Leginon

h1. Image Shift matrix calibration

Image shift matrix calibrations are used at each magnification that Leginon uses. All 2x2

matrix calibrations covered by the "Matrix" node works in the same way. For a particular type

of movement, in this case an "image shift" using the electromagnetic lenses of the microscope,

a 2x2 transformation matrix needs to be created that relates the values sent to the microscope

and the amount of "image shift" movement seen on the CCD imaging area. Only one set of

measurement is sufficient for image shift matrix calibration.

_How does matrix calibration work?_

bq. Matrix calibration is made by making N sets of measurements (specified by "N

Average"). Each measurement set acquires three images, first at a given origin, second

with an x-axis movement in the specified "Parameter" by the specified "Shift Fraction" of

the image, and third with an y-axis movement by the same shift fraction. The resulting

shifts in the acquired images are obtained by cross correlation. A transformation matrix

is then generated for the measurement set. The origin is shifted by the "Interval"

specified in the node, in meters before the next set of measurements is taken. At the end,

the N matrixes obtained are averaged and saved in the database at the specific

magnification and movement type and can be applied to any camera configuration.

"Tolerance", expressed in fraction of image, is used as an error check. The calibration is

considered failed when the measured movement is much different from that calculated from

pixel calibration

*  Leginon/Presets Manager> Select a preset for the calibration and send its

parameter to the microscope. Matrix calibration depends only on magnification and

microscope high tension. Therefore, only one preset per combination needs to be

calibrated.

*  Scope> Make sure that the CCD is imaging an area with distinct feature.

preferable isotropic, i.e., a single line is not appropriate but lines crossing each

other is good.

*  Leginon/NodeSelector> select "Matrix" node.

*  Leginon/Matrix/Toolbar> left-click "acquire image" to obtain a test image with

current parameters.

*  If the camera settings are not ideal-

Leginon/Presets Manager> If you have presets set up, you can change the camera

setting of the preset and send it to scope.

OR

Leginon/Matrix/Toolbar> open "settings" window by clicking the icon to select

camera configuration and correlation method. The former will take into effect only if

"Overwrite Preset" is checked. Click "OK" to save the settings and close the window when

done.

*Tip: Use this step to set the camera configuration to 512x512 binned by 8 (and a

short exposure time, of course) for presets with larger dimension and lower bin can save

a lot of image acquisition time during the calibration.

*  Leginon/Matrix/Settings> select correlation method. Phase correlation is

especially efficient in cases where periodic pattern exist. The pattern often causes

cross correlation peak search to misidentify the correct peak in the multiple peak

correlation map.

*  Leginon/Matrix/Toolbar> select "image shift" as the Parameter and open the

"Parameter Setting" window by clicking on the icon to the right of the selector.

*  Leginon/Matrix/Matrix Settings> "Average # position"=1 is sufficient. The rest

can be left in default values. "Interval" is not a relavent parameter since " average #

position"=1.

*  Leginon/Matrix/Toolbar> left-click (Execute icon) to calibrate.

*  The image should be shifting 10-30% of the imaging area. If this is not the case,

then adjust the shift fraction so that this occurs. The images can be monitored in Image

Display Panel with display selection in image control panel set to "image". The beam

should also be covering the entire imaging area at all time. If significant beam shift

is produced during the calibration, then the microscope alignments need to be adjusted,

especially image/beam calibration through the FEI software).

*  Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]

Image Shift Matrix calibration need for the Example MSI:

|<filename>Preset</filename>|<filename>magnification</filename>|

|gr|120|

|sq|550|

|hl|5000|

|fc,fa,en,ef|50000|

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[[Bright and Dark reference images|< Bright and Dark reference images]] | [[Beam Shift matrix calibration|Beam Shift matrix calibration >]]

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