Stage Position matrix calibration » History » Version 8
Anchi Cheng, 06/06/2012 07:22 PM
1 | 1 | Amber Herold | h1. Stage Position matrix calibration |
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5 | Stage Position matrix calibrations can used to navigate at low magnifications (lower than |
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6 | ~1000x when accuracy of better than 2 um is not required. However, since the Modeled Stage |
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7 | Position Rotation/Scale calibration also saves such matrix, this calibration is not necessary. |
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8 | The procedure is provided here for reference. |
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14 | 5 | Amber Herold | [[Image Shift matrix calibration|How does matrix calibration work?]] |
15 | 3 | Alex Kadokura | |
16 | 1 | Amber Herold | |
17 | 7 | Amber Herold | # Leginon/Presets Manager> Select the low mag preset for the calibration and send |
18 | 1 | Amber Herold | its parameter to the microscope. |
19 | 7 | Amber Herold | |
20 | # Microscope> Make sure there are distinguishable features for cross correlation |
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21 | 8 | Anchi Cheng | in the range of movement to be used and that the beam is not clipping the area of the digital camera |
22 | 1 | Amber Herold | acquisition. Removing the objective aperture may be necessary. |
23 | 7 | Amber Herold | |
24 | # Leginon/NodeSelector> select "Matrix" node. |
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26 | # Acquire test image and change the Camera Configuration in "setting" window to values |
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27 | 1 | Amber Herold | that will produce a good image in a reasonable exposure time. Don't forget that |
28 | "Overwrite Preset" has to be checked if you want to change the Camera Configuration in |
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29 | the node. |
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30 | 7 | Amber Herold | |
31 | # Leginon/Matrix/Toolbar/Settings> select correlation method in the window. Phase |
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32 | 1 | Amber Herold | correlation is especially efficient in cases where periodic pattern exist. The pattern |
33 | often causes cross correlation peak search to misidentify the correct peak in the |
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34 | multiple peak correlation map. |
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35 | 7 | Amber Herold | |
36 | # Leginon/Matrix/Toolbar> select "stage position" as the Parameter and open the |
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37 | 1 | Amber Herold | "Parameter Setting" window. |
38 | 7 | Amber Herold | |
39 | # Leginon/Matrix/Matrix Settings> Change "Average # position" to a number 1+ (less |
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40 | 1 | Amber Herold | than 10 for a faster calibration). The value 1 will give a moderate to poor calibration. |
41 | Recommendations are as follow: |
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42 | 7 | Amber Herold | |
43 | 5 | Amber Herold | ** Phase correlation |
44 | 7 | Amber Herold | |
45 | 5 | Amber Herold | ** Stage position |
46 | 7 | Amber Herold | |
47 | 5 | Amber Herold | ** Tolerance = 50% |
48 | 7 | Amber Herold | |
49 | 1 | Amber Herold | ** Shift fraction = 25% |
50 | 7 | Amber Herold | |
51 | 1 | Amber Herold | ** Average = 5 |
52 | 7 | Amber Herold | |
53 | 1 | Amber Herold | ** Interval = 1.5e-05 meters |
54 | 7 | Amber Herold | |
55 | 1 | Amber Herold | Because the measurements are variable depending of stage position, an averaging |
56 | technique is used to create a matrix that can be more generally applied to positions |
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57 | over a greater range. A better method is to model the stage position ( "http://emg.nysbc.org/publications/techreports/99-001/":http://emg.nysbc.org/publications/techreports/99-001/ ). |
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58 | 7 | Amber Herold | |
59 | # Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
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61 | # The image should be shifting 10-30% of the imaging area. The images can be |
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62 | 1 | Amber Herold | monitored in Image Display Panel with display selection in image control panel set to |
63 | "image". The cross correlation and its peak can also be displayed. There has to be |
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64 | recognizable imaging feature that moves with stage movement for good correlation at all |
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65 | time for a good calibration. For example, if the CCD is covered completely by the grid |
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66 | bar, the calibration will certainly fail. |
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67 | 7 | Amber Herold | |
68 | # Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]. |
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73 | ______ |
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75 | [[Beam Shift matrix calibration|< Beam Shift matrix calibration]] | [[Modeled Stage Position calibration|Modeled Stage Position calibration >]] |
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77 | ______ |