Image Shift matrix calibration » History » Version 9
Anchi Cheng, 07/29/2015 01:18 AM
1 | 1 | Amber Herold | h1. Image Shift matrix calibration |
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4 | Image shift matrix calibrations are used at each magnification that Leginon uses. All 2x2 |
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5 | matrix calibrations covered by the "Matrix" node works in the same way. For a particular type |
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6 | of movement, in this case an "image shift" using the electromagnetic lenses of the microscope, |
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7 | a 2x2 transformation matrix needs to be created that relates the values sent to the microscope |
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8 | 7 | Anchi Cheng | and the amount of "image shift" movement seen on the digital camera imaging area. Only one set of |
9 | 1 | Amber Herold | measurement is sufficient for image shift matrix calibration. |
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14 | 3 | Alex Kadokura | |
15 | 1 | Amber Herold | _How does matrix calibration work?_ |
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18 | 3 | Alex Kadokura | bq. Matrix calibration is made by making N sets of measurements (specified by "N |
19 | 1 | Amber Herold | Average"). Each measurement set acquires three images, first at a given origin, second |
20 | with an x-axis movement in the specified "Parameter" by the specified "Shift Fraction" of |
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21 | the image, and third with an y-axis movement by the same shift fraction. The resulting |
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22 | shifts in the acquired images are obtained by cross correlation. A transformation matrix |
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23 | is then generated for the measurement set. The origin is shifted by the "Interval" |
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24 | specified in the node, in meters before the next set of measurements is taken. At the end, |
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25 | the N matrixes obtained are averaged and saved in the database at the specific |
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26 | magnification and movement type and can be applied to any camera configuration. |
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27 | "Tolerance", expressed in fraction of image, is used as an error check. The calibration is |
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28 | considered failed when the measured movement is much different from that calculated from |
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29 | pixel calibration |
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32 | 6 | Amber Herold | # Leginon/Presets Manager> Select a preset for the calibration and send its |
33 | 1 | Amber Herold | parameter to the microscope. Matrix calibration depends only on magnification and |
34 | microscope high tension. Therefore, only one preset per combination needs to be |
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35 | calibrated. |
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36 | 6 | Amber Herold | |
37 | 7 | Anchi Cheng | # Scope> Make sure that the digital camera is imaging an area with distinct feature. |
38 | 1 | Amber Herold | preferable isotropic, i.e., a single line is not appropriate but lines crossing each |
39 | other is good. |
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40 | 6 | Amber Herold | |
41 | # Leginon/NodeSelector> select "Matrix" node. |
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43 | # Leginon/Matrix/Toolbar> left-click "acquire image" to obtain a test image with |
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44 | 1 | Amber Herold | current parameters. |
45 | 6 | Amber Herold | |
46 | # If the camera settings are not ideal- |
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47 | |
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48 | 1 | Amber Herold | Leginon/Presets Manager> If you have presets set up, you can change the camera |
49 | setting of the preset and send it to scope. |
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50 | 6 | Amber Herold | |
51 | 1 | Amber Herold | OR |
52 | 6 | Amber Herold | |
53 | 1 | Amber Herold | Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select |
54 | camera configuration and correlation method. The former will take into effect only if |
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55 | "Overwrite Preset" is checked. Click "OK" to save the settings and close the window when |
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56 | done. |
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57 | 6 | Amber Herold | |
58 | 1 | Amber Herold | *Tip: Use this step to set the camera configuration to 512x512 binned by 8 (and a |
59 | short exposure time, of course) for presets with larger dimension and lower bin can save |
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60 | a lot of image acquisition time during the calibration. |
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61 | 6 | Amber Herold | |
62 | # Leginon/Matrix/Settings> select correlation method. Phase correlation is |
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63 | 1 | Amber Herold | especially efficient in cases where periodic pattern exist. The pattern often causes |
64 | cross correlation peak search to misidentify the correct peak in the multiple peak |
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65 | correlation map. |
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66 | 6 | Amber Herold | |
67 | # Leginon/Matrix/Toolbar> select "image shift" as the Parameter and open the |
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68 | 1 | Amber Herold | "Parameter Setting" window by clicking on the icon to the right of the selector. |
69 | 6 | Amber Herold | |
70 | # Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest |
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71 | 1 | Amber Herold | can be left in default values. "Interval" is not a relavent parameter since " average # |
72 | position"=1. |
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73 | 6 | Amber Herold | |
74 | # Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
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76 | # The image should be shifting 10-30% of the imaging area. If this is not the case, |
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77 | 1 | Amber Herold | then adjust the shift fraction so that this occurs. The images can be monitored in Image |
78 | Display Panel with display selection in image control panel set to "image". The beam |
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79 | should also be covering the entire imaging area at all time. If significant beam shift |
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80 | is produced during the calibration, then the microscope alignments need to be adjusted, |
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81 | 5 | Amber Herold | especially image/beam calibration through the FEI software). |
82 | 6 | Amber Herold | |
83 | # Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]] |
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84 | 1 | Amber Herold | |
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87 | 6 | Amber Herold | *Image Shift Matrix calibration need for the Example MSI:* |
88 | 1 | Amber Herold | |
89 | 9 | Anchi Cheng | |*Preset*|*magnification*| |
90 | 1 | Amber Herold | |gr|120| |
91 | |sq|550| |
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92 | |hl|5000| |
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93 | |fc,fa,en,ef|50000| |
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94 | 2 | Amber Herold | |
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97 | ______ |
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99 | 8 | Anchi Cheng | [[Bright and Dark reference images|< Bright and Dark reference images]] | [[Beam Shift matrix calibration|Beam Shift matrix calibration (FEI scopes)>]] |
100 | [[Bright and Dark reference images|< Bright and Dark reference images]] | [[Image Beam Compensation calibration|Image Beam Compensation calibration (JEOL scopes)>]] |
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101 | 2 | Amber Herold | |
102 | ______ |