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Beam Shift matrix calibration » History » Version 6

Alex Kadokura, 05/28/2010 02:09 PM

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h1. Beam Shift matrix calibration
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Beam shift matrix calibrations are used at each magnification that Leginon uses. These
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calibrations are not absolutely necessary, but can be very helpful to center the beam in the
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navigator node. In this case, the image of a small beam within the CCD is treated as an object
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in the image. When the beam is shifted by the electromagnetic lenses of the microscope, the
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imprint of the beam moves relative to the CCD. The 2x2 transformation matrix created then
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relates the values sent to the microscope and the amount of "beam shift" movement seen on the
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CCD imaging area. Only one set of measurement is sufficient for beam shift matrix
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calibration.
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[[Image Shift matrix calibration|How does matrix calibration
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work?]]
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* Leginon/Presets Manager> Select a preset for the calibration and send its
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parameter to the microscope. Matrix calibration depends only on magnification and
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microscope high tension. Therefore, only one preset per combination needs to be
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calibrated.
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*  Scope> contract the beam sufficiently so that it remains in the area of CCD
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acquisition during the calibration. It is also preferable that the CCD is imaging an
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area with no distinct feature such as an empty grid square to minimize false peak from
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unmoved object during a beam shift. At low magnifications, stage can be pulled out and
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parked with a spacer to create the empty field.
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*  Leginon/NodeSelector> select "Matrix" node.
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*  Leginon/Matrix> the preset CCD configuration is almost certainly bad for imaging
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contracted beam. Therefore, DO NOT use "test acquire" at this point.
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*  Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select
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camera configuration and correlation method. The former will take into effect only if
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"Overwrite Preset" is checked. Click "OK" to save the settings and close the window when
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done.
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*Tip: 1024x1024 binned by 4 and a VERY short exposure time can save time but still
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keep the contracted beam from burning the CCD.
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*  Leginon/Matrix/Toolbar> left-click "Acquire Image" to obtain a test image with
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current parameters.
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*  Leginon/Matrix/Toolbar> select "beam shift" as the Parameter and open the
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"Parameter Setting" window by clicking on the icon to the right of the selector.
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*  Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest
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can be left in default values. "Interval" is not a relavent parameter since " average #
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position"=1.
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*  Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate.
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*  The image of the beam should be shifting 10-30% of the imaging area. If this is not
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the case, then adjust shift fraction so that this occurs. The images can be monitored in
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Image Display Panel with display selection in image control panel set to "image". The
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cross correlation and its peak can also be displayed. The beam need to be contained in
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the imaging area at all time.
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*  Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the
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calibration]].
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|<filename>Preset</filename>|<filename>magnification</filename>|
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|gr|120 (rarely used)|
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|sq|550 (rarely used)|
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|hl|5000 (seldom used)|
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||11000 (used in beam shift alignment tool in Presets Manager to align the beam at
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50000x)|
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|fc,fa,en,ef|50000 (useful)|
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* The Presets Manager beam shift alignment tool uses ~5x lower magnification than the
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preset meant to be aligned in order to see the whole beam in view. This means that for
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fc,fa,en,ef that are at 50000x, a calibration at 11000x is required at the similar defocus
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range.
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[[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]]
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