Special Operation Preference setup » History » Version 2
Amber Herold, 04/27/2010 11:38 AM
1 | 1 | Amber Herold | h1. Special Operation Preference setup |
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5 | h2. Taking final exposures at very high magnification |
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9 | Hysteresis of image shift at very high mags such as 200 kx can be reduced by setting the |
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10 | following configuration |
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13 | * Presets Manager/Settings> |
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16 | Cycle Magnification Only = no |
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19 | * If <link linkend="QExpTarget">queuing is used at exposure targeting</link>, |
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22 | Exposure Targeting/Settings> |
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25 | Declare drift when queue submitted = yes |
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33 | h2. Avoiding drift correction that uses LM sq |
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34 | preset |
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38 | If the grid is flat and the offset of targets is small enough that it can be corrected |
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39 | in the hole image, we recommand using the <link linkend="QExpTarget">Queuing option at |
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40 | Exposure Targeting</link>. The sq preset is still used after Stage Z adjustment to correct |
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41 | the hole targets but will not be used when queued exposure targets are processed. |
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44 | If the offset of targets is minimal even after stage Z adjustment, set the following to |
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45 | avoid using ancestor images obtained in LM for drift management purpose, queuing or |
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46 | not. |
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49 | * Target Adjustment/Settings> |
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52 | Minimum Magnification =Lowest Magnification you want to allow the node to use for |
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53 | determining the new target. |
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61 | h2. Minimize the use of image shift for the final exposure (Approach 1) |
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65 | Large image shift can cause sufficient beam tilt that creates problems such as bad |
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66 | autofocus, beam shift, and loss of resolution (but probably only if better than 4 angstrum |
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67 | is needed). Image shift is used in Leginon for targeting exposure because it is much more |
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68 | accurate than a single movement by the specimen goniometer, even after it is modeled for |
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69 | mechanical periodicity. |
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72 | The accuracy of the stage movement is lower when it moves a long distance. Therefore, |
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73 | using iterative stage movement can improve the targeting, and therefore reduce the amount of |
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74 | image shift required for the final exposure. To use this feature, change the following |
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75 | preference in Hole node (or Subsquare node in MSI-Raster). |
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78 | It is important to know that in order to check whether the precision is reached, image |
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79 | is taken at the preset at which the target is selected on (in this case, sq preset), so the |
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80 | dose should be kept at minimal. On our microscope 0.2 micron precision can be obtained |
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81 | within 2 to 3 moves. |
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84 | Hole/Settings/Image Acquisition> |
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87 | * Mover=navigator |
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90 | * Navigator Target Tolerance = 2 e-7 m (or whatever tolerance you like): This sets the |
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91 | goal for multiple movement |
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94 | * Navigator Acceptable Tolerance = 1 e-6 m (or whatever tolerance you like): If |
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95 | further movement causes an increase rather than a decrease of targeting accuracy, this |
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96 | value determines whether the target is aborted or not. |
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99 | * Final Image Shift = No |
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104 | Navigation/Settings/Error Checking and Correction> |
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107 | * Preset cycle after each move = yes if your sq preset is in LM mode and you don't |
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108 | mind wait a little longer; = no if you don't have hysteresis problem staying in sq |
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109 | preset for the unknown amount of time during the iterative move. |
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117 | h2. Minimize the use of image shift for the final exposure (Approach 2) |
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121 | A different approach is being developed to minimize image shift while maintaining final |
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122 | targeting accuracy-A combination of stage movement and image shift. This approach can only |
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123 | be used in limited cases such as targets selected for the tomography node or exposure node, |
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124 | and is only experimental in the latter case. |
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127 | Tomography or Exposure/Settings/Image Acquisition> |
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130 | * Move Type = modeled stage position |
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133 | * Mover=navigator |
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136 | * Navigator Target Tolerance = 1 e-7 m (or whatever tolerance you like) |
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139 | * Navigator Acceptable Tolerance = 1 e-6 m (or whatever tolerance you like) |
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142 | * Final Image Shift = Yes |
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150 | h2. Optimize autofocusing sequence |
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154 | The focus sequence in Focus and Z Focus nodes can and should be optimize for specific |
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155 | cases. The activated sequence in the default setting is good for a flat holey grid and is |
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156 | meant for high resolution imaging at 50k x or higher. If accurate defocus is not important, |
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157 | focusing once per grid square may be sufficient, for which all focus sequence in Focus node |
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158 | can be deactivated and the same autofocus step can be added to Z Focus node instead. |
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161 | There are two methods to determine the defocus automatically : Stage tilt (Equivalent to |
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162 | stage wobbling) and Beam tilt. There are also two possible ways for correcting the defocus |
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163 | measured: Defocus (Equivalent to turning the focusing knob on the scope and reset the |
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164 | defocus) and Stage Z (Moving the stage to the zero defocus height). |
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167 | The following observations at NRAMM may help you determine what is the best to |
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168 | use |
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171 | * Both defocus determination method requires calculation correlation between two |
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172 | images. Therefore, the magnification and the location of the autofocusing should include |
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173 | area with contrast. |
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176 | * The higher the magnification, the more accurate the defocus determination but the |
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177 | smaller the range of defocus the defocus determination can handle. |
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180 | * Beam Tilt is more reproducible and preferred method to determing defocus in HM |
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181 | mode. |
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184 | * Stage Tilt (Wobbling) is the preferred method to determine defocus in LM |
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185 | mode. |
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190 | MSI-Raster Chapter contains an example of an <link linkend="MSI-R_auto_focus" |
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191 | >alternative Z Focus node focus sequence</link> for grid that show little contrast at |
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192 | medium magnifications. |
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193 | 2 | Amber Herold | |
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196 | ______ |
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198 | [[Initial MSI application preferences|< Initial MSI application preferences]] | [[MSI Quick-start|MSI Quick-start >]] |
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200 | ______ |