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Image Shift matrix calibration » History » Version 12

Anchi Cheng, 08/16/2016 07:53 PM

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h1. Image Shift matrix calibration
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Image shift matrix calibrations are used at each magnification that Leginon uses. All 2x2
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matrix calibrations covered by the "Matrix" node works in the same way. For a particular type
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of movement, in this case an "image shift" using the electromagnetic lenses of the microscope,
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a 2x2 transformation matrix needs to be created that relates the values sent to the microscope
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and the amount of "image shift" movement seen on the digital camera imaging area. Only one set of
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measurement is sufficient for image shift matrix calibration.
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h2. Image Shift matrix calibration on JEOL microscope is also used for iteratively [[refine IMAGE_SHIFT_SCALE in jeol.cfg]]
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_How does matrix calibration work?_
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bq. Matrix calibration is made by making N sets of measurements (specified by "N
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Average"). Each measurement set acquires three images, first at a given origin, second
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with an x-axis movement in the specified "Parameter" by the specified "Shift Fraction" of
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the image, and third with an y-axis movement by the same shift fraction. The resulting
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shifts in the acquired images are obtained by cross correlation. A transformation matrix
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is then generated for the measurement set. The origin is shifted by the "Interval"
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specified in the node, in meters before the next set of measurements is taken. At the end,
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the N matrixes obtained are averaged and saved in the database at the specific
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magnification and movement type and can be applied to any camera configuration.
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"Tolerance", expressed in fraction of image, is used as an error check. The calibration is
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considered failed when the measured movement is much different from that calculated from
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pixel calibration
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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> Make sure that the digital camera is imaging an area with distinct feature.
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preferable isotropic, i.e., a single line is not appropriate but lines crossing each
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other is good.
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#  Leginon/NodeSelector> select "Matrix" node.
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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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#  If the camera settings are not ideal-
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Leginon/Presets Manager> If you have presets set up, you can change the camera
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setting of the preset and send it to scope.
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OR
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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: Use this step to set the camera configuration to 512x512 binned by 8 (and a
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short exposure time, of course) for presets with larger dimension and lower bin can save
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a lot of image acquisition time during the calibration.
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#  Leginon/Matrix/Settings> select correlation method. Phase correlation is
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especially efficient in cases where periodic pattern exist. The pattern often causes
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cross correlation peak search to misidentify the correct peak in the multiple peak
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correlation map.
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#  Leginon/Matrix/Toolbar> select "image 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 should be shifting 10-30% of the imaging area. If this is not the case,
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then adjust the shift fraction so that this occurs. The images can be monitored in Image
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Display Panel with display selection in image control panel set to "image". The beam
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should also be covering the entire imaging area at all time. If significant beam shift
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is produced during the calibration, then the microscope alignments need to be adjusted,
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especially image/beam calibration through the FEI software).
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#  Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]
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*Image Shift Matrix calibration need for the Example MSI:*
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|*Preset*|*magnification*|
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|gr|120|
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|sq|550|
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|hl|5000|
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|fc,fa,en,ef|50000|
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{{include(Scaling Image Shift Matrix Calibration)}}
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[[Bright and Dark reference images|< Bright and Dark reference images]] | [[Image Beam Compensation calibration|Image Beam Compensation calibration (JEOL scopes)>]]
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