD (Gatan K2, DE-12, DE-20, Falcon unless you have ways to reduce the beam intensity at the same magnification by using spot size that gives you week enough beam). |
6 | 1 | Amber Herold | |
7 | Beam shift matrix calibrations are used at each magnification that Leginon uses. These |
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8 | calibrations are not absolutely necessary, but can be very helpful to center the beam in the |
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9 | 11 | Anchi Cheng | navigator node. In this case, *the image of a small beam within the CCD is treated as an object |
10 | in the image.* When the beam is shifted by the electromagnetic lenses of the microscope, the |
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11 | 1 | Amber Herold | imprint of the beam moves relative to the CCD. The 2x2 transformation matrix created then |
12 | relates the values sent to the microscope and the amount of "beam shift" movement seen on the |
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13 | CCD imaging area. Only one set of measurement is sufficient for beam shift matrix |
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14 | calibration. |
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19 | 8 | Amber Herold | [[Image Shift matrix calibration|How does matrix calibration work?]] |
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22 | 3 | Alex Kadokura | |
23 | 9 | Amber Herold | # Leginon/Presets Manager> Select a preset for the calibration and send its |
24 | 1 | Amber Herold | parameter to the microscope. Matrix calibration depends only on magnification and |
25 | microscope high tension. Therefore, only one preset per combination needs to be |
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26 | calibrated. |
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27 | 9 | Amber Herold | |
28 | # Scope> contract the beam sufficiently so that it remains in the area of CCD |
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29 | 1 | Amber Herold | acquisition during the calibration. It is also preferable that the CCD is imaging an |
30 | area with no distinct feature such as an empty grid square to minimize false peak from |
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31 | unmoved object during a beam shift. At low magnifications, stage can be pulled out and |
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32 | parked with a spacer to create the empty field. |
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33 | 9 | Amber Herold | |
34 | # Leginon/NodeSelector> select "Matrix" node. |
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35 | |
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36 | # Leginon/Matrix> the preset CCD configuration is almost certainly bad for imaging |
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37 | 1 | Amber Herold | contracted beam. Therefore, DO NOT use "test acquire" at this point. |
38 | 9 | Amber Herold | |
39 | # Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select |
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40 | 1 | Amber Herold | camera configuration and correlation method. The former will take into effect only if |
41 | "Overwrite Preset" is checked. Click "OK" to save the settings and close the window when |
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42 | done. |
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43 | 9 | Amber Herold | |
44 | 1 | Amber Herold | *Tip: 1024x1024 binned by 4 and a VERY short exposure time can save time but still |
45 | keep the contracted beam from burning the CCD. |
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46 | 9 | Amber Herold | |
47 | # Leginon/Matrix/Toolbar> left-click "Acquire Image" to obtain a test image with |
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48 | 1 | Amber Herold | current parameters. |
49 | 9 | Amber Herold | |
50 | # Leginon/Matrix/Toolbar> select "beam shift" as the Parameter and open the |
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51 | 1 | Amber Herold | "Parameter Setting" window by clicking on the icon to the right of the selector. |
52 | 9 | Amber Herold | |
53 | # Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest |
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54 | 1 | Amber Herold | can be left in default values. "Interval" is not a relavent parameter since " average # |
55 | position"=1. |
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56 | 9 | Amber Herold | |
57 | # Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
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58 | |
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59 | # The image of the beam should be shifting 10-30% of the imaging area. If this is not |
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60 | 1 | Amber Herold | the case, then adjust shift fraction so that this occurs. The images can be monitored in |
61 | Image Display Panel with display selection in image control panel set to "image". The |
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62 | cross correlation and its peak can also be displayed. The beam need to be contained in |
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63 | the imaging area at all time. |
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64 | 9 | Amber Herold | |
65 | # Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]. |
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70 | 9 | Amber Herold | *Beam Shift Calibration Need for the Example MSI:* |
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73 | 17 | Anchi Cheng | |*Preset*|*magnification*| |
74 | 1 | Amber Herold | |gr|120 (rarely used)| |
75 | |sq|550 (rarely used)| |
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76 | |hl|5000 (seldom used)| |
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77 | 7 | Anchi Cheng | ||11000 (useful in beam shift alignment tool in Presets Manager to align the beam at |
78 | 1 | Amber Herold | 50000x)| |
79 | |fc,fa,en,ef|50000 (useful)| |
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84 | 8 | Amber Herold | *The Presets Manager beam shift alignment tool works best using ~5x lower magnification than the |
85 | 1 | Amber Herold | preset meant to be aligned in order to see the whole beam in view. This means that for |
86 | fc,fa,en,ef that are at 50000x, a calibration at 11000x is required at the similar defocus |
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87 | range. |
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88 | 2 | Amber Herold | |
89 | ______ |
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91 | [[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]] |
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93 | ______ |