1278 UserManual

SkyScan-1278 User Manual V1.
0 10/2015 0
In-Vivo X-Ray Microtomograph
SkyScan 1278
User Manual
© Bruker microCT 2015
Designed and manufactured by Bruker microCT in Belgium
Kartuizersweg 3B
2550 Kontich
Belgium
SkyScan-1278 User Manual V1.0 10/2015 1

TABLE OF CONTENTS
1 INTRODUCTION IN X-RAY MICROTOMOGRAPHY .......................................... 6

1.1 Introduction .................................................................................................. 6
1.2 Basic principles of microtomography ............................................................ 7
1.3 In-vivo time-resolve (4D) microtomography ................................................ 10
2 SKYSCAN-1278 SYSTEM OVERVIEW ............................................................ 12

2.1 Specifications ............................................................................................. 13
2.1.1 General ............................................................................................... 13
2.1.2 X-Ray Source ...................................................................................... 13
2.1.3 X-ray detector:..................................................................................... 13
2.1.4 Animal handling system ...................................................................... 13
2.1.5 Integrated physiological monitoring ..................................................... 13
2.2 Supplied software ....................................................................................... 13
2.2.1 Scanner control and data acquisition software .................................... 13
2.2.2 Physiological monitoring software “SkyscanVisual” ............................ 14
2.2.3 Reconstruction software “NRecon” with GPU acceleration ................. 14
2.2.4 Software for time –resolved (4D) reconstruction “TSort” ..................... 14
2.2.5 Visualization software “DataViewer” .................................................... 14
2.2.6 Format Converter “TConv” and “DICOM converter” ............................ 15
2.2.7 2D/3D morphological analysis software “CTan” .................................. 15
2.2.8 Realistic visualization by surface rendering “CTvol” ............................ 15
2.2.9 Realistic volume rendering software “CTvox” ...................................... 16
2.2.10 Control and Reconstruction Workstation ............................................. 16
2.2.11 Physical: .............................................................................................. 16
2.3 Installation requirements ............................................................................ 17
3 INSTALLATION PROCEDURE ......................................................................... 18

3.1 Site requirements ....................................................................................... 18
3.2 Unpacking .................................................................................................. 19
3.3 Installation of the scanner .......................................................................... 22
3.4 Supplied toolkit ........................................................................................... 24
4 SCANNER’S CONSTRUCTION ........................................................................ 25

4.1 Main parts of the scanner ........................................................................... 25
4.2 Software components and dataflow between them .................................... 27
5 GETTING STARTED ......................................................................................... 29

5.1 Acquiring images and collecting datasets .................................................. 29
5.2 Reconstruction ........................................................................................... 33
5.3 Visualization of reconstructed results ......................................................... 34
5.4 Visualization by volume rendering .............................................................. 35
5.5 2D / 3D image analysis and surface rendering ........................................... 37
5.6 How to get help .......................................................................................... 39
6 TOUCHSCREEN FUNCTIONS ......................................................................... 41

7 PHYSIOLOGICAL MONITORING SUBSYSTEM .............................................. 42
7.1 Physiological monitoring electronics........................................................... 42
7.2 Physiological monitoring software .............................................................. 44
8 CONTROL PROGRAM FUNCTIONS................................................................ 47

8.1 General layout ............................................................................................ 47
8.2 Toolbar ....................................................................................................... 48
8.3 Status bar ................................................................................................... 50
8.4 Actions menu ............................................................................................. 51
8.4.1 X-Ray Start/Stop ................................................................................. 52
8.4.2 Grab Image ......................................................................................... 53
8.4.3 Snap Image ......................................................................................... 53
8.4.4 Open Image… ..................................................................................... 53
8.4.5 Save Image… ..................................................................................... 54
8.4.6 Delete Dataset .................................................................................... 54
8.4.7 Start Scanning..................................................................................... 55
8.4.8 Start Connected Scanning .................................................................. 57

8.4.9 Start Reconstruction ............................................................................ 58
8.4.10 Start Volume Rendering ...................................................................... 58
8.4.11 Start DataViewer ................................................................................. 58
8.4.12 Start 2D/3D Image Analysis ................................................................ 59
8.4.13 Exit ...................................................................................................... 59
8.5 Options Menu ............................................................................................. 60
8.5.1 Acquisition ........................................................................................... 61
8.5.2 Data Folder... ...................................................................................... 61
8.5.3 X-ray source… .................................................................................... 61
8.5.4 Filters .................................................................................................. 61
8.5.5 Visual Camera ON/OFF ...................................................................... 62
8.5.6 Dose Meter SHOW/HIDE .................................................................... 62
8.5.7 Preferences... ...................................................................................... 63
8.5.8 Configurations ..................................................................................... 64
8.5.9 View .................................................................................................... 64
8.5.10 Annotation ........................................................................................... 64
8.5.11 Update Current Flat-Field .................................................................... 65
8.5.12 Recover log-file from Encrypted Copy ................................................. 65
8.5.13 Scanner Settings… ............................................................................. 65
8.5.14 Scanning Modes... .............................................................................. 66
8.6 Help Menu .................................................................................................. 68
8.6.1 About SkyScan1278… ........................................................................ 68
9 4D (TIME-RESOLVED) ACQUISITION AND RECONSTRUCTION .................. 69

9.1 Time-resolved method................................................................................ 69
9.2 Sorting time-resolved data ......................................................................... 70
9.3 Data sorting process .................................................................................. 72
9.4 Reconstruction of time-resolved data ......................................................... 73
9.5 Visualization of time-resolved results ......................................................... 73
10 GLP (GOOD LABORATORY PRACTICE) MODULE ........................................ 74
10.1 Access rights .............................................................................................. 74
10.2 Installation .................................................................................................. 75
10.3 Adding New User ....................................................................................... 76
10.4 Managing user rights .................................................................................. 76
10.5 Required user management to run control software................................... 76
10.6 Deleting user account................................................................................. 76
10.7 Change password for the user account ...................................................... 76
10.8 Specify number of logon attempts .............................................................. 77
10.9 Uninstalling user management ................................................................... 77
11 SERVICE AND SUPPORT ................................................................................ 78

12 DOCUMENT VERSION..................................................................................... 79

1 INTRODUCTION IN X-RAY MICROTOMOGRAPHY
1.1 Introduction
Conventional optical or electron microscopy allows visualizing two-dimensional images of a specimen
surface or thin slices. However, in most cases a conclusion about original three-dimensional object
structures cannot be made on the base of two-dimensional information.
One can obtain the three-dimensional information of object structures by cutting them into very thin
slices, which can then be visualized in the light microscope and interpolate the two-dimensional
information into a three-dimensional structure model. This method however is not only very
cumbersome but also not very reliable since the object structure itself can be altered by the
preparation technique and the distance between the slices is usually too coarse to avoid loss of 3D
information.
An X-ray (radiography) system produces two-dimensional shadow images of complete internal three-
dimensional structures, but in a single two-dimensional shadow projection the depth information is
completely mixed. Only an X-ray tomography system allows us to visualize and measure complete
three-dimensional object structures without sample preparation or chemical fixation. Typically, the
spatial resolution of conventional medical CT-scanners is in the range of 1 - 2.5 mm, which
corresponds to 1 - 10 cubic mm voxel (volume element) size. Computerized X-ray microscopy and
microtomography now gives possibilities to improve the spatial resolution by seven to ten orders in
the volume terms. The system “SkyScan-1278” allows reaching a spatial resolution in the level of fifty
microns, which corresponding to near 1x10-4 cubic mm voxel size. As in the “macro” CT-scanners, the
internal structure can be reconstructed and analysed fully non-destructively.

1.2 Basic principles of microtomography
An X-ray shadow image represents a two-dimensional projection from a three-dimensional object. In
the simplest case, we can describe the X-ray illumination as parallel. In this approximation, each
point on the shadow image contains the integration of absorption information inside the three-
dimensional object along the path of the corresponding partial X-ray beam.
For parallel geometry one can divide the problem of three-dimensional reconstruction from two-
dimensional projections into the serial reconstruction of two-dimensional object slices from one-
dimensional shadow lines.
Let us show the possibility of this reconstruction on a simple example, an object with only one point
with significant absorption in an unknown place. In the one-dimensional shadow line a decreasing of
intensity of the shadow of absorption in the object area will be seen (see the next picture). Now we
can initialize in the computer memory an empty array of pixels (picture elements) corresponding to
possible object displacement. Of course, one must be sure that all parts of the reconstructed object
will be inside the field of view. Because we have the position of the shadow from the absorption
points of the object, we can mark on the area of reconstruction in the computer memory all possible
positions of absorption points inside the object as lines.
Now we can rotate our object and repeat this operation. In each new rotation position of the object,
we will add to the area of reconstruction the lines of possible object positions corresponding to the
position of the shadow. This operation is named "back-projection". After certain number of rotation
steps we can localize the position of the absorption point inside the area of reconstruction. As we
increase the number of shadow projections from different views, this localization becomes better
defined.

