Leginon

h1. Pixel Size Calibration

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.

h2.  Enter a known pixel size

*  Leginon/Pixel Size/Toolbar> Click the Calibrate button !http://emg.nysbc.org/software/leginon/images/icons/play.png!.

*  Leginon/Pixel Size/Pixel Size Calibration> Highlight the desired magnification

and click Edit.

*  Leginon/Pixel Size/Pixel Size Calibration/Edit Pixel Size> Enter the pixel

size in m/pixel.

*  Leginon/Pixel Size/Pixel Size Calibration/Edit Pixel Size> Enter a comment to

describe how this pixel size was determined.

*  Leginon/Pixel Size/Pixel Size Calibration/Edit Pixel Size> Click Save

*  Leginon/Pixel Size/Pixel Size Calibration> Click Done

h2.  Extrapolate a pixel size

*  Leginon/Pixel Size/Toolbar> Click the Calibrate button !http://emg.nysbc.org/software/leginon/images/icons/play.png!.

*  Leginon/Pixel Size/Pixel Size Calibration> Highlight 1 or more magnifications

to extrapolate the new mag. pixel size from.

*  Leginon/Pixel Size/Pixel Size Calibration> Click Extrapolate

*  Leginon/Pixel Size/Pixel Size Calibration/Extrapolate Pixel Size> Highlight

the desired magnification to extrapolate the pixel size for.

*  Leginon/Pixel Size/Pixel Size Calibration/Extrapolate Pixel Size> Enter a

comment to describe how the new size was determined.

*  Leginon/Pixel Size/Pixel Size Calibration/Extrapolate Pixel Size> Click

Extrapolate and Save

*  Leginon/Pixel Size/Pixel Size Calibration> Click Done

|_.Preset|_.magnification|

|gr|120|

|sq|550|

|hl|5000|

|fc,fa,en,ef|50000|

h2.  Acquire images of a standard crystal and calculate the pixel size from distance

between the diffraction spots

*  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.

*  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.

*  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.

*  Leginon/Pixel Size/Pixel Size Measurement> Enter the lattice parameters of the

crystal. The default is that of catalase.

*  Leginon/Pixel Size/Panel> Use the ruler tool to measure the distance of two

well-separated diffraction spots.

*  Leginon/Pixel Size/Pixel Size Measurement> Enter the Miller indices of the

spots and the distance measured in pixels on the spectrum.

*  Leginon/Pixel Size/Pixel Size Measurement> Click on "Calculate Pixel Size".

The result is shown below.

*  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.

*  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".

*  Leginon/Pixel Size/Pixel Size Measurement> Click Done