Beam Shift matrix calibration » History » Version 8
Amber Herold, 06/23/2010 12:59 PM
1 | 1 | Amber Herold | h1. Beam Shift matrix calibration |
---|---|---|---|
2 | |||
3 | |||
4 | |||
5 | Beam shift matrix calibrations are used at each magnification that Leginon uses. These |
||
6 | calibrations are not absolutely necessary, but can be very helpful to center the beam in the |
||
7 | 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 |
||
9 | 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 |
||
11 | CCD imaging area. Only one set of measurement is sufficient for beam shift matrix |
||
12 | calibration. |
||
13 | |||
14 | |||
15 | |||
16 | |||
17 | 8 | Amber Herold | [[Image Shift matrix calibration|How does matrix calibration work?]] |
18 | 1 | Amber Herold | |
19 | |||
20 | 3 | Alex Kadokura | |
21 | 5 | Alex Kadokura | * 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 |
||
24 | calibrated. |
||
25 | |||
26 | |||
27 | * Scope> contract the beam sufficiently so that it remains in the area of CCD |
||
28 | acquisition during the calibration. It is also preferable that the CCD is imaging an |
||
29 | area with no distinct feature such as an empty grid square to minimize false peak from |
||
30 | unmoved object during a beam shift. At low magnifications, stage can be pulled out and |
||
31 | parked with a spacer to create the empty field. |
||
32 | |||
33 | |||
34 | * Leginon/NodeSelector> select "Matrix" node. |
||
35 | |||
36 | |||
37 | * Leginon/Matrix> the preset CCD configuration is almost certainly bad for imaging |
||
38 | contracted beam. Therefore, DO NOT use "test acquire" at this point. |
||
39 | |||
40 | |||
41 | * Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select |
||
42 | camera configuration and correlation method. The former will take into effect only if |
||
43 | "Overwrite Preset" is checked. Click "OK" to save the settings and close the window when |
||
44 | done. |
||
45 | |||
46 | |||
47 | *Tip: 1024x1024 binned by 4 and a VERY short exposure time can save time but still |
||
48 | keep the contracted beam from burning the CCD. |
||
49 | |||
50 | |||
51 | * Leginon/Matrix/Toolbar> left-click "Acquire Image" to obtain a test image with |
||
52 | current parameters. |
||
53 | |||
54 | |||
55 | * Leginon/Matrix/Toolbar> select "beam shift" as the Parameter and open the |
||
56 | "Parameter Setting" window by clicking on the icon to the right of the selector. |
||
57 | |||
58 | |||
59 | * Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest |
||
60 | can be left in default values. "Interval" is not a relavent parameter since " average # |
||
61 | position"=1. |
||
62 | |||
63 | |||
64 | * Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate. |
||
65 | |||
66 | |||
67 | * The image of the beam should be shifting 10-30% of the imaging area. If this is not |
||
68 | the case, then adjust shift fraction so that this occurs. The images can be monitored in |
||
69 | Image Display Panel with display selection in image control panel set to "image". The |
||
70 | cross correlation and its peak can also be displayed. The beam need to be contained in |
||
71 | the imaging area at all time. |
||
72 | |||
73 | 6 | Alex Kadokura | |
74 | 8 | Amber Herold | * Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]. |
75 | 1 | Amber Herold | |
76 | |||
77 | |||
78 | |||
79 | 8 | Amber Herold | Beam Shift Calibration Need for the Example MSI: |
80 | 1 | Amber Herold | |
81 | |||
82 | |<filename>Preset</filename>|<filename>magnification</filename>| |
||
83 | |gr|120 (rarely used)| |
||
84 | |sq|550 (rarely used)| |
||
85 | |hl|5000 (seldom used)| |
||
86 | 7 | Anchi Cheng | ||11000 (useful in beam shift alignment tool in Presets Manager to align the beam at |
87 | 1 | Amber Herold | 50000x)| |
88 | |fc,fa,en,ef|50000 (useful)| |
||
89 | |||
90 | |||
91 | |||
92 | |||
93 | 8 | Amber Herold | *The Presets Manager beam shift alignment tool works best using ~5x lower magnification than the |
94 | 1 | Amber Herold | preset meant to be aligned in order to see the whole beam in view. This means that for |
95 | fc,fa,en,ef that are at 50000x, a calibration at 11000x is required at the similar defocus |
||
96 | range. |
||
97 | 2 | Amber Herold | |
98 | ______ |
||
99 | |||
100 | [[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]] |
||
101 | |||
102 | ______ |