In the case of reconstruction from an infinite number of projections one can get an image with a
good definition of the absorption area position inside the initial object. At the same time a blur area
will accompany the point image because it is produced as a superposition of lines from all directions
Now that we know what image will be produced from the point object, we can ``pre-correct'' the
initial information from the absorption lines to make the resulting image correspond more closely to
the real object.
This correction named “convolution” adds some ``negative absorption'' outside the region of the
object shadow to compensate the positive blur in the back projection process which is shown in the
figure above.
The same algorithm can produce cross section images not only from a single point object but from
any real object. Each object can be represented as a large number of separate absorption voxels and
the linear absorption in any X-ray beam corresponds to the sum of all absorption from all voxels
inside this beam. In this way the two-dimensional cross sections of the object can be reconstructed
from the one-dimensional shadow lines in different views.
However, most laboratory X-ray sources are not able to generate parallel beams. In the real case,
one will use a point source which produces a cone X-ray beam encompassing the object.

For tomographical reconstruction the solution of this problem can be found by taking into account
the cone-beam geometry in the back-projection procedure. In the cone-beam geometry the rays
going through the front and the back of the object will not be projected on the same row of the
detector. The fastest slice to reconstruct will be the one corresponding to the optical axis because no
thickness information has to be used here.
In X-ray imaging, the shadow image contains information about the intensity reduction inside the
three-dimensional object. Because the X-ray absorption corresponds to an exponential law (Lambert-
Beer), the linear absorption information from the shadow image can be restored by taking the
logarithm. This is a non-linear operation, and a consequence of this is that any noise in small signal
areas can produce significant errors in reconstruction. To eliminate these errors, an averaging of
initial data can be used. On the other hand we can try to improve the signal to noise ratio in the
shadow images by optimizing the exposure time in order to obtain the most representative
information. A more effective way of noise reduction in the reconstruction process is special
selection of a correction or filter function for convolution before back projection. In the simplest case
(described above) the correction function produces two "negative absorption" reactions around any
signal or noise peak in the shadow line and this behavior becomes very dangerous for noisy initial
information. Special selection of a convolution function for correction with spectral limitation by a
"Hamming window" prevents noise from increasing during the reconstruction procedure. In X-ray
micro -tomography, information from a voxel with a very small physical size should be detected and
the right choice of parameters for noise reduction becomes very important.
During acquisition the object will rotate over 180 (or a little more for cone-beam geometry) or 360
degrees with a fixed rotation step. At each angular position a shadow (or transmission) image will be
acquired. The acquisition program will save all these projection images on the disk. The number of
files after this acquisition is dependent upon the rotation step selected and the total rotation which
is chosen. When the acquisition is finished the reconstruction can be started. The obtained shadow
angular projections will be used for the reconstruction of the virtual slices through the object. A raw
data cross section is then generated using the reconstruction algorithm. This raw data is not yet an
image; it is a matrix of numbers corresponding to absorption values in the reconstructed cross
section. The size of the reconstructed array NxN is defined by the number of pixels in the lines of the
angular projection images N. The reconstruction results can be saved directly (typically - by
conversion to a 16bit image) or after interactive selection by the operator of a density window, with
subsequent conversion to 8bit or 16bit images. During selection of the density window, minimum
and maximum values are selected. All values between these will be displayed as half tone image.
Depending on the choice of the user, all attenuation values below the minimum will be black while

everything above the maximum will then be displayed as white. The reconstructed array will be
shown as a half-tone image of the cross section with linear conversion to gray-scale inside the
selected density interval.
1.3 In-vivo time-resolve (4D) microtomography

The SkyScan1278 includes integrated physiological monitoring subsystem, which allows saving time
marks of animals’ physiological processes, such as heartbeat, breathing, etc. and using this
information to create time-resolve 4D reconstructed results. The physiological monitoring subsystem
contains a color camera with real-time body movement detection software, an ECG electrodes and
sensitive amplifier to reveal cardio activity and an airflow sensor for direct breathing detection. The
information from all sensors digitized and sends to control computer where operator can select
thresholds for generating time marks of physiological processes.
During image acquisition, the scanner is acquiring number of images with short exposure in every
angular position and saving exact time mark for every image. After the scanning, acquired images can
be sorted according to time marks saved by physiological monitoring subsystem.
Following picture shows example with acquisition of 10 images in every angular position:
Every physiological cycle, for example – heartbeat interval, divided by selected number of time bins,
four in the shown example, named A, B, C and D. All images with acquisition time marks inside time
bin A will go to the first set or projections A0, A1, ...; all images with time marks inside time bin B will
go to the second set or projections B0, B1, ... and so on. All four sets of angular projections are
reconstructed separately; everyone will create sharp reconstructed results without motion blurring
because they are reconstructed from the images taken in relatively short time window inside
physiological cycle. All four reconstructed results can be visualized together with possibility to scroll

in space XYZ and in time T by switching from one set of results to another. This allows seeing
dynamics of working heart by 4-dimensional or time-resolve reconstruction.
Because all images and time marks from all physiological processes are saved after a single scan, we
can sort the images again using another physiological information, for example – respiratory cycles.
After such new sorting of the data, reconstructed results will allow to see dynamics of breathing in
the same animal without rescanning and applying additional dose to the animal.

2 SKYSCAN-1278 SYSTEM OVERVIEW
The in-vivo X-ray Microtomograph SkyScan-1278 is a desk-top laboratory system with possibility for
imaging and 3D reconstruction of small laboratory animals, such as mice and rats, as well as tissue
and bone samples and samples or other materials. It consists of the combination of Micro-CT system
and a computer with system control software, reconstruction and application software. This system
allows reconstructing non-invasively any cross-section through the animal body with possibilities to
convert the reconstructed dataset into a realistic 3D-image and calculate internal morphological
parameters. The instrument contains a micro-focus X-ray tube with high-voltage power supply and a
two-dimensional X-ray detector on a rotating gantry, animal transport system with possibility to hold
one of supplied animal cassettes with different sizes and an associated electronics.

2.1 Specifications
2.1.1 General
 Scanning diameter – 80mm,
 Scanning length – 200mm (80mm in one scan),
 Nominal spatial resolution (pixel size) – <52um independent on scanning size,
 Shortest scanning time – 7.2 sec,
 Gantry opening – 150mm diameter,
 Scanning modes – step and shot or continuous gantry rotation,
 Scanner control – Windows graphical user interface or force-sensitive touch screen (can be
operated in gloves),
 Reconstructed volume (after a single scan) - 1536x1536x1550 pixels with possibility of 2x2
and 4x4 binning.
2.1.2 X-Ray Source

 Peak energy – 20…65kV, maximum power – 50W.
 Spot size – 50um (power and peak energy independent),
 Filters – motorized filter changer, 4 positions (no filter, Al 0.5mm, Al 1mm, dose reducing
filter),
2.1.3 X-ray detector:

 Type - Active pixel CMOS flat panel,
 Image format – 1944 x 1536 pixels,
 Dynamic range – typ. 66dB, 14 bit digitalization,
 Readout rate – more than 30 frames/s (4x4 binning), 8 frames/s full format.
2.1.4 Animal handling system

 Easy replicable mouse and rat cassettes (three cassettes with different sizes supplied),
 Connections – anesthetic gas, 3-way ECG connector, temperature sensor,
2.1.5 Integrated physiological monitoring

 Sensors – color camera, breathing sensor, ECG with carbon electrodes and wires,
temperature sensor,
 Video monitoring – 5Mp CMOS camera, white LED illumination, real time movement
detection from user-selected region of interest,
 Breathing and ECG signals – 12bit digitalization, computer controlled amplification,
 Sampling rate – up to 150/sec simultaneously color video, ECG, breathing, external gating
signal, temperature,
 Temperature stabilization by warm air, adjustable set point 20...40C,
 Recording exact time marks from any (or multiple) physiological processes for 4D time-
resolved tomography.
2.2 Supplied software
2.2.1 Scanner control and data acquisition software

The acquisition software provides source and camera control, shadow image acquisition, scanning
parameter adjustments including different sets of measurement protocols. Pre-processing includes
flat-field correction, geometrical correction, averaging of number of frames in every angular position,
etc.

