Beam Shift matrix calibration » History » Version 7
Anchi Cheng, 06/06/2010 08:21 PM
1 | 1 | Amber Herold | h1. Beam Shift matrix calibration |
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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 | navigator node. In this case, the image of a small beam within the CCD is treated as an object |
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8 | in the image. When the beam is shifted by the electromagnetic lenses of the microscope, the |
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9 | imprint of the beam moves relative to the CCD. The 2x2 transformation matrix created then |
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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 | 5 | Alex Kadokura | [[Image Shift matrix calibration|How does matrix calibration |
18 | work?]] |
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19 | 1 | Amber Herold | |
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21 | 3 | Alex Kadokura | |
22 | 5 | Alex Kadokura | * Leginon/Presets Manager> Select a preset for the calibration and send its |
23 | 1 | Amber Herold | parameter to the microscope. Matrix calibration depends only on magnification and |
24 | microscope high tension. Therefore, only one preset per combination needs to be |
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25 | calibrated. |
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28 | * Scope> contract the beam sufficiently so that it remains in the area of CCD |
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29 | acquisition during the calibration. It is also preferable that the CCD is imaging an |
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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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35 | * Leginon/NodeSelector> select "Matrix" node. |
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38 | * Leginon/Matrix> the preset CCD configuration is almost certainly bad for imaging |
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39 | contracted beam. Therefore, DO NOT use "test acquire" at this point. |
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42 | * Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select |
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43 | camera configuration and correlation method. The former will take into effect only if |
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44 | "Overwrite Preset" is checked. Click "OK" to save the settings and close the window when |
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45 | done. |
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48 | *Tip: 1024x1024 binned by 4 and a VERY short exposure time can save time but still |
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49 | keep the contracted beam from burning the CCD. |
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52 | * Leginon/Matrix/Toolbar> left-click "Acquire Image" to obtain a test image with |
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53 | current parameters. |
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56 | * Leginon/Matrix/Toolbar> select "beam shift" as the Parameter and open the |
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57 | "Parameter Setting" window by clicking on the icon to the right of the selector. |
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60 | * Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest |
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61 | can be left in default values. "Interval" is not a relavent parameter since " average # |
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62 | position"=1. |
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65 | * Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
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68 | * The image of the beam should be shifting 10-30% of the imaging area. If this is not |
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69 | the case, then adjust shift fraction so that this occurs. The images can be monitored in |
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70 | Image Display Panel with display selection in image control panel set to "image". The |
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71 | cross correlation and its peak can also be displayed. The beam need to be contained in |
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72 | the imaging area at all time. |
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75 | 6 | Alex Kadokura | * Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the |
76 | calibration]]. |
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77 | 1 | Amber Herold | |
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84 | |<filename>Preset</filename>|<filename>magnification</filename>| |
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85 | |gr|120 (rarely used)| |
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86 | |sq|550 (rarely used)| |
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87 | |hl|5000 (seldom used)| |
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88 | 7 | Anchi Cheng | ||11000 (useful in beam shift alignment tool in Presets Manager to align the beam at |
89 | 1 | Amber Herold | 50000x)| |
90 | |fc,fa,en,ef|50000 (useful)| |
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95 | 7 | Anchi Cheng | * The Presets Manager beam shift alignment tool works best using ~5x lower magnification than the |
96 | 1 | Amber Herold | preset meant to be aligned in order to see the whole beam in view. This means that for |
97 | fc,fa,en,ef that are at 50000x, a calibration at 11000x is required at the similar defocus |
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98 | range. |
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99 | 2 | Amber Herold | |
100 | ______ |
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102 | [[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]] |
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104 | ______ |