Troubles with Calibrations - Troubleshooting¶

• <link linkend="pixeloff">Available magnification from pixal size calibration is
  different from that said on the scope (See Installation Trouble Shoot)</link>

• <link linkend="tr_matrx">Matrix calibration fails due to large pixel error</link>

• <link linkend="tr_matrx_beam">Beam shift calibration fails</link>

Matrix calibration fails¶

• Display correlation map in the matrix calibration node during the calibration can help
  identify the source of the failure.

Observations and Why:

• The image appears normal with most pixels in medium gray but the correlation
  images show peaks moving randomly during the calibration - No image contrast for
  correlation due to no object in view, at Gaussian focus, or bad image intensity either
  too low or too high

• One or both images appear white or black and the correlation images show peaks
  moving randomly during the calibration - Artifacts in the images such as spikes not
  corrected by the corrector node that fool the correlation procedure to consider the
  image is never moved or moved a lot.

• The correlation image give consistent multiple peaks or bars - Bright/Dark
  correction images are not created.

• Both images and correlation peaks behave normally, i.e., there is one correlation
  peak and its location corresponds well to the movement seen in the images and the set
  shift fraction - Pixel calibration may be off.

Solutions:

• No object in view

• EM> move the specimen holder to an area with an isotropic feature well
  centered within the CCD.

• No constrast

• Leginon/Presets Manager> Adjust defocus, and/or exposure time of the preset
  that the calibraion uses and send the new values to scope.

• Spikes in the image

• Leginon/Presets Manager> Reduce exposure time? Might reduce number of
  random event

• Leginon/Correction/Settings> Select the camera configuration of the problem
  image.

• Leginon/Correction/Settings> Reduce the despike threshold and/or increase
  the neighborhood size. The aim is to allow spikes with lower values and larger
  footprint, respectively, to be removed.

• No bright/dark images

• Leginon/Correction/Settings> Select the camera configuration of the problem
  image.

• Leginon/Correction> Acquire bright/dark images

• Pixel Calibration is off

• Leginon/Matrix/Settings> Increase Tolerance to allow the error to pass
  through.

• Leginon/Matrix> redo the calibration. If it is successful, test the
  calibration in Navigation

• If the calibration test is satisfactory, the result is acceptable. Pixel
  calibration can be off since it is only an estimate for lower mags. You may want
  to modify the pixel calibration entry according to the calculated value in matrix
  calibration. Leaving the value as is will not cause major problem.

Beam shift matrix calibration fails¶

• Other than the <link linkend="tr_matrx">failures common for all matrix
  calibraion</link>, there are some additional reasons for beam shift calibration to
  fail.

Observations and Why:

• The images shows not just a circle of the beam but a treak - The beam is too
  intense that the CCD picks up the movement of the beam when the beam shutter is opened
  and closed.

• The second images shows a shadow of the first- The CCD is saturated from the first
  image acquisition.

• Not the whole image moves during the beam shift - This calibration have to see
  only the beam not grid bars or objects on the grid . Neither of the latter will move
  when the beam is shifted and therefore will show as false peak in the correlation
  image.

• Part of the beam moves out of the view during beam shift - The applied shift or
  the beam too large.

Solutions:

• Intense beam, saturated CCD

• EM> reduce the intensity by a change in spot size.

• Leginon> reduce the binning so that the exposure time can be increased
  without saturating the camera. The longer exposure also reduces the relative
  contribution of the shutter effect.

• Unmoved object

• EM> move to an empty square.

• EM> If not possible to exclude the grid bars in the empty square at low
  magnifications, pull out the holder by about 3 cm (1 inch) and park it with a
  spacer during the calibration.

• Beam shift too large

• Leginon/Matrix/Settings> Reduce shift fraction.

• Beam too large

• EM> Reduce the beam size.

• Leginon/Matrix> Acquire test images and adjust exposure time, beam spot
  size etc. to match.