2.2.2 Physiological monitoring software “SkyscanVisual”
This software allows real-time imaging from scanners’ colour camera with real time movement
detection from selected area inside the image, acquiring digitized signals from ECG amplifier, air/gas
flow sensor and temperature sensor, acquiring signals from the connector for external TTL pulses (for
example, from ventilator), setting gain individually for every acquisition channel, adjusting individual
thresholds, saving exact time marks from selected / all channels and control animal heating system
for temperature stabilization at selected by operator level.
2.2.3 Reconstruction software “NRecon” with GPU acceleration

The software uses modified Feldkamp multi-slice volumetric (cone-beam) reconstruction algorithm.
Single slice or selected / full volume can be reconstructed after one scan. Full cross section size (full
image mode), partial reconstruction mode, and possibility for detail local reconstruction with object
larger than field of view.
Automatic misalignment correction, ring artifact reduction, adjustable smoothing, beam hardening
correction, detector’s dead pixel correction, thermo drift compensation, drawing rulers, automatic
and manual selection for grey-scale window, etc. Output file formats: 16bit TIFF, greyscale JPEG, 8-bit
BMP, text format. The software supplied with two types of reconstruction engines switchable by
operator: multithreading reconstruction using only CPU (NReconServer) and hybrid CPU/GPU
reconstruction accelerated by GPU (GPUReconServer). GPU-accelerated version provides x3…x10
speed-up dependent on performance of installed graphical card. Typical total reconstruction time for
1K x 1K x 600 pixels from 400 angular projections is less than 1 min, for 2K x 2K x 1200 pixels from
800 projections is around 12 min.
2.2.4 Software for time –resolved (4D) reconstruction “TSort”
The program “TSort” allows sorting acquired images according to information saved by physiological
monitoring subsystem for creating time-resolve reconstruction results. With this program all
acquired projection files will be distributed according to selected number of time bins inside every
cycle of breathing or heart activity for following reconstruction in number of time points inside
selected cycle. It also provides averaging of multiple images in every time bin and filling empty bins in
the case of pure primary information.
2.2.5 Visualization software “DataViewer”
The reconstructed set of slices can be flexibly viewed in "Data Viewer" program. Images are
displayed as a slice-by-slice movie. DataViewer also has a viewing mode with three intersecting
orthogonal slices centred at any selected point inside the reconstructed volume, which can be turned
and each intersecting slice independently moved by simple mouse control. DataViewer includes
possibility to rotate reconstructed volume around any axis and resample reconstructed dataset in
any alternative orientation. Additional features include 4th dimension for compression/tension and
time-resolved tomography, variable smoothing, saving interpolated datasets in saggital or coronal
section, measuring and saving distances and intensity profiles.

2.2.6 Format Converter “TConv” and “DICOM converter”
The format converter utility "TConv" converts between TIFF, BMP and JPEG files with adjustment of
colour palette, inversion, renaming, resizing and combining of datasets. The DICOM converter
provides conversion from the set of reconstructed slices to file(s) in DICOM 3 format.
2.2.7 2D/3D morphological analysis software “CTan”
“CT-analyzer” builds 3D models from micro-CT scans and measures comprehensive 2D and 3D
morphometric parameters. The software features an advanced, rapid and user-friendly region-of-
interest (ROI) free-hand selection tool, which by auto-interpolation between layers becomes the
volume-of-interest (VOI), the essential basis for all quantitative analysis. CT density analysis is also
provided within any VOI, which by calibration can provide Hounsfield units or volumetric bone
mineral density (see BMD phantoms). The 3D models created by CT-analyzer are loaded and viewed
from the accompanying “CTvol” software (see below).
The capabilities of “CT-analyzer” are in summary:

• Flexible dataset opening including variable resizing and conversion from formats of other
micro-CT producers,
• Slice tool for density profile and longitudinal section from transverse sections
• Advanced, rapid and user-friendly region-of-interest (ROI) resizable standard shapes or free-
hand selection tool, auto-interpolated between layers to give the volume-of-interest (VOI)
• Saves VOI selections and VOI-sampled datasets
• Creates 3D triangularized models for precise 3D viewing
• Volume rendering tools or full reconstructed space or volume of interest
• Possibility to create STL models suitable for finite element analysis
• Flexible binarization tool with linear/logarithmic grey histogram
• Outputs grey histogram from selected VOI for density measurements (HU, BMD)
• Customizable printed analysis reports, txt and html reports for QA/GLP
• Batch mode possible
Full list of functions can be found at: http://www.skyscan.be/next/CTAn02.pdf,
Descriptions of measured parameters: http://www.skyscan.be/next/CTAn03.pdf,
User Manual – at: http://www.skyscan.be/next/CTan_UserManual.pdf
2.2.8 Realistic visualization by surface rendering “CTvol”
“CTvol” (CT-volume) provides viewing, intuitive manipulation and flexible control of 3D-model
texture and transparency, plus a versatile moviemaker.
A virtual 3D viewing environment is created by the user that allows:

• Selection of background including scenery;
• Moving and rotation of single or multiple models, together or separately;
• Advanced control of object texture, color, lighting and transparency;
• Ability to view inside models by cutting away a part or making a part transparent;
 A “flight recorder” for flexible and fast creation of “movies” for animated presentation in a
3D virtual environment by automatic interpolation between several selected key frames.
 Stereo imaging using red-green or red-cyan glasses
More details can be found in User Manual at:
http://www.skyscan.be/next/CTvol_UserManual.pdf

2.2.9 Realistic volume rendering software “CTvox”
The "CTvox" software also offers 3D visualization, based on a different approach (volume rendering,
as opposed to surface rendering for CTvol). CTvox does not rely on geometric models generated by
CT-analyzer but works directly on the reconstructed cross sections. Volume rendering is ideally suited
to visualize in 3D the inner structure of scanned objects in a very flexible and intuitive manner.
Features include:
 3D navigation controls allows manipulating both object and camera,
 A flexible clipping tool allows producing cut-away views.
 Three different rendering modes are supported (volume render, maximum intensity
projection = MIP, attenuation maps).
 Transfer Function Editor is used to control appearance of the rendering.
 Background selection, including custom scenery.
 A "flight recorder" for fast creation of "fly around" and "fly through" animations based on the
selection of several key frames with automatic interpolation in between.
 Imaging possibilities include 3D stereo viewing.
 Possibility to combine results from multiple datasets, for example – from results of
reconstruction in absorption, phase-contrast and dark-field modes. Individually adjusted
transfer functions (colors and transparency curves) for every dataset and control one
weighted mixture of datasets during rendering.
 Export to mobile devices operating under iOS and Android. The rendering software from
Bruker-microCT for mobile devices is available for free downloads: mobile devices under iOS
on the AppStore and for Android mobiles – on the GooglePlay
1
2.2.10 Control and Reconstruction Workstation
Dell Workstation with all preinstalled software:
 2x Intel XEON processor E5-2640 v3 (eight core HT, 2.6 GHz Turbo 20 MB, 90W)
 Windows 7 Professional (64-bit)
 64 GB DDR3 2133 MHz RAM
 4GB NVIDIA graphics card
 8 TB (2x 4 TB) SATA HDD in RAID 0 for data
 512GB SSD (Solid State Drive) for operating system and programs
 24” UltraSharp wide LCD with LED backlit, 1920x1200 native resolution
 DVD+/- RW drive
 QWERTY keyboard
 Optical scroll mouse
 Soundbar
2.2.11 Physical:
 Enclosure – desk-top fully shielded system,
 Radiation safety - <1uSv/h at any place on the instrument surface,
 Size / weight – 850W x 960H x 1240L mm (keep available 1620L mm) / 240kg,
 Electrical power – 100…240V AC, 50-60Hz, <150W (excluding workstation).
1
The computer configuration can change from time to time.

