Leginon

h1. Beam Shift matrix calibration

Beam shift matrix calibrations are used at each magnification that Leginon uses. These

calibrations are not absolutely necessary, but can be very helpful to center the beam in the

navigator node. In this case, the image of a small beam within the CCD is treated as an object

in the image. When the beam is shifted by the electromagnetic lenses of the microscope, the

imprint of the beam moves relative to the CCD. The 2x2 transformation matrix created then

relates the values sent to the microscope and the amount of "beam shift" movement seen on the

CCD imaging area. Only one set of measurement is sufficient for beam shift matrix

calibration.

<blockquote>

_<link linkend="mcal_how"/>How does matrix calibration

work?_

</blockquote>

*  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> contract the beam sufficiently so that it remains in the area of CCD

acquisition during the calibration. It is also preferable that the CCD is imaging an

area with no distinct feature such as an empty grid square to minimize false peak from

unmoved object during a beam shift. At low magnifications, stage can be pulled out and

parked with a spacer to create the empty field.

*  Leginon/NodeSelector> select "Matrix" node.

*  Leginon/Matrix> the preset CCD configuration is almost certainly bad for imaging

contracted beam. Therefore, DO NOT use "test acquire" at this point.

*  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: 1024x1024 binned by 4 and a VERY short exposure time can save time but still

keep the contracted beam from burning the CCD.

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

current parameters.

*  Leginon/Matrix/Toolbar> select "beam 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 of the beam should be shifting 10-30% of the imaging area. If this is not

the case, then adjust 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

cross correlation and its peak can also be displayed. The beam need to be contained in

the imaging area at all time.

*  Use Navigation node to <link linkend="nav">check the result of the

calibration</link>.

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

|gr|120 (rarely used)|

|sq|550 (rarely used)|

|hl|5000 (seldom used)|

||11000 (used in beam shift alignment tool in Presets Manager to align the beam at

50000x)|

|fc,fa,en,ef|50000 (useful)|

* The Presets Manager beam shift alignment tool uses ~5x lower magnification than the

preset meant to be aligned in order to see the whole beam in view. This means that for

fc,fa,en,ef that are at 50000x, a calibration at 11000x is required at the similar defocus

range.