SkyScan 1275

How to set up a scan?

Method note
MCT-098

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Overview workflow

1. Sample preparation and mounting on a sample holder

2. Sample positioning in the SkyScan 1275

i. Fix the sample holder on the sample stage

ii. Close the door
iii. Switch on the x-ray source
iv. Position region of interest sample in the camera field of view
v. Set the pixel size
3. Optimize transmission through the sample

i. Set the correct filter

ii. Adjust voltage
4. Update the flat-field correction

i. Remove the sample

ii. Inactivate the flat-field correction in the ‘scanner setup’ menu
iii. Adjust the exposure time and current in the ‘scanner setup’ menu
iv. Update the flat-field correction
v. Activate flat-field again in the ‘scanner setup’ menu
5. Reposition the sample (cfr step 2)

6. Evaluate image

7. Set acquisition settings in ‘acquisition’ menu

i. Rotation step
ii. Frame averaging
iii. Random movement
iv. 180/360° scan
v. Partial width
8. Start scan

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Workflow in detail

1. Sample preparation and mounting on a sample holder

i. Different samples require different preparation/mounting techniques:

o Scan dry or wet?

o Scan at room temperature or keep the sample cool/frozen?
o Scan in air, water, ethanol…?
o Prevent movement of the sample!
o Mount using polystyrene foam, double sided tape, wax, …?
o …
ii. If possible resize your sample but make sure the size is still large enough to
give representable data.

iii. The ideal shape of an object is a cylinder.

iv. Position the sample in the center of rotation to avoid misalignment artifacts
and to allow for maximal zooming.

1. Sample positioning in the SkyScan 1275

i. Fix the sample holder on the sample stage.

ii. Close the door.
iii. Switch on the x-ray source.
iv. If possible make the sample rotate completely inside the field of view:
o The parts of the sample that rotate outside the field of view can’t be
reconstructed due to missing data.
v. Define a pixel size:
o The pixel size is defined by a combination of the sample position
(‘zoom’) and the camera binning mode.
o Camera binning will increase the signal to noise ratio.

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2. Optimize transmission through the sample

One key aspect of microCT imaging is partial absorption of X-rays in the sample. Too
much transmission will reduce the contrast between different densities, while a low
transmission will increase the noise level in the images. The transmission should be
evaluated by inspecting the profile line in the acquisition software (activated by a
single right click on the projection image). Adjust filter and voltage settings to get a
minimum transmission between 10 and 50% (aim for 30% if possible). Be mindful to
take in to account that the attenuation of samples can be different at different angular
positions and that enough transmission is needed from all angles.

i. Set the correct filter

o A filter absorbs X-rays below a certain energy level and thus increases
the average energy of the X-ray beam. As a result, applying a (denser)
filter will increase the transmission through the sample and reduce
beam hardening artifacts.
o 2 different filters are standard available with the SkyScan 1275 system
resulting in 3 filter options (no filter, 1mm Al and 1mm Cu filter).
Additional filters can be custom made. The filters have to be inserted
manually or can be swapped by moving the slider inside the sample
chamber (from serial number 9 onwards).
o After changing the filter, select the right configuration corresponding
to the installed filter in the actions < configuration < load menu.
ii. Adjust voltage

o Changing the applied voltage will change the average energy of the X-
ray spectrum. Increasing (decreasing) the applied voltage will increase
(decrease) the average energy of the X-ray beam and thus increase
(decrease) the transmission through the sample.
o The source voltage of the SkyScan 1275 system is limited to 100kV
(10W).

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3. Update the flat-field correction

The flat-field correction is a background correction that will make sure the background
is always represented in the same grey level and will level out interpixel intensity
variations that would otherwise result in ring artifacts. As such the flat-field correction
is essential when a comparison is needed between multiple scans generated on
different time points.

One should always update the flat-field correction upon changes in the following
settings: filter, voltage, current, power of the source and camera binning mode.

iii. Remove the sample from the field of view (either lower the sample below the
camera field of view or take it out of the micro-CT).
iv. Inactivate the flat-field correction by double clicking in the top left corner of
the field of view (indicated by ‘ff’ or ‘flat-field correction off’).
v. Adjust the exposure time and current in the ‘scanning settings’ menu to get
an average transmission in air between 40 and 50% without flat-field
correction (aim for 45%). The ‘scanning settings’ menu is activated by pressing
the “Ctrl+Alt+Shift+S” key combination.
vi. In case the voltage/current are changed, update the numbers in the ‘scanning
settings’ window accordingly.
vii. Activate flat-field again by double clicking in the top left corner of the field of
view (indicated by ‘ff’ or ‘flat-field correction off’).
viii. Update the flat-field correction in the ‘update flat-field references’ menu.
Note that in this menu one has the option to define the exposure time
automatically. In case this option is ticked, steps ii.-v. can be skipped. In
addition, the sample stage is moved completely down during this procedure,
which makes that if the sample is small enough it will not be in the field of
view anymore and also step i. can be skipped.

Note that this flat-field correction can be saved and re-used for similar samples. We
recommend updating the flat-field correction at the start of the day, and when the
above described settings are changed.

4. Reposition the sample

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Cfr. step 1 and 2.

5. Evaluate image

Evaluate the transmission through the sample (cfr step 3). If the transmission is fine,
proceed to step 7. If the transmission is too low or too high, repeat steps 3 and 4.

6. Set acquisition settings in ‘acquisition’ menu

ix. Rotation step

o A smaller rotation step will increase the signal to noise ratio.

Preferentially lower the rotation step (instead of increasing frame
averaging) for low dense samples when the signal to noise ratio is too
low.
o Guidelines for choosing the rotation step
Rotation step
Binning

≤ 0.5°
1K (std. resolution) mode

≤ 0.3°
2K (high resolution) mode

x. Frame averaging
o A higher number for frame averaging will increase the signal to noise
ratio. Preferentially increase the frame averaging (instead of
decreasing the rotation step) for high dense samples when the signal
to noise ratio is too low.
o Guidelines for choosing the frame averaging

Binning Frames

1K (std. resolution) mode

1-4

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1-4 (low dense materials)

2K (high resolution) mode 4-8 (high dense materials)

xi. Random movement

o Can be activated to reduce ring artifacts.
o Don’t use random movement with unstable samples.
xii. 180/360° scan
o 360° scans should be selected for samples consisting of a combination
of high (radio-)dense materials inside low (radio-) dense materials to
avoid depletion artifacts.
xiii. Partial width
o By activating the partial width, the width of the projection imaged is
cropped. Make sure the sample rotates within the new field of view
(boundaries) at all angles. By activating the partial width, the rotation
step can be slightly increased.

7. Start scan

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