Image Shift matrix calibration » History » Version 11
Anchi Cheng, 12/15/2015 08:53 PM
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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11 | 11 | Anchi Cheng | h2. Image Shift matrix calibration on JEOL microscope is also used for iteratively [[refine IMAGE_SHIFT_SCALE in jeol.cfg]] |
12 | 3 | Alex Kadokura | |
13 | 1 | Amber Herold | _How does matrix calibration work?_ |
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16 | 3 | Alex Kadokura | bq. Matrix calibration is made by making N sets of measurements (specified by "N |
17 | 1 | Amber Herold | Average"). Each measurement set acquires three images, first at a given origin, second |
18 | with an x-axis movement in the specified "Parameter" by the specified "Shift Fraction" of |
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19 | the image, and third with an y-axis movement by the same shift fraction. The resulting |
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20 | shifts in the acquired images are obtained by cross correlation. A transformation matrix |
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21 | is then generated for the measurement set. The origin is shifted by the "Interval" |
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22 | specified in the node, in meters before the next set of measurements is taken. At the end, |
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23 | the N matrixes obtained are averaged and saved in the database at the specific |
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24 | magnification and movement type and can be applied to any camera configuration. |
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25 | "Tolerance", expressed in fraction of image, is used as an error check. The calibration is |
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26 | considered failed when the measured movement is much different from that calculated from |
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27 | pixel calibration |
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30 | 6 | Amber Herold | # Leginon/Presets Manager> Select a preset for the calibration and send its |
31 | 1 | Amber Herold | parameter to the microscope. Matrix calibration depends only on magnification and |
32 | microscope high tension. Therefore, only one preset per combination needs to be |
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33 | calibrated. |
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34 | 6 | Amber Herold | |
35 | 7 | Anchi Cheng | # Scope> Make sure that the digital camera is imaging an area with distinct feature. |
36 | 1 | Amber Herold | preferable isotropic, i.e., a single line is not appropriate but lines crossing each |
37 | other is good. |
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38 | 6 | Amber Herold | |
39 | # Leginon/NodeSelector> select "Matrix" node. |
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40 | |
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41 | # Leginon/Matrix/Toolbar> left-click "acquire image" to obtain a test image with |
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42 | 1 | Amber Herold | current parameters. |
43 | 6 | Amber Herold | |
44 | # If the camera settings are not ideal- |
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45 | |
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46 | 1 | Amber Herold | Leginon/Presets Manager> If you have presets set up, you can change the camera |
47 | setting of the preset and send it to scope. |
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48 | 6 | Amber Herold | |
49 | 1 | Amber Herold | OR |
50 | 6 | Amber Herold | |
51 | 1 | Amber Herold | Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select |
52 | camera configuration and correlation method. The former will take into effect only if |
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53 | "Overwrite Preset" is checked. Click "OK" to save the settings and close the window when |
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54 | done. |
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55 | 6 | Amber Herold | |
56 | 1 | Amber Herold | *Tip: Use this step to set the camera configuration to 512x512 binned by 8 (and a |
57 | short exposure time, of course) for presets with larger dimension and lower bin can save |
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58 | a lot of image acquisition time during the calibration. |
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59 | 6 | Amber Herold | |
60 | # Leginon/Matrix/Settings> select correlation method. Phase correlation is |
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61 | 1 | Amber Herold | especially efficient in cases where periodic pattern exist. The pattern often causes |
62 | cross correlation peak search to misidentify the correct peak in the multiple peak |
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63 | correlation map. |
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64 | 6 | Amber Herold | |
65 | # Leginon/Matrix/Toolbar> select "image shift" as the Parameter and open the |
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66 | 1 | Amber Herold | "Parameter Setting" window by clicking on the icon to the right of the selector. |
67 | 6 | Amber Herold | |
68 | # Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest |
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69 | 1 | Amber Herold | can be left in default values. "Interval" is not a relavent parameter since " average # |
70 | position"=1. |
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71 | 6 | Amber Herold | |
72 | # Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
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74 | # The image should be shifting 10-30% of the imaging area. If this is not the case, |
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75 | 1 | Amber Herold | then adjust the shift fraction so that this occurs. The images can be monitored in Image |
76 | Display Panel with display selection in image control panel set to "image". The beam |
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77 | should also be covering the entire imaging area at all time. If significant beam shift |
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78 | is produced during the calibration, then the microscope alignments need to be adjusted, |
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79 | 5 | Amber Herold | especially image/beam calibration through the FEI software). |
80 | 6 | Amber Herold | |
81 | # Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]] |
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82 | 1 | Amber Herold | |
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85 | 6 | Amber Herold | *Image Shift Matrix calibration need for the Example MSI:* |
86 | 1 | Amber Herold | |
87 | 9 | Anchi Cheng | |*Preset*|*magnification*| |
88 | 1 | Amber Herold | |gr|120| |
89 | |sq|550| |
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90 | |hl|5000| |
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91 | |fc,fa,en,ef|50000| |
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92 | 2 | Amber Herold | |
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95 | ______ |
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97 | 8 | Anchi Cheng | [[Bright and Dark reference images|< Bright and Dark reference images]] | [[Image Beam Compensation calibration|Image Beam Compensation calibration (JEOL scopes)>]] |
98 | 2 | Amber Herold | |
99 | ______ |