Leginon

h1. 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>

h2. 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.

h2. 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.