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Special Operation Preference setup » History » Revision 3

Revision 2 (Amber Herold, 04/27/2010 11:38 AM) → Revision 3/9 (Alex Kadokura, 06/04/2010 03:28 PM)

h1. Special Operation Preference setup 



 h2.    Taking final exposures at very high magnification 



 Hysteresis of image shift at very high mags such as 200 kx can be reduced by setting the 
 following configuration 


 *    Presets Manager/Settings> 


 Cycle Magnification Only = no 


 *    If [[Queuing Example 1 - Exposure Targeting|queuing <link linkend="QExpTarget">queuing is used at exposure targeting]], targeting</link>, 


 Exposure Targeting/Settings> 


 Declare drift when queue submitted = yes 







 h2.    Avoiding drift correction that uses LM sq 
 preset 



 If the grid is flat and the offset of targets is small enough that it can be corrected 
 in the hole image, we recommand using the <[[Queuing Example 1 - Exposure Targeting|Queuing <link linkend="QExpTarget">Queuing option at 
 Exposure Targeting]]. Targeting</link>. The sq preset is still used after Stage Z adjustment to correct 
 the hole targets but will not be used when queued exposure targets are processed. 


 If the offset of targets is minimal even after stage Z adjustment, set the following to 
 avoid using ancestor images obtained in LM for drift management purpose, queuing or 
 not. 


 *    Target Adjustment/Settings> 


 Minimum Magnification =Lowest Magnification you want to allow the node to use for 
 determining the new target. 







 h2.    Minimize the use of image shift for the final exposure (Approach 1) 



 Large image shift can cause sufficient beam tilt that creates problems such as bad 
 autofocus, beam shift, and loss of resolution (but probably only if better than 4 angstrum 
 is needed). Image shift is used in Leginon for targeting exposure because it is much more 
 accurate than a single movement by the specimen goniometer, even after it is modeled for 
 mechanical periodicity. 


 The accuracy of the stage movement is lower when it moves a long distance. Therefore, 
 using iterative stage movement can improve the targeting, and therefore reduce the amount of 
 image shift required for the final exposure. To use this feature, change the following 
 preference in Hole node (or Subsquare node in MSI-Raster). 


 It is important to know that in order to check whether the precision is reached, image 
 is taken at the preset at which the target is selected on (in this case, sq preset), so the 
 dose should be kept at minimal. On our microscope 0.2 micron precision can be obtained 
 within 2 to 3 moves. 


 Hole/Settings/Image Acquisition> 


 * Mover=navigator 


 * Navigator Target Tolerance = 2 e-7 m (or whatever tolerance you like): This sets the 
 goal for multiple movement 


 * Navigator Acceptable Tolerance = 1 e-6 m (or whatever tolerance you like): If 
 further movement causes an increase rather than a decrease of targeting accuracy, this 
 value determines whether the target is aborted or not. 


 * Final Image Shift = No 




 Navigation/Settings/Error Checking and Correction> 


 *    Preset cycle after each move = yes if your sq preset is in LM mode and you don't 
 mind wait a little longer; = no if you don't have hysteresis problem staying in sq 
 preset for the unknown amount of time during the iterative move. 







 h2.    Minimize the use of image shift for the final exposure (Approach 2) 



 A different approach is being developed to minimize image shift while maintaining final 
 targeting accuracy-A combination of stage movement and image shift. This approach can only 
 be used in limited cases such as targets selected for the tomography node or exposure node, 
 and is only experimental in the latter case. 


 Tomography or Exposure/Settings/Image Acquisition> 


 * Move Type = modeled stage position 


 * Mover=navigator 


 * Navigator Target Tolerance = 1 e-7 m (or whatever tolerance you like) 


 * Navigator Acceptable Tolerance = 1 e-6 m (or whatever tolerance you like) 


 * Final Image Shift = Yes 







 h2. Optimize autofocusing sequence 



 The focus sequence in Focus and Z Focus nodes can and should be optimize for specific 
 cases. The activated sequence in the default setting is good for a flat holey grid and is 
 meant for high resolution imaging at 50k x or higher. If accurate defocus is not important, 
 focusing once per grid square may be sufficient, for which all focus sequence in Focus node 
 can be deactivated and the same autofocus step can be added to Z Focus node instead. 


 There are two methods to determine the defocus automatically : Stage tilt (Equivalent to 
 stage wobbling) and Beam tilt. There are also two possible ways for correcting the defocus 
 measured: Defocus (Equivalent to turning the focusing knob on the scope and reset the 
 defocus) and Stage Z (Moving the stage to the zero defocus height). 


 The following observations at NRAMM may help you determine what is the best to 
 use 


 *    Both defocus determination method requires calculation correlation between two 
 images. Therefore, the magnification and the location of the autofocusing should include 
 area with contrast. 


 *    The higher the magnification, the more accurate the defocus determination but the 
 smaller the range of defocus the defocus determination can handle. 


 *    Beam Tilt is more reproducible and preferred method to determing defocus in HM 
 mode. 


 *    Stage Tilt (Wobbling) is the preferred method to determine defocus in LM 
 mode. 




 MSI-Raster Chapter contains an example of an [[Improving Autofocusing|alternative <link linkend="MSI-R_auto_focus" 
 >alternative Z Focus node focus sequence]] sequence</link> for grid that show little contrast at 
 medium magnifications. 



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 [[Initial MSI application preferences|< Initial MSI application preferences]] | [[MSI Quick-start|MSI Quick-start >]] 

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