Pixel Size Calibration » History » Version 3
Amber Herold, 06/23/2010 12:44 PM
| 1 | 1 | Amber Herold | h1. Pixel Size Calibration |
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| 4 | 3 | Amber Herold | Pixel Size Calibration allows entry and simple extrapolation of pixel size values for various magnifications. The entry value should be calculated in (m/pixel). Enter pixel size for all the magnifications that will be used. Extrapolation can be used to enter the pixel sizes for magnifications that have not been calibrated at the microscope with a standard specimen, such as catalase crystals. |
| 5 | 1 | Amber Herold | |
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| 8 | h2. Enter a known pixel size |
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| 14 | * Leginon/Pixel Size/Toolbar> Click the Calibrate button !http://emg.nysbc.org/software/leginon/images/icons/play.png!. |
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| 17 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration> Highlight the desired magnification and click Edit. |
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| 20 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration/Edit Pixel Size> Enter the pixel size in m/pixel. |
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| 23 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration/Edit Pixel Size> Enter a comment to describe how this pixel size was determined. |
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| 26 | * Leginon/Pixel Size/Pixel Size Calibration/Edit Pixel Size> Click Save |
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| 29 | * Leginon/Pixel Size/Pixel Size Calibration> Click Done |
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| 33 | h2. Extrapolate a pixel size |
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| 38 | * Leginon/Pixel Size/Toolbar> Click the Calibrate button !http://emg.nysbc.org/software/leginon/images/icons/play.png!. |
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| 41 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration> Highlight 1 or more magnifications to extrapolate the new mag. pixel size from. |
| 42 | 1 | Amber Herold | |
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| 44 | * Leginon/Pixel Size/Pixel Size Calibration> Click Extrapolate |
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| 47 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration/Extrapolate Pixel Size> Highlight the desired magnification to extrapolate the pixel size for. |
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| 50 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration/Extrapolate Pixel Size> Enter a comment to describe how the new size was determined. |
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| 53 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Calibration/Extrapolate Pixel Size> Click Extrapolate and Save |
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| 56 | * Leginon/Pixel Size/Pixel Size Calibration> Click Done |
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| 60 | 3 | Amber Herold | Pixel Calibration Need for the Example MSI: |
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| 62 | |_.Preset|_.magnification| |
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| 63 | |gr|120| |
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| 64 | |sq|550| |
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| 65 | |hl|5000| |
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| 66 | |fc,fa,en,ef|50000| |
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| 71 | 3 | Amber Herold | h2. Acquire images of a standard crystal and calculate the pixel size from distance between the diffraction spots |
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| 74 | 3 | Amber Herold | * TEM>Insert the standard crystal such as catalase, aligned to eucentric height, and centerred on a well ordered area at 0.5-2 um. defocus. |
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| 77 | * Leginon/Pixel Size/Toolbar> Click the Acquire button !http://emg.nysbc.org/software/leginon/images/icons/acquire.png!. The power spectrum of the image will be displayed. |
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| 80 | * Leginon/Pixel Size/Toolbar> Click on the Measure button !http://emg.nysbc.org/software/leginon/images/icons/ruler.png! if several orders of diffractions can be seen. |
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| 83 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Measurement> Enter the lattice parameters of the crystal. The default is that of catalase. |
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| 86 | 3 | Amber Herold | * Leginon/Pixel Size/Panel> Use the ruler tool to measure the distance of two well-separated diffraction spots. |
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| 89 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Measurement> Enter the Miller indices of the spots and the distance measured in pixels on the spectrum. |
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| 92 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Measurement> Click on "Calculate Pixel Size". The result is shown below. |
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| 95 | 3 | Amber Herold | * repeat 5-7 on other pairs of spots or repeat the measurement. Alternatively, go to another crystal and repeat 2. (There is no need to close the settings window. The values calculate will stay until the TEM magnification of the image has changed. |
| 96 | 1 | Amber Herold | |
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| 98 | 3 | Amber Herold | * Leginon/Pixel Size/Pixel Size Measurement> Select from the pixel size calculated so far by highlighting them for averaging and save to database with a click on "Save Averaged Pixel Size From Selected". |
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| 101 | * Leginon/Pixel Size/Pixel Size Measurement> Click Done |
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| 107 | ______ |
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| 109 | [[Calibration without presets|< Calibration without presets]] | [[Bright and Dark reference images|Bright and Dark reference images >]] |
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| 111 | ______ |