Skyscan 1072 Micro CT:

Image Acquisition User Guide

System initialisation:
a. Determine the state the system is in:
i. Turn on both monitors
ii. Turn the green power switch on the front of the Skyscan
1072 unit on
iii. Open the Skyscan MicroCT software
• If software is not open on screen turn on the CPU and
wait for Windows XP to open.
• At the password screen type in Skyscan

b. Logon to the EMU server:

i. Click blue button on the switching box
ii. Click on Manual Login at EMU Client software
iii. Enter your user name and password
iv. If you have more than one account number you may need
to select the appropriate account number to be charged.
v. Delete previous sessions acquired images
vi. Click blue button to return to Skyscan MicroCT software

c. Load a baseline system configuration:

i. Go to the File menu at the top of the screen and select
System Configuration then click Load
ii. Go to the C drive, open the Results folder and double
click on Configuration Files
iii. Double click on the desired kV and uA setting (80kV &
100uA is full power. Specimens lacking density eg.
polyurethane foams, may require reduced voltage and
current)

d. Setup the source:

i. If the source has not been used in the previous 8 hours it
will need to power up slowly, this process is referred to as
“aging”.
 ii. To determine if the source needs to be aged, click to
turn the source on.
• If the source immediately ramps up to 80kv and
104uA, it is ready for use.
• If a dialog box opens indicating that aging has begun,
the software will prevent further use until the aging
process is complete. Remaining time is indicated
within the dialog box.

Acquiring images:
e. Load the sample:
i. The three specimen mounts are kept in the small box in the
top drawer. The specimen size will determine the most
appropriate mount to use
ii. Take care to attach the specimen as near to the center of
the mount and as vertically as possible

iii. Click to open the door of unit

iv. Lock the specimen holder in position taking care to not exert
downward or sideways pressure on the stage

v. Click to close door of Skyscan unit

vi. Click to turn on x-ray source, wait whilst voltage

increases

vii. Click to obtain a shadow image

f. Set the specimen height:

i. Click and type in a positive number to raise or a

negative number to lower the height of the specimen

ii. Click to obtain an updated image

g. Set the magnification:

PLEASE NOTE: The absolute maximum magnification in 150x. If your

intend using magnifications higher than 70x, you must turn on the internal

camera by clicking and watching carefully as you increase the

magnification to make sure that you do not run into the source. Please
seek advice if you are unsure.
 i. If the required magnification has been determined during

previous sessions, click , type in the magnification then

click to obtain an updated image

ii. To increase magnification stepwise, click , then click

to obtain an updated image

iii. To decrease magnification click , then click to

obtain an updated image

h. Check if the aluminium filter is required:

i. Click to overlay an image profile onto the shadow

image
ii. If the green profile line shows a sharp drop as the x-rays
enter your specimen, or if the minimum value indicated at
the top right of the screen is < 10%, the aluminium filter
should be used.
iii. To insert the aluminium filter, open the Control menu at the
top of the screen, click on Filters, select Al filter then click

OK, then click to obtain an updated image

i. Check the acquisition parameters:

i. Click on to enter acquisition parameters.

ii. For low to medium magnifications reasonable resolutions are
obtained by rotating specimens through 180º at steps of
0.9º.
iii. For high magnifications where increased resolution is
required, specimens may be rotated through 360º and/or
reduced rotation steps of 0.45º or 0.23º may be used.
iv. Exposures for acquisitions without the aluminium filter are
normally 1.8 sec, exposures with the aluminium filter in
place should default to 5.7 sec. These settings can be
changed to suit unusual specimens. Please seek advice if
uncertain.

j. Check specimen centration;

i. If the specimen is not perfectly centred it may swing out of
the field of view as the rotation angle changes. To ensure
 this will not happen it is a good idea to check a number of
rotation angles prior to image acquisition.

ii. Click and set rotation angle to 30º, click ok then click

to obtain an updated image

iii. Click again, click Next Step then click to obtain

an updated image
iv. Repeat this process through entire rotation angle ie. 180º or
360º.

v. Finally, click and set rotation angle back to 0º, then

click to obtain an updated image.

k. Set the pathway for saving your acquired images

i. Open the File menu at the top of the screen
ii. Click on Data Directories and select Browse
iii. Select the M drive Results directory (the M drive can be
VERY slow to respond, please be patient, repeated mouse
clicking will result in the software hanging)
iv. Create a new folder and name it (with a name that will be
recognizable to staff if they ever need to contact you prior to
deleting files), then click OK

l. Begin the acquisition;

i. Open the Acquisition and Reconstruction menu at the
top of the screen.
ii. Click Acquire for Cone and Spiral.
iii. Type in a name for the data set, then click OK.
iv. The acquisition will begin and after acquiring the first couple
of images the software will display the time remaining for
completion of imaging.

m. Ending your session:

i. Close the Skyscan MicroCT software
ii. A message will appear asking you to wait while the Skyscan
shuts down, when the dialog box closes, turn off the
MicroCT at the green power switch
iii. Click blue button on the switching box
iv. At the EMU Client software screen click Manual Logout
then click No Consumables Used
 Skyscan 1072 Micro CT:

Reconstruction
User Guide

1. In order to undertake a reconstruction, the two associated alignment

bmp. Files, and the txt. file written during acquisition, must be in the
same folder as the tif. files. If the dataset has been written to CD or DVD
it must be written back to the hard drive for the reconstruction process.

2. To start the software double click on the NRecon icon

3. Minimise the NRecon Server(local) dialog box

4. Select any tiff file within the dataset you wish to reconstruct, click Open

5. Open the Parameters screen

Turn Smoothing off

Tick Post Alignment

Tick if object extends

beyond field of view

Set Ring artifact

reduction to ~ 8
6. Click on Reconstruction tab

Click Fine tuning

Select Post-alignment
Select ~ 5 trials
Set the parameter step to 2 or 3
Click Start and OK

7. Use the ▲ and ▼ in the top databar to move through the 5 trial
images and note the value of the best aligned image

8. Return to the Parameters tab and plug in this post-alignment value

9. Return to the Reconstruction tab and repeat trials using a parameter step
of 0.5 or 1

10. Determine the most appropriate post-alignment value then return to the
Parameters tab and plug in this value

11. You can return to the Reconstruction tab and repeat fine tuning for both
ring artifact and beam hardening if you think your image is affected by
either of these imaging artifacts

• Ring artifacts can be reduced by utilizing random movement during

the acquisition step
• Beam hardening is recognisable as extra density at the border of
the specimen. The correction reduces the signal to noise ratio of
the image so should only be used when necessary
12. Go to Output options tab

Try clicking Auto

To further refine the image you can

drag the boundary lines left or right
to remove the background and set
for the best image contrast

Tick to turn scales on or unclick to

turn off

13. Return to Reconstruction tab, set top and bottom lines, select step 1 or 2
depending on resolution required then click Start.