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Special Operation Preference setup » History » Version 2

Amber Herold, 04/27/2010 11:38 AM

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h1. Special Operation Preference setup
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h2.  Taking final exposures at very high magnification
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Hysteresis of image shift at very high mags such as 200 kx can be reduced by setting the
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following configuration
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*  Presets Manager/Settings>
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Cycle Magnification Only = no
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*  If <link linkend="QExpTarget">queuing is used at exposure targeting</link>,
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Exposure Targeting/Settings>
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Declare drift when queue submitted = yes
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h2.  Avoiding drift correction that uses LM sq
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preset
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If the grid is flat and the offset of targets is small enough that it can be corrected
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in the hole image, we recommand using the <link linkend="QExpTarget">Queuing option at
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Exposure Targeting</link>. The sq preset is still used after Stage Z adjustment to correct
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the hole targets but will not be used when queued exposure targets are processed.
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If the offset of targets is minimal even after stage Z adjustment, set the following to
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avoid using ancestor images obtained in LM for drift management purpose, queuing or
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not.
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*  Target Adjustment/Settings>
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Minimum Magnification =Lowest Magnification you want to allow the node to use for
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determining the new target.
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h2.  Minimize the use of image shift for the final exposure (Approach 1)
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Large image shift can cause sufficient beam tilt that creates problems such as bad
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autofocus, beam shift, and loss of resolution (but probably only if better than 4 angstrum
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is needed). Image shift is used in Leginon for targeting exposure because it is much more
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accurate than a single movement by the specimen goniometer, even after it is modeled for
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mechanical periodicity.
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The accuracy of the stage movement is lower when it moves a long distance. Therefore,
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using iterative stage movement can improve the targeting, and therefore reduce the amount of
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image shift required for the final exposure. To use this feature, change the following
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preference in Hole node (or Subsquare node in MSI-Raster).
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It is important to know that in order to check whether the precision is reached, image
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is taken at the preset at which the target is selected on (in this case, sq preset), so the
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dose should be kept at minimal. On our microscope 0.2 micron precision can be obtained
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within 2 to 3 moves.
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Hole/Settings/Image Acquisition>
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* Mover=navigator
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* Navigator Target Tolerance = 2 e-7 m (or whatever tolerance you like): This sets the
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goal for multiple movement
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* Navigator Acceptable Tolerance = 1 e-6 m (or whatever tolerance you like): If
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further movement causes an increase rather than a decrease of targeting accuracy, this
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value determines whether the target is aborted or not.
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* Final Image Shift = No
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Navigation/Settings/Error Checking and Correction>
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*  Preset cycle after each move = yes if your sq preset is in LM mode and you don't
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mind wait a little longer; = no if you don't have hysteresis problem staying in sq
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preset for the unknown amount of time during the iterative move.
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h2.  Minimize the use of image shift for the final exposure (Approach 2)
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A different approach is being developed to minimize image shift while maintaining final
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targeting accuracy-A combination of stage movement and image shift. This approach can only
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be used in limited cases such as targets selected for the tomography node or exposure node,
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and is only experimental in the latter case.
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Tomography or Exposure/Settings/Image Acquisition>
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* Move Type = modeled stage position
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* Mover=navigator
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* Navigator Target Tolerance = 1 e-7 m (or whatever tolerance you like)
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* Navigator Acceptable Tolerance = 1 e-6 m (or whatever tolerance you like)
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* Final Image Shift = Yes
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h2. Optimize autofocusing sequence
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The focus sequence in Focus and Z Focus nodes can and should be optimize for specific
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cases. The activated sequence in the default setting is good for a flat holey grid and is
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meant for high resolution imaging at 50k x or higher. If accurate defocus is not important,
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focusing once per grid square may be sufficient, for which all focus sequence in Focus node
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can be deactivated and the same autofocus step can be added to Z Focus node instead.
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There are two methods to determine the defocus automatically : Stage tilt (Equivalent to
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stage wobbling) and Beam tilt. There are also two possible ways for correcting the defocus
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measured: Defocus (Equivalent to turning the focusing knob on the scope and reset the
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defocus) and Stage Z (Moving the stage to the zero defocus height).
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The following observations at NRAMM may help you determine what is the best to
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use
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*  Both defocus determination method requires calculation correlation between two
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images. Therefore, the magnification and the location of the autofocusing should include
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area with contrast.
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*  The higher the magnification, the more accurate the defocus determination but the
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smaller the range of defocus the defocus determination can handle.
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*  Beam Tilt is more reproducible and preferred method to determing defocus in HM
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mode.
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*  Stage Tilt (Wobbling) is the preferred method to determine defocus in LM
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mode.
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MSI-Raster Chapter contains an example of an <link linkend="MSI-R_auto_focus"
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>alternative Z Focus node focus sequence</link> for grid that show little contrast at
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medium magnifications.
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[[Initial MSI application preferences|< Initial MSI application preferences]] | [[MSI Quick-start|MSI Quick-start >]]
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