Troubles with Tomography¶

• <link linkend="tomo_intensity">Image appears oversaturated with overflow to negative
  values</link>

• <link linkend="tomo_intensity">Images acquired in tomography have different
  intensity range from that acquired from other nodes with the same preset and exposure
  time.</link>

• <link linkend="tomo_large_move">Images move by a large amount between
  tilts.</link>

Unusual intensity range in the tomography image¶

Two possible reasons:

• The exposure time has been modified by the tomography node to spread the total dose
  to all images in the tomogram.

Solution: Reduce the total dose or reduce preset beam intensity. You can find the
real exposure time from the log panel of the tomography node or through the information
page of the image in the web image viewers.

• The image intensity of images collected by the Tomography class node does not have
  the same meaning as in other images in Leginoon. The flat-field corrected intensity
  values are multiplied by 10 before the image is saved and displayed as MRC image as
  signed 16-bit integer. Therefore any original CCD count of 3276.8 or larger will
  overflow. All other images in Leginon are saved without manipulation as float.
  Therefore, the images obtained through tomography node and another acquisition nodes
  will appear differently in the both the web image viewer and within Leginon.

Solution: Reduce the total dose.

Find out what exposure time corresponds to the fractionated dose from your tilt
angle step and range and total dose and take an image at tomo preset with such an
exposure in Navigation node. You will need to reduce the total dose if a good fraction
of the counts are larger than 3200 even though it would not appear to be saturated in
the float scale without the 10x factor.

Large movement between tilted images¶

Find out how smooth the movement is by comparing the images.

If transition is smooth and linear:

• Magnification too high

Solution: Lower the magnification or perform <link linkend="Tomo_low_mag_fitting"

low-magnification rough model fitting</link>.

• Optical axis offset model is too different from the initial guess for the
  non-linear least-square fitting.

Solution: Perform <link linkend="Tomo_low_mag_fitting">low-magnification rough model
fitting</link>.

If transition is not smooth nor linear:

• Goniometer behavior unpredictable

Solution: Service the goniometer.