Image Beam Compensation Calibration » History » Version 1
Anchi Cheng, 07/27/2015 06:50 PM
1 | 1 | Anchi Cheng | h1. Image Beam Compensation Calibration (Required by JEM microscopes) |
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3 | h1. DO NOT GO THROUGH THIS CALIBRATION ON FEI SCOPES. DO [Beam Shift matrix calibration]] instead. |
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5 | This calibration is used to estimate the beam shift required to bring the beam back to the center when an image shift is applied to reach a target. It is saved as beam shift matrix and is only relevant to JEM microscopes. Such compensation is applied by microscope software with FEI scopes. |
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7 | # Leginon/Presets Manager> Select a preset for the calibration and send its |
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8 | parameter to the microscope. Matrix calibration depends on the instruments, i.e., the scope and camera used, magnification and |
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9 | microscope high tension. Therefore, only one preset per combination needs to be |
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10 | calibrated. |
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11 | # Scope> Lower the main screen. This calibration does not actually acquire digital camera images. |
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12 | # Scope> contract the beam sufficiently so that the center of the beam can be located easily on the main screen. |
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13 | # Leginon/NodeSelector> select "Image Beam Comp" node. |
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14 | # Leginon/Image Beam Comp/Toolbar> open "settings" window by clicking the icon to change the amount of image shift applied during the calibration. Click "OK" to save the settings and close the window when done. |
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15 | # Leginon/Image Beam Comp/Toolbar> left-click "Calibrate" to open the calibration dialog. |
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16 | # Leginon/Image Beam Comp/Calibrate> Follow the instruction for each step. Left-click Done when you have perform what it asks you to do at each step. |
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17 | # Leginon/Image Beam Comp/Calibrate> Click OK when all steps are completed and satisfied to save the calibration. Click Cancel otherwise. |
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19 | Testing: |
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21 | # Leginon/Presets Manager> Select the preset sent above for the calibration and send its parameters to microscope and camera. |
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22 | # Use Navigation node to [[Checking Matrix and Modeled Stage Position Calibration|check the result of the calibration]]. Select "Image Beam Shift" as the move type. Feature on the image should be shifted but the beam remains centered. |
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24 | *Beam Shift Calibration Need for the Example MSI:* |
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26 | |<filename>Preset</filename>|<filename>magnification</filename>| |
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27 | |fc,fa,en,ef|50000| |
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29 | ______ |
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31 | [[Image Shift matrix calibration|< Image Shift matrix calibration]] | [[Stage Position matrix calibration|Stage Position matrix calibration >]] |
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33 | ______ |