2.3 Installation requirements
The necessary installation space is shown in the following image:
The system should be installed on enough strong table, which can safely handle 250kg without
vibrations. The same table (if it is large enough) or another one close by can be used for computer
screen, keyboard and mouse. The control computer can be placed on or under the table. The cables
between the scanner and control computer are approximately 1.5m long. The system needs three
power sockets: one for the scanner and two for computer and the monitor. All connections between
computer and scanner and between computer and monitor should be done before connecting any
part to the main power. All three power sockets should have ground connections with common
ground.
To access animal transport system during installing/removing cassettes with the animals, top part of
the “nose” of the scanner can be slide out. It requires approximately 40 cm additional space for
sliding part of the animal transport system plus certain space for operator arm because the handle
for the sliding part located in the end of the “nose” of the scanner.
Typical operator position during installing / removing animal cassettes is on the side of the scanner
where touch screen is located. The same side contains emergency stop and key switch, which
controls X-Ray source. The opposite side wall contains all connectors for cables between the scanner
and control computer and for cable to main power. The cable connections may require some space
(10-15cm) between the side of the scanner and surrounded obstacles. There is no need to keep
access to the power switch integrated in the power inlet – keep this switch always ON. The scanner
will be switched ON or OFF by control software. Keeping power switch in ON position also allows
unlocking access to the animal by pushing emergency stop button when scanner power is not
activated by control program.

3 INSTALLATION PROCEDURE
In case of damage during transportation or any defect in the scanner operation, please contact your
local Bruker microCT distributor (see http://www.skyscan.be/company/distributors.htm).
Alternatively, you can consult Bruker microCT directly:
BRUKER MICROCT, Kartuizersweg 3B, Kontich B-2550, BELGIUM.
Email: [email protected], Tel: +32 3 877 5705, Fax: +32 3 877 5769
Only specialists trained by Bruker microCT are authorized to do service and repair on the scanner!
The system is not intended to be placed in public areas. If the equipment is used in a manner not
specified by the manufacturer, the protection provided by the equipment may be impaired. We
recommend you to consult national authorities to determine all local operational requirements.
Scope of this part of the User Manual:
This part is meant as a guideline to unpack, connect and startup the SkyScan1278 X-ray
microtomograph. Always use your common sense, specific onsite difficulties with transportation and
installation are not described in this manual.
Please wait for trained service personnel from Bruker microCT or its certified
distributor to unpack and to install the system.
3.1 Site requirements

The SkyScan1278 X-ray microtomograph delivered in flight case with size of 1340 x 1960 x 1200mm
and with total weight of packaged system around 330kg. The control computer, monitor, keyboard,
mouse, box with accessories and all necessary cables are inside this flight case.
Make sure that the flight case can be unloaded from the truck that will make the delivery. The
customer will need a suitable forklift to unload and to move the system to the final destination.
All parts are for indoor use. Make sure that the reserved room for the CT scanner is large enough and
the table for scanner installation is strong enough to handle 250+ kg of weight safely and without
collecting vibrations from possible unstable floor surface. During scanner movement to final
destination keep flight case in horizontal orientation. Turning flight case to any side surface or upside
down will damage the scanner. The doors and elevators should be big enough to move 1200mm size
box through the openings.
The SkyScan1278 microtomograph needs 3 wall sockets with common earth connection: 2 for the
computer + monitor and one more for the scanner. The sockets should be able to deliver 4A each for
200-240V line voltage or 6A each in the case of 100-130V line voltage.

3.2 Unpacking
The scanner and all associated parts are supplied in the flight case shown in following picture:
The flight case has attached shock (left image) and tilt (right image) sensors:
Before opening flight case, check all attached sensors. Red central part of the plastic tube in the
shock sensor indicates that scanner got unaccepted shocks during transportation. Red indication in
the round central part of the tilt sensor indicates that scanner was transported in wrong orientation.
In both cases scanner may be severely damaged. In the case of activated shock or tilt sensors, don’t
open the scanner, inform transportation and insurance company and continue opening only with
presence of insurance expert. All damages during transportation should be covered by insurance
company connected to transportation carrier.

Keep 1-1.5m free available space around flight case before continuing unpacking. Two top parts of
the case can be disconnected from the bottom part:
The top part shown on the right in previous image contains compartment with a monitor (if
computer shipped inside the flight case) and probably some extra accessories. Remove all content
from this compartment:
Move both top parts out of the bottom part of packaging. The bottom part supports the scanner and
also contains an accessory box and a computer (if it shipped with the scanner). The computer and
accessory box hold by the belts. Remove the belts and take out the computer and accessory box.

Open accessory box and take out two steel handles. The handles should be screwed and tightened
into two holes on the back side of the scanner:
To lift up the scanner use the belts wrapped around two inserted handles on the back side of the
scanner and around two integrated handles in the front of the scanner body. Put belts by such way
that they will not slide out during lifting up the scanner.

ATTENTION: Newer use front “nose” of the scanner to lift it up. Any force applied to the front part of
the scanner will damage precision animal transport system inside the “nose”. Use only four handles
to lift scanner up.
To lift up the scanner, a forklift with enough long vertical travel or other lifting equipment, which can
handle 300kg, can be used:
After unpacking and installing to the table, check again for possible transportation damages and in
the case of discovering any damages on the external surfaces of the scanner body, contact carrier
and insurance company.
3.3 Installation of the scanner

Before starting the scanner one should make the connections shown in the figures below. All
interconnections with signal cables should be made before connection of the main power plugs to
the wall sockets.
Firstly unpack computer and monitor and install them close to the scanner. Connect computer to
monitor by video cable, connect keyboard and mouse to any UBS sockets on the back side of
computer. Alternatively the keyboard and mouse can be connected to USB hub in the monitor with
single cable USB connection between USB hub in the monitor and USB socket on the back of the
computer.
If computer supplied with soundbar, attach soundbar to the bottom of the monitor from the back
side, connect power cable of soundbar to the monitor and signal cable with green plug to the green
socket on the back side of the computer.
Next step is to connect the computer and the scanner.

There are two places on the side of the scanner opposite to the side with touchscreen where the
cables should be connected: one – on the main body of the scanner and another – on the animal
transport system:
Before connecting the scanner, the computer and the monitor to the main power, make following
connections:
 Use the supplied cable to connect “positioning” connectors on the scanner body and on the
animal transport system.
 Using supplied so called “camera link” cable connect “computer” socket on the scanner body
to similar socket on frame grabber installed in the computer.
 Using the supplied USB cable connect USB socket on the scanner body to any USB port on
the back side of the computer.
 Using another supplied USB cable connect USB socket on the animal transport system to any
USB port on the back side of computer.
The main switch on the system body close to the inlet of the main power can be always on. The
scanner will be switched ON or OFF by signals from control software.
Now you can connect the computer, the monitor and the system to properly grounded wall sockets.
Before starting the system check that emergency stop button on the scanner is released. If it is
pushed during transportation or packaging/unpackaging, release the button by small turn in the
direction shown by arrows printed on the button.
If the computer supplied with the system, all software is already pre-installed and configured by the
producer or distributor. A back-up CD supplied with the system contains back-ups for all software, an
electronic version of all User Manuals and the necessary device drivers. Most recent versions of the
Bruker microCT software can be downloaded from our website: www.bruker-
microct.com/products/downloads.htm
The key switch on the scanner is enabling or disabling activation of X-ray generator. This key can be
removed only in OFF position. In this case X-ray cannot be started and control software may
complain that connection to X-ray source cannot be established.
3.4 Supplied toolkit
The supplied toolkit in the plastic box located during transportation aside the scanner.
It contains three animal cassettes with different sizes (small mouse cassette, big mouse/small rat
cassette and big rat cassette), two handles removing scanner from transportation box and plastic bag
with ECG electrodes and temperature sensor.

4 SCANNER’S CONSTRUCTION
4.1 Main parts of the scanner
The scanner contains number of subsystems inside the steel enclosure:
Main body of the scanner contains most X-ray, mechanical and electronic parts of the system. The X-
ray source with adjustable energy in the range of 20-65kV and flat panel detector are placed on the
gantry, which can rotate around animal bed to acquire angular projections necessary for
tomographical reconstruction. The source assembly also contains a collimator and a motorized
changer of energy filters. This changer has four available positions: first position without any filter is
used for imaging soft tissues in combination with low peak energy in X-ray source; the second and
third positions are occupied by flat Al filters with 0.5mm and 1mm thicknesses correspondingly and
are used for full body scanning of mice and rats; the forth position contains specially shaped filter in
Al alloy, which can be used in combination with high source energy for low-dose scanning.
The gantry turns by powerful stepping motor and can travel over 362 degree. Back part of the system
occupied by electronics, which includes control board for all stepping motors and X-ray source, high-
voltage power supply for x-ray source, all low-voltage power supplies and other electronic parts. A
heater with fan to create warm air flow over central opening of the gantry is also located in the back
side of the scanner, but mechanically integrated to the gantry. This heater allows keeping animal
body under controlled temperature to avoid dangerous loss of temperature under anesthesia.

