Beam Shift matrix calibration » History » Version 11
Anchi Cheng, 05/15/2012 07:27 PM
1 | 10 | Anchi Cheng | h1. Beam Shift matrix calibration (Optional) |
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2 | 1 | Amber Herold | |
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5 | Beam shift matrix calibrations are used at each magnification that Leginon uses. These |
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6 | calibrations are not absolutely necessary, but can be very helpful to center the beam in the |
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7 | 11 | Anchi Cheng | navigator node. In this case, *the image of a small beam within the CCD is treated as an object |
8 | in the image.* When the beam is shifted by the electromagnetic lenses of the microscope, the |
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9 | 1 | Amber Herold | imprint of the beam moves relative to the CCD. The 2x2 transformation matrix created then |
10 | relates the values sent to the microscope and the amount of "beam shift" movement seen on the |
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11 | CCD imaging area. Only one set of measurement is sufficient for beam shift matrix |
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12 | calibration. |
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17 | 8 | Amber Herold | [[Image Shift matrix calibration|How does matrix calibration work?]] |
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20 | 3 | Alex Kadokura | |
21 | 9 | Amber Herold | # Leginon/Presets Manager> Select a preset for the calibration and send its |
22 | 1 | Amber Herold | parameter to the microscope. Matrix calibration depends only on magnification and |
23 | microscope high tension. Therefore, only one preset per combination needs to be |
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24 | calibrated. |
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25 | 9 | Amber Herold | |
26 | # Scope> contract the beam sufficiently so that it remains in the area of CCD |
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27 | 1 | Amber Herold | acquisition during the calibration. It is also preferable that the CCD is imaging an |
28 | area with no distinct feature such as an empty grid square to minimize false peak from |
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29 | unmoved object during a beam shift. At low magnifications, stage can be pulled out and |
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30 | parked with a spacer to create the empty field. |
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31 | 9 | Amber Herold | |
32 | # Leginon/NodeSelector> select "Matrix" node. |
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34 | # Leginon/Matrix> the preset CCD configuration is almost certainly bad for imaging |
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35 | 1 | Amber Herold | contracted beam. Therefore, DO NOT use "test acquire" at this point. |
36 | 9 | Amber Herold | |
37 | # Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select |
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38 | 1 | Amber Herold | camera configuration and correlation method. The former will take into effect only if |
39 | "Overwrite Preset" is checked. Click "OK" to save the settings and close the window when |
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40 | done. |
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41 | 9 | Amber Herold | |
42 | 1 | Amber Herold | *Tip: 1024x1024 binned by 4 and a VERY short exposure time can save time but still |
43 | keep the contracted beam from burning the CCD. |
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44 | 9 | Amber Herold | |
45 | # Leginon/Matrix/Toolbar> left-click "Acquire Image" to obtain a test image with |
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46 | 1 | Amber Herold | current parameters. |
47 | 9 | Amber Herold | |
48 | # Leginon/Matrix/Toolbar> select "beam shift" as the Parameter and open the |
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49 | 1 | Amber Herold | "Parameter Setting" window by clicking on the icon to the right of the selector. |
50 | 9 | Amber Herold | |
51 | # Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest |
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52 | 1 | Amber Herold | can be left in default values. "Interval" is not a relavent parameter since " average # |
53 | position"=1. |
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54 | 9 | Amber Herold | |
55 | # Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
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57 | # The image of the beam should be shifting 10-30% of the imaging area. If this is not |
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58 | 1 | Amber Herold | the case, then adjust shift fraction so that this occurs. The images can be monitored in |
59 | Image Display Panel with display selection in image control panel set to "image". The |
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60 | cross correlation and its peak can also be displayed. The beam need to be contained in |
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61 | the imaging area at all time. |
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62 | 9 | Amber Herold | |
63 | # Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]. |
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64 | 1 | Amber Herold | |
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68 | 9 | Amber Herold | *Beam Shift Calibration Need for the Example MSI:* |
69 | 1 | Amber Herold | |
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71 | |<filename>Preset</filename>|<filename>magnification</filename>| |
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72 | |gr|120 (rarely used)| |
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73 | |sq|550 (rarely used)| |
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74 | |hl|5000 (seldom used)| |
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75 | 7 | Anchi Cheng | ||11000 (useful in beam shift alignment tool in Presets Manager to align the beam at |
76 | 1 | Amber Herold | 50000x)| |
77 | |fc,fa,en,ef|50000 (useful)| |
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82 | 8 | Amber Herold | *The Presets Manager beam shift alignment tool works best using ~5x lower magnification than the |
83 | 1 | Amber Herold | preset meant to be aligned in order to see the whole beam in view. This means that for |
84 | fc,fa,en,ef that are at 50000x, a calibration at 11000x is required at the similar defocus |
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85 | range. |
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86 | 2 | Amber Herold | |
87 | ______ |
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89 | [[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]] |
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91 | ______ |