Leginon

h1. Matrix Calibrator

Matrix calibrator performs four different calibrations that based on linear transformation

conversion: Image shift, beam shift, stage position, and image/beam shift

<highlights>

Required bindings

Required bindings to use preset instrument configuration set by presets manager

<simplelist type="vert">

<member> PresetsManagerNode - (PresetChangedEvent) -> MatrixCalibratorNode</member>

</simplelist>

</highlights>

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

Because the calibration is based on correlation of the acquired images, well contrasted

images with the intended movement clearly shown but not by such a large amount that the

apparent feature is altered is the key for sucessful calibrations.

Image shift calibration is useful only on FEI microscope where image shift/beam shift

compensation is calibrated and stored at the scope. Without such stored calibration, Image

shift/Beam shift calibration is required instead.

h2.  Toolbar

*  Settings = Adjust the manual image acquisition parameters.

*  Acquire Image = Acquire a current image.

*  Stage Position | Image Shift | Beam Shift = Choose the type of calibration to

complete

*  Parameter Settings = Adjust the parameters (and limits) for the calibration

process

*  Calibrate = Start the calibration.

*  Abort = Stop the Continuous Acquire function.

*  Edit Current Calibration = Edit the matrix when the calibration is completed. Not

recommended for beginner.

h2.  Settings

*  Use "phase | cross" correlation = Select the type of correlation used to

calculate the calibration.

*  Override Preset = use this node's <link linkend="camconfig">Instrument and Camera

Configuration</link> to acquire the images in this node

h2.  Parameter Settings

*  Tolerance = percent error allowed when calculating the calibration

*  Shift Fraction = amount sequential images should shift relative to each

other

*  Average = the number of sequential images that are acquired in order to calculate

the calibration

*  Interval "2e-6" = the interval (m) that is used to move the stage/beam/image

position to take images required for the image sequence

*  Use current positon as starting point = When enabled (default), the current stage

postion is used to begin the calibration

*  Base (x,y) = If "Use current position as starting point" is not enabled, this

position will be used to start the calibration

h2.  Image Control Panel

This panel controls which image is shown in the Image Display area.

*  Image = shows the corrected images as they are acquired

*  Correlation = shows the correlation image between sequential images in a

calibration

*  Peak = shows an orange crosshair over the Peak that has been identified from the

correlation image