Bottom part of the main scanner body includes resistive (force-sensitive) touch screen in the
operator’s side of the scanner, emergency stop and key switch. In contrast to most other touch-
screen displays with capacitive sensitive element, which requires physical contact by human fingers,
used force-sensitive touch screen can be activated using hands with gloves or by any object in
operator’s hands. The emergency stop, when pushed, interrupts scanner’s main power and disables
all movements and X-ray emission. In the same time activating emergency stop unlocks animal
transport system (if power switch in the main inlet is ON) and allows removing animal from the
scanner. The key switch can be used for preventing starting X-ray when removed. The key can be
removed from the lock only in OFF position.
The opposite side of the bottom of the scanner body contains all electrical and signal connections of
the scanner. It includes a main power connector with a filter, a switch and two fuses behind the
switch; a USB socket and a CameraLink connector for scanner control and image streaming; a 25-pin
connector to control animal transport system. The switch above the inlet of main power is for service
purposes (switch it OFF for fuse replacement) and should be always in ON position for normal
scanner operations. The scanner will be switched ON or OFF by commands from control program and
doesn’t require activation of any physical switching elements.
The right part of the system in the image on previous page contains animal transport system and
physiological monitoring subsystem. The animal transport system attached to the main body of the
scanner by two threaded handles. It can be in one of two possible configurations: a long travel
transport system (620mm travel) or a short travel transport system (310mm travel). The long travel
animal transport system connected to the main scanner body by extendable rails and allows inserting
additional modules in the front of scanner body. The short travel animal transport system can be
detached from the scanner completely for passing through narrow door in laboratory or in elevator
during scanner installation. Both versions of animal transport system are working fully identically
with this type of the scanner.
The animal transport system has a special connector, which allows easy attaching and detaching of
any animal cassette. It contains 3-pin ECG connection, 2-pin connection to the temperature sensor
on the animal cassette, inlet and outlet of anesthetic gas and other connections. The pipe for
anesthetic gas has a valve, which prevents gas leak without animal cassette installed. All listed
connections between animal transport system and animal cassette are connected together by simple
turn of the slider in the top of the connector.
Bottom part of the animal transport system contains a physiological monitoring electronics, the
connections to the stepping motor on the animal transport system and to the safety lock. The
physiological monitoring subsystem described in all details in the chapter 7 of this Manual.

4.2 Software components and dataflow between them
The system is supplied with a number of software programs: the SkyScan1278 control program,
NRecon, DataViewer, CTVox, CTAn, CTVol, etc. Also software for physiological monitoring described
in following chapter is included.
The dataflow between these programs is shown in the following image:
The control program acquires images from the X-ray camera, controls gantry rotation, filter changer,
animal transport system and X-ray source. It can acquire X-ray images through the animal, perform
all necessary corrections and image processing procedures, save individual X-ray images or complete
sets of angular projections for a tomographical reconstruction. During acquisition the control
program saves all angular projections as 16-bit TIFF images with filenames “prefixNNNNNNNN.tif”,
where “prefix” corresponds to the selected name for the dataset and “NNNNNNNN” indicates the
number of angular projection in an 8-digit format. The minimal index corresponds to first acquired
angular projection and it is always 00000000. The set of acquired projection images can be opened
and shown as a movie by DataViewer. Any individual projection can be opened by double clicking to
the corresponding file or by an imaging program, which supports 16-bit TIFF encoding, for example
“Adobe Photoshop”.
Every set of projections is accompanying by a log-file. Once the acquisition of the angular projections
is completed, the control program will save a “prefix.log” file, where “prefix” corresponds to the
dataset filename. This text file contains all the necessary information about the scanner, full
description of scanning geometry and all settings used during the acquisition process. The
reconstruction program uses this file to extract the acquisition geometry for a particular scanner, the
object position and image format.
The reconstruction is performed by the NRecon program, which can use NReconServer for
reconstruction using CPU only or GPUReconServer for reconstruction accelerated by GPU in graphics
card. The operator can select one of two listed server program for the reconstruction calculations.
The program loads the angular projections in 16-bit TIFF format and all necessary information about
scanning geometry from the corresponding “*.log” file. The NRecon program works with floating-
point data values for internal calculations during reconstruction. After first reconstruction of a single
slice, the operator can define a density window and all reconstructed slices will be saved as the

grayscale images with from the selected density range. The format of these images can be 16-bit
TIFF, 8-bit BMP / PNG or 24-bit (grayscale) JPEG. The results can be also saved in DICOM format.
Filenames of the reconstructed cross section images contain the same prefix as the angular
projections extended by “_rec” and a four or eight-digit index, which indicates now the vertical
position of the reconstructed cross section inside the three-dimensional reconstructed space. The
minimal index corresponds to selected bottom of the reconstructed space counted in respect to the
bottom line in the projection images, which corresponds to index 0000. The reconstruction program
updates the dataset’s log-file by adding the program version and all reconstruction parameters. The
full set of reconstruction results can be opened by one of the listed below programs for visualization
of results.
The DataViewer allows visualizing reconstructed results as a slice-by-slice movie or in the form of
three orthogonal slices crossed at any point inside the reconstructed volume. It also supports
resampling of the reconstructed results in any orientation and simple measurements such as
distance measurements in 2D and 3D.
The program for volume rendering, CTvox, uses the reconstructed dataset to create a realistic
visualization of the reconstructed object by volume rendering. The results of this rendering can be
saved as BMP or JPG images. The program also supports automated movie creation, which can be
saved as a (compressed or uncompressed) *.avi file. The program can export datasets through any
file transfer service, such as DropBox, or by a wired connection to mobile devices. A mobile version
of CTvox makes volume rendering on iPhone, iPad and Android devices.
The CTAn program for 2D/3D processing and analysis can load reconstructed datasets in TIFF, BMP,
PNG or JPG formats, and can save the results of processing and analysis into text files and tables
which are suitable for import into Microsoft Excel. It also accepts results from many other micro-CT
scanners (Zeiss/XRadia, Scanco, etc.) and can work with datasets in DICOM-format, which is a
commonly used format for 3D scanners and clinical CT systems. The CTAn program can save 3D-
models of the reconstructed objects in standard STL format “*.stl” for 3D printers to create physical
model of the scanned object. It can also save triangulated models in number of different formats,
such as “*.ply” or internal “*.p3g” and “*.ctm” formats. The “*.stl”, “*.p3g” and “*.ctm” formats are
supported by CTVol, which is a program for surface rendering of 3D models. Results of the rendering
can be saved as BMP images or as an animated “movie” in compressed or uncompressed “*.avi” files.

5 GETTING STARTED
The control program of the SkyScan1278 has the same operational principles as any other Windows-
based program. It is possible to select a function from the menu/submenu in the top line of the
program window and by pushing toolbar buttons under menu line, and also change modes and
parameters using the corresponding control buttons or sliders in the status bar in the bottom of
program window. To start the SkyScan1278 control software double click to the corresponding
shortcut on the desktop:
After starting the program an initialization window will be shown on the screen. During initialization
the program will wake-up the scanner and will establish connection to all parts of the system.
5.1 Acquiring images and collecting datasets

The start window of the control program on the screen contains the main menu bar in the top of the
window, the toolbar under main menu, the status bars at the bottom of program window and four
imaging areas in the middle dedicated to image from the camera (left top), extracted from phase
stepping absorption image (right top), extracted differential phase-contrast image (left bottom) and
extracted dark-field image (right bottom).

To insert an object, to start the X-ray source and to obtain an on-screen projection image, you can
use one of the first three buttons at the left side of the toolbar:
X-RAY ON / OFF with necessary start-up procedures.
Live imaging mode (Grab Image).
Single image mode (Snap Image).
If X-ray is OFF (first shown button is not “pressed”), the lock in the animal transport system is open
and top cover can be moved out by hand using handle in the end of the cover. During opening the
cover, animal bed holder will be moved automatically in the position, which allows easy installation
of the animal bed. Animal bed can be installed by pushing black connector of the bed to the socket in
the animal transport system and locked by moving red lever in the top to “close” position. The
animal bed can be released by moving red lever to “open” position:
After installing the bed, slide top cover of the animal transport system towards the main body of the
scanner till fully closed position. Now press “Live Image” button on the toolbar. It will start X-Ray
source. In the first start of the day automatic preheating procedure with gradual increase of voltage
and current can take from tens of seconds to couple of minutes. If system was not in use for a long
time, this procedure can take up to tens of minutes. In following starts the X-ray source will be able
to start very shortly.

