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.

Enter a known pixel size¶

• Leginon/Pixel Size/Toolbar> Click the Calibrate button .

• 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

Extrapolate a pixel size¶

• Leginon/Pixel Size/Toolbar> Click the Calibrate button .

• 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

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 . The power spectrum of the image will be displayed.

• Leginon/Pixel Size/Toolbar> Click on the Measure button 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