Leginon

h1. 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>

h2. 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.

h2. 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.