After rising voltage and current in X-ray source, the image will appear in the “imaging area” in the left
side of the program window. You can adjust position of the object by short mouse push to the small
buttons with green arrows in the status bar. Clicking the “Grab Image” button once more will stop
continuous acquisition. The “Snap Image” function will also turn on the X-ray source and acquires a
single image, keeping the X-rays ON. Clicking to leftmost toolbar button can deactivate X-ray and
open lock on the top cover of animal transport system.
When the X-ray source is activated, an indicator appears on the screen:
The image will be updated after every exposure (which can take from tens of milliseconds to several
seconds, update rate indicated in top left corner of imaging area) in the imaging field. You can move
object up or down by using small button with green arrows in the status bar in the bottom of
program window. Alternatively, you can move animal bed by dragging on the image with pressed left
mouse button and Ctrl in keyboard – the movement will be executed after releasing left mouse
button. Clicking to the left slider allows rotating the gantry (don’t drag, just click). Clicking to
numerical value aside of rotation slider or in the right side of vertical positioning buttons with arrows
will call dialog window, which allows setting both positions numerically. Using third pane in the
status bar one can select camera image format, which allows changing number of pixels and pixel
size in the images. The pixel size, shown in this pane, corresponds to the size of pixels on the object.
Next pane in the status bar allows selecting of filters. Clicking to this pane will open pop-up submenu
with available options. Rest panes of the status bar are used only for indications.
To get images properly corrected, the flat-field references (without object) should be acquired. The
flat-field reference for every filter / camera format combination contains two images acquired
without an object: bright-field reference acquired with X-ray illumination and dark-field reference
acquired without X-rays. The flat-field references should be acquired without any animal cassettes
installed. If X-Ray is ON, remove the animal cassette by clicking to left toolbar button, close the
animal transport system cover, start x-ray and select menu item Options -> Update Flat-Field for
Current Mode. This procedure will collect reference, save them to the disk and will use them for
correction of corresponding imaging modalities during following image acquisitions. You don’t need
to repeat this procedure every time. Update flat-field references only if you will see severe ring
artifacts in reconstructed slices.
Install animal cassette and start live imaging again by using this toolbar button:

You can compare corrected and uncorrected images by switching flat-field correction ON and OFF
using checkbox in Options -> Preferences or by double click to text “ff”/”flat-field correction OFF” in
the left top corner of the imaging area.
Try to snap single image by using this button:
In this case image acquisition can take longer time because of integration of several images to
improve image quality. More individual images integrated, better image quality will be. Number of
integrated images can be adjusted in Options-> Acquisition as a number of frames for averaging
(scanning mode “step and shoot” should be selected). The same averaging will be used during
scanning for tomographical reconstruction.
To start scanning with acquisition of angular projections for tomographical reconstruction, use next
button in the toolbar – “Start Scanning” – or corresponding command in menu Actions -> Start
Scanning:
The control program will open the “Scanning Options” dialog to adjust scanning parameters and the
location for storage the projection image files:

Type the filename prefix and select (by “browse” button) the target folder for file location. For a first
attempt use “step and shoot” mode, rotation step between 0.5 and 1 degree and averaging of
several frames. You can make your selection of scanning parameters in advance with following
clicking to “Close” button, which will save selected parameters without starting scanning. The same
pre-selection of parameters can be done by calling menu function Options -> Acquisition, which will
open identical dialog window without “Scan” button.
Clicking the “Scan” button will start process of collecting and saving to disk angular projections,
which will be used in 3D reconstruction. After the start of the scan the control software will show a
progress dialog:
During acquisition all angular projections will be saved to the hard disk of your computer in the
selected folder.
If imaging area is too small to get necessary part or full animal be scanned, you can select scanning
area longer than one imaging field. In this case the scanning volume will be covered by number of
partial scans, which will be combined automatically to continuously reconstructed volume in the
reconstructing program. For selecting long scanning volume move animal bed to the position where
you can see the beginning of total scanning volume and select first limit by right mouse double click.
Then move animal bed to the position where you can see the end of scanning volume and also select
it by right mouse double click. Only last two selected positions will be taken into account so you can
redo your selection. The order of selection (top after bottom or bottom after top) is not important.
After finishing the scan the progress dialog will disappear from the screen and you can start the
reconstruction of virtual slices across your object by selecting menu item Actions -> Start
Reconstruction or by using the next button on the toolbar:
If more than one dataset exists in the current folder, the control software will show you list of
available datasets for reconstruction. Click on the name of your dataset and the OK button or just
double click to dataset name. If only one dataset exists in the current data folder, the reconstruction
software will start immediately.
5.2 Reconstruction
The reconstruction process will be executed by a separate program NRecon in combination with the
reconstruction server, which can be NReconServer, GPUreconServer or InstaRecon® (last one can be

supplied optionally). Dependent on the security settings in your computer, during first start of this
program it may ask you to unlock access – do so.
The reconstruction program NRecon will show you the first acquired angular projection image on the
left side and several control panels on the right side (select “Start” tab). Click the “Preview” button to
reconstruct one central cross sectional slice through your object. The reconstructed slice will then be
displayed with automatic switching to the “output options” tab. This tab allows you to select the
density window by moving the coloured vertical lines in the histogram, to obtain optimal contrast of
the tissue inside the animal body. Then switch the control panel back to the “Start” tab and select
the top and bottom (vertical range) of the reconstructing space by the numerical position of the first
and last slices or by moving the top and bottom horizontal lines in the shadow image with the
mouse. You can also select a step between reconstruction slices. A step value of one corresponds to
reconstruction of all cross sectional slices. Other reconstruction parameters such as smoothing,
misalignment correction, ring artefact reduction and beam hardening correction, are set in the
second “Settings” tab. After changing any parameters in this tab, you can try to reconstruct single
slice again by selecting “Preview” in the “Start” tab. Finally when all reconstruction parameters are
set, reconstruction can either be started immediately by the “Start” button in the “Start “ tab, or
placed in the batch manager by pressing “Add to batch” to execute the reconstruction later. After
reconstruction, all reconstructed slices will be saved to the same folder on your hard disk (or in
subfolder if it is selected in Options -> Preferences). In the case of acquiring differential phase-
contrast and dark-field modalities, click to leftmost button in the toolbar and click to any file with
“_dfc” or “_dfi” after filename prefix and repeat reconstruction procedure like it described above.
5.3 Visualization of reconstructed results

To show the reconstruction results you can start the DataViewer program directly from the
reconstruction program by using following button in the toolbar or reconstruction program:
This program displays the reconstructed cross sections as a slice-by-slice animation. Second button in
the toolbar of DataViewer starts and stops such animation. You can also load the full reconstructed
3D space into DataViewer and visualize three orthogonal slices crossing at any selected point inside
the object using the third button in the toolbar. The next toolbar button opens a “3D Navigator”
display to show the spatial position of three selected slices:

The “Navigation” window can be detached from the control area and attached to any other controls
in DataViewer window or freely placed anywhere (keep Ctrl button pushed to avoid attaching during
movement of “Navigation” window).
You can select any position for the crossing point of the three virtual slices by moving colour crosses
in the images or the slice planes in the 3D Navigation window by left mouse button. Right mouse
button drag-and-drop inside the 3D Navigation window allows rotation of the spatial model. Moving
mouse with left mouse button in any of three slices while keeping Ctrl pressed allows rotating the
reconstruction volume to any orientation. You can create a new dataset in any alternative
orientation by saving it after rotation using the Actions -> Save command.
5.4 Visualization by volume rendering

To start the volume rendering program from the reconstruction software, press the following button:
It will start the CTvox program, which can perform a realistic 3D visualization of the reconstructed
object using volume rendering. Once a dataset has been loaded into CTvox, the transfer function plot
area (in the Transfer Function pane, in the upper left corner) will display a histogram of the data.
Likewise, the low-intensity contributions (which dominate the periphery of reconstructed images)
tend to obscure the core of the volume data. Therefore, it is usually useful to suppress these low
intensities in the rendering. The purple “opacity” curve (initially a straight line) shows the conversion
between the intensity in the reconstructed slices (low - left, high - right) and the opacity of the
object’s parts, shown in the image.
Add a knot to the opacity curve by clicking in the lower left side of the purple curve in the transfer
function window. Move the knot down to get the low-intensity clouds around the object more
transparent.

