Beam Shift matrix calibration » History » Revision 5
Revision 4 (Alex Kadokura, 05/28/2010 02:07 PM) → Revision 5/17 (Alex Kadokura, 05/28/2010 02:07 PM)
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. [[Image Shift matrix calibration|How _<link linkend="mcal_how"/>How does matrix calibration work?]] work?_ * bq. 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. ______ [[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]] ______