Stage Position matrix calibration¶

Stage Position matrix calibrations can used to navigate at low magnifications (lower than
~1000x when accuracy of better than 2 um is not required. However, since the Modeled Stage
Position Rotation/Scale calibration also saves such matrix, this calibration is not necessary.
The procedure is provided here for reference.

How does matrix calibration work?

• Leginon/Presets Manager> Select the low mag preset for the calibration and send
  its parameter to the microscope.

• Microscope> Make sure there are distinguishable features for cross correlation
  in the range of movement to be used and that the beam is not clipping the area of CCD
  acquisition. Removing the objective aperture may be necessary.

• Leginon/NodeSelector> select "Matrix" node.

• Acquire test image and change the Camera Configuration in "setting" window to values
  that will produce a good image in a reasonable exposure time. Don't forget that
  "Overwrite Preset" has to be checked if you want to change the Camera Configuration in
  the node.

• Leginon/Matrix/Toolbar/Settings> select correlation method in the window. 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 "stage position" as the Parameter and open the
  "Parameter Setting" window.

• Leginon/Matrix/Matrix Settings> Change "Average # position" to a number 1+ (less
  than 10 for a faster calibration). The value 1 will give a moderate to poor calibration.
  Recommendations are as follow:
  • Phase correlation
  • Stage position
  • Tolerance = 50%
  • Shift fraction = 25%
  • Average = 5
  • Interval = 1.5e-05 meters

Because the measurements are variable depending of stage position, an averaging
technique is used to create a matrix that can be more generally applied to positions
over a greater range. A better method is to model the stage position ( http://emg.nysbc.org/publications/techreports/99-001/ ).

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

• The image should be shifting 10-30% of the imaging area. The images can be
  monitored in Image Display Panel with display selection in image control panel set to
  "image". The cross correlation and its peak can also be displayed. There has to be
  recognizable imaging feature that moves with stage movement for good correlation at all
  time for a good calibration. For example, if the CCD is covered completely by the grid
  bar, the calibration will certainly fail.

• Use Navigation node to check the result of the calibration.

< Beam Shift matrix calibration | Modeled Stage Position calibration >