There are two visualization modes for navigating the scene:
 Object movement: the orientation (rotation) and position (translation) of the object
can be adjusted using the right and left mouse button respectively; the camera can be
moved closer to or further away from the object using the mouse wheel.
 Camera movement: the object is held in place; the camera can be rotated around the
object (right mouse button) and the camera viewing angle can be adjusted (left mouse
button); again, the mouse wheel moves the camera forward or backward.
The right mouse button controls the rotation in both modes. In object movement mode, the left
button controls the translation in the viewing plane. Out-of-plane translation (i.e. perpendicular to
the viewing plane) is performed by moving the mouse vertically with the mouse wheel pressed. In
camera movement mode, the left button controls the camera viewing angle (acting as a zoom, but
introducing perspective distortion when the camera is close to the object; the viewing angle can also
be set in the View Options pane). By holding the Shift key down while left clicking, the face of the
clipping box under the mouse pointer can be 'grabbed' and subsequently dragged to clip a portion of
the object. Holding the Ctrl key during rotation or translation (in both modes) will keep the object in
place and move only the clipping box, allowing appropriate positioning the clipping plane. The mouse
wheel controls the distance between camera and object in both modes. Double clicking either mouse
button in the imaging window toggles the movement mode.
Object’s colour can be adjusted by manipulating the partial colour transfer functions (red, green and
blue) which show after the corresponding selection in the drop-down list “Channel” in the transfer
function pane.
The Flight Recorder functionality can be used to produce fly-around or fly-through animations for
your 3D data. Start the Flight Recorder dialog by selecting Actions -> Flight Recorder command or
click on the toolbar button:
The idea is to set up the scene and to tag it as a key frame by clicking the Add button. After preparing
the next scene, click Add again and so on. When creating the movie, the program will generate the
specified number of intermediate frames by appropriately interpolating the positions and all
adjusted parameters between the key frames.

When ready, the movie can be generated by clicking “Save movie”. The output is either an AVI movie
file or a series of movie frames in BMP, JPG or PNG format.
More details on CTvox functions can be found in its “Quick Start Guide” available for downloading
from the Bruker microCT website.
5.5 2D / 3D image analysis and surface rendering

Following button in the toolbar of the control program and in the toolbar of the reconstruction
program starts the CTAn software package for 2D/3D image analysis:
The software package for image analysis and visualization of reconstructed datasets practically
contains two programs: CTAn for 2D/3D analysis and CTVol for 3D visualization by surface rendered
object model(s). To use the two programs together, for direct export of the 3D object models for
visualization, connect CTVol to CTAn: in CTAn menu go to File -> Preferences -> Tools and define
CTVol.exe as the 3D visualization program. At the first start of CTAn, it is better to change the units
from pixels to microns or milimeters. This can be done in File -> Preferences -> General.
If CTAn is started from another program, the selected dataset will be opened automatically.
Alternatively you can open any set of results by the button in the toolbar of CTAn. The shadow
image (if present) and the list of files will be shown in the top part of the program window and one of
the cross sections in the bottom part. You can animate through the selected dataset by pushing
or by using the slider on the left side of the image files list. Right mouse click in the cross section
image to open a submenu for image zoom. Drag and drop the left mouse button in the cross section
image or the projection image to measure distances. Different colour look-up tables can be selected
in the “Palette” tab. Click the sign to invert the image colour scheme.
After loading a dataset, several buttons will appear in the main toolbar in the top of the program
window:
 original image view,
 selection of region or volume of interest,
 conversion of images to binary images for analysis,
 image analysis (activated after conversion to binary).
If you wish to select a region/volume of interest, click the button and draw on the image with the
left mouse button held any shape around the area you want inside the region of interest. This shape
can be copied to all cross sections in the dataset by the toolbar button. To select a 3D volume of
interest you can draw different regions in different cross sections, and the software will interpolate
them automatically through all intermediate cross sections. Use the toolbar button with

pop-down submenu to select regular shapes for the region-of-interest. Volume-of-interest can be
limited in the vertical direction by two sliders to the right of the files list. Double-click on the blue bar
between these sliders to enter upper and lower limits numerically. One can reset all regions-of-
interests by the button to “start again” with VOI selection.
Go to conversion to binary images with the button. If the “Histogram” pane cannot be seen,
open it by dragging down the top border of the “Palette” window by the mouse:
Select the upper and lower global threshold levels by sliders above and under the histogram. The
white part of the binary images represents the objects selected for the subsequent 2D and 3D
analysis.
Use the button in the main toolbar for image analysis. Distributions of size, perimeter, form,
orientation and internal porosity from the current 2D slice are shown as colour-coded histograms in
the “Analysis” part of the program window. Colours or brightness (dependent on the selected
“Palette”) of the histogram’s bars match the colours of the objects in the image with corresponding
2D parameter values. To enhance this colour coding of the 2D histogram select “colour” or “colour2”
from the “Palette” drop-menu and use sliders under the colour scale in the “Palette” pane . To see
the results from another cross section, select it in the list of available files. Use the local toolbar or
right mouse button in the “Analysis” area to start a full individual 2D object analysis from the current
image ( button) or to start a full 3D analysis ( button) from the selected volume of interest. A
further 2D analysis giving integrated 2D parameters for all selected dataset images is possible by
selecting the button, which will create a tabular comma-delineated text file, which can be
imported to Microsoft Excel.
To send the selected volume of interest to CTVol for realistic visualization, go back to the binary
images by the button in the main toolbar and then push the button in the local toolbar. We
recommend that you select a small volume of interest in the central part of the object for your first
visualization attempt, to avoid memory limitations and slow reaction for the object movements in
3D-space. Select checkbox “Launch associated program to show model” in the “Create 3D Model”
dialog to start CTVol after the model is created. If the model will be used only for visualization, select
the “p3g” file format, which creates smaller file sizes with possibility to control smoothness of the
model during visualization. CTAn will export a 3D-model of the selected part of the object into the
CTVol program for visualization. The CTVol program starts in a separate window with its own controls
as explained below. It can also be started independently.
From the same function in CTAn, any 3D model can be saved in STL format. This file type is often
used for 3D printers, can be imported to most CAD packages and is also used in a number of
programs for finite element analysis.
The CTVol toolbar contains buttons to select object movement modes and object(s)/space
properties. Object and camera movement functions have similar behaviour as the corresponding
functions and buttons in CTVox.

object movement mode,
camera movement mode,
show/hide object properties dialog,
show/hide stage properties dialog,
show/hide light properties dialog.
Object and camera can be moved by the mouse. By holding the right mouse button one can rotate
the object or camera depending on the selected mode in the toolbar. The mouse wheel always
changes the distance from the camera to the object. The left mouse button can shift the object in the
case of selection of object movement, or zoom in / zoom out in the case if camera movement has
been selected. Double click on either mouse button to toggle between object movement and camera
movement modes.
The object properties dialog allows adjustment of the surface colour and other visual properties for
the selected object and the object can be set as movable/unmovable and visible/invisible. One
predefined object – the plate – is generated automatically and can be used to cut the selected object
using the “cut by plane” button.
The stage properties dialog allows adjustment of the camera viewing angle and selection of the
background: single selected colour, a 3D colour box or scenery. It also allows displaying the object in
stereo mode for red-cyan or red-green glasses (use in the toolbar for quick ON/OFF stereo) and
the adding of a fog effect with adjustable density to the scene.
The light properties dialog allows adjusting the colour and the direction of the light for object
illumination.
Making movies is similar to the corresponding function in CTVox with a limited number of options.
The toolbar button opens the “Flight recorder” window. This option allows storing a number of
key frames with subsequent smooth interpolation in between. The resulting movie can be shown
directly on the screen and saved as a number of BMP or JPG files as well as a compressed and
uncompressed movie in AVI format.
5.6 How to get help

Most application programs provide a context help function. Just click to the “Context help” button in
toolbar:

The mouse cursor will change from an arrow to a question mark. Now you can click to any function in
the menu, to any button in the toolbar or to any other control element of the program workspace. In
the popup window you will get a detailed explanation for the selected function or item.
For the main control program all functions are described in all details in the chapter 8 of this manual.
All other programs are supported by a corresponding User Manuals and/or by a “Getting Started”
guide, which can be found in the “Manuals” subfolder in the program folder of the computer
supplied with the scanner. Most recent versions of the programs and User Manuals can be
downloaded from the Bruker microCT website.
The documents available at the moment of writing this Manual are:
NRecon User Guide: http://www.bruker-microct.com/next/NReconUserGuide.pdf
GPUReconServer Installation Guide: http://www.bruker-microct.com/next/GPU_Nrecon.pdf
CTvox Quick Start Guide: http://www.bruker-microct.com/next/CTvox_QuickStartGuide.pdf
CTvox for iPhone/iPod: http://www.bruker-microct.com/next/CTvoxForIPhone.pdf
CTvox for iPad: http://www.bruker-microct.com/next/CTvoxForIPad.pdf
CTvox for Android: http://www.bruker-microct.com/next/CTvoxForAndroid.pdf
CTan/CTvol Getting Started: http://www.bruker-microct.com/next/CTan_CTvol_getting_started.pdf
CTan User Manual: http://www.bruker-microct.com/next/CTan_UserManual.pdf
CTvol User Manual: http://www.bruker-microct.com/next/CTvol_UserManual.pdf
CTan List of Functions: http://www.bruker-microct.com/next/CTAn02.pdf
CTan Description of Measured Parameters: http://www.bruker-microct.com/next/CTAn03.pdf
CTan Creating User Plug-Ins: http://www.bruker-microct.com/next/CTanPlugIns.pdf
Most recent versions of all application programs can be downloaded from:
http://www.bruker-microct.com/products/downloads.htm
To close the control program, double click on the icon in the top left corner of the program window
or click once on the rightmost box with a cross in the top right corner of program window. The
program also can be closed through menu Actions -> Exit. Closing the program will switch OFF the
scanner and save all settings.

6 TOUCHSCREEN FUNCTIONS
The touchscreen of SkyScan1278 system allows quick access to frequently used control functions and
indicates current status of the system:
The left bottom part of the touchscreen indicates current status of X-ray source.
The “Animal position” area in the left top part allows moving animal cassette forward and backward.
The movement will be executed as long as an operator keeps corresponding button on the
touchscreen “pushed”.
Right top area of the touch screen occupied by four buttons for energy and filter selection. Selecting
new filter will readjust accelerating voltage in X-ray tube according to settings in the control
program. Touching any button in this area will change colour of corresponding button to yellow for a
short time to indicate that command is received and will switch to yellow colour permanently after
executing filter changing.
The right bottom area of the touchscreen allows imaging and scanning control. The “IMAGE” button
activates/deactivates the lock on animal transport system, the X-ray source and image acquisition.
Next to “IMAGE” button is a “START SCANNING” button. The text on this button corresponds to the
function, which will be executed after pushing to corresponding button. After execution of
corresponding command, the text on the buttons will be changed to reflect next possible actions.
Yellow colour in this button indicates that scanning process is running. In this case the progress
indicator in the bottom of this area of touchscreen will display scanning process and text on the
button will be changed to “STOP SCANNING”.
Take into account that control command from the touchscreen may activate execution of
corresponding functions not immediately, but rather sending requests to command queue, with first
priority for commands selected on the computer screen. The operator has to wait until requested
touchscreen command will be executed before selecting next one to avoid that multiple selected
queries will be executed one after another and will block normal software operations.

7 PHYSIOLOGICAL MONITORING SUBSYSTEM
Supplied physiological monitoring subsystem contains specific electronics integrated into the scanner
and physiological monitoring software, which can be started from the scanner’s control software
using menu item Options -> Visual Camera ON/OFF or by this button on the toolbar:
The physiological monitoring software can be also started from the shortcut on the desktop:
In the case if it is started from desktop, the image from the visual camera inside the system can be
dark because there is no illumination inside the gantry, which is normally provided by the scanner
when physiological monitoring started by scanner’s control software.
The hardware of physiological monitoring subsystem contains several sensors connected to the
sockets in animal cassette, a colour camera in the top of the gantry opening and electronic board
with all amplification, digitalization and communication circuits.
7.1 Physiological monitoring electronics

The physiological monitoring electronic board diagram is shown on the following picture:
The subsystem includes a color 5Mp CMOS camera connected to USB port of computer through
internal USB hub inside the scanner, an ECG channel with non-metallic (carbon fiber) electrodes in

the animal cassette, ECG amplifier, fifth-order frequency filter and optical isolated signal connection,
a breathing detection channel with air-flow sensor connected to face mask on the animal bed and
corresponding amplifier, a temperature sensor on the animal bed and an input for external
synchronization pulses, for example – from external ventilator. The ECG and breathing channels have
controlled gain. In the case of ECG channel, the gain control is also optically isolated from all other
parts of the subsystem. Optically isolated front part of ECG channel takes power from isolated DC-DC
converters. Full electrical isolation of ECG channel from the parts connected to computer allows
maintaining very high sensitivity and immunity against electrical noise.
All signals from four input channels connected to a microprocessor controller, which digitizes analog
inputs by 12-bit analog-to-digital converters (ADC), controls gain in ECG and breathing signal
amplifiers and provides communication with computer through USB port under control of internal
firmware.
All electronics in physiological monitoring subsystem is powered from USB port and has no electrical
connections to other parts of the scanner.
On the animal cassette side, the electronics has five connections through spring contacts and two air
pipes for air-flow sensor. One of the pipes connected through air flow sensor to input connector for
anesthetic gas, another one – directly to output connector. The input line ended to animal face mask.
Direct connection of air flow sensor to animal face mask allows breathing detection with or without
using any anesthetic gas: keeping both gas connections open is also allowing animal breathing
detection.
There are several electrical connectors on every animal cassette:
Two supplied carbon-fiber ECG electrodes with red and white plugs should be connected to the
sockets with red and white rings correspondingly. If necessary, third electrode can be added for
connection to the socket with black ring. A temperature probe should be connected to 2-pin socket.
All tubes are already installed in the animal cassettes and don’t require reconnection. The face mask
can be installed to the front or to the back of every animal cassette. The mask can be repositioned by
user. Installing face mask in the side of cassette opposite to the connector side makes easy access for
the tail injection of contrast agents.

The ECG electrodes can be connected to two arms of the animal or to diagonal arm and leg:
7.2 Physiological monitoring software

A “SkyScanVisual” software package supports all functionality of physiological monitoring subsystem,
displays all signals in real-time on the screen, saves time marks for image sorting in time-resolved
studies and sends signals to control the heated inside the scanner for maintaining selected animal
temperature.
The physiological monitoring window on the screen shows image from the colour camera and real-
time readings from all sensors. Top yellow plot displays movement detection curve. The movement
detection based on the analysis of image changes inside selected region of interest in the image
window. Current region of interest is shown by dotted rectangle and can be dragging rectangle
corners using left mouse button. The detection area should be positioned in the place where body
movements can be seen with largest amplitude. The gain in video stream can be adjusted by slider
on the left side of the curve. You can move the slider by left mouse button or by mouse wheel. The
update rate for all measurements is defined by image update rate and dependent on camera
exposure and image format. Both parameters can be selected by right mouse click to the title bar of
the window with following selection of “SkyScan Visual Settings”:
For good sampling of breathing signal shown above Resolution and Exposure are appropriate. For
good sampling of ECG signal from small mice with high heartbeat rate, the resolution of 648x486
pixels and shorter exposure (8-10ms) may produce better ECG signal. The settings dialog also allows
adjusting proper white balance for the camera images.
The second field in the right top corner of the SkyScan Visual window with red curve and red slider
shows ECG signal. The gain for this signal can be adjusted by the slider using left mouse button. After
first click to any slider aside of physiological monitoring curve, mouse wheel control will be
redirected to corresponding slider and following adjustments can be done by mouse wheel until next
click to a different slider. Next light blue curve shows breathing signal and corresponding slider on
the left from the curve adjusts gain for this signal. Next green area shows signals from the connector
(BNC socket) for external synchronization pulses. The bottom magenta plot shows temperature
measurements from the temperature sensor on the animal bed and corresponding numerical value.
Every display area for physiological monitoring signals contains dotted line(s), which define
thresholds for activation time mark saving. The thresholds can be adjusted by dragging dotted lines
using left mouse button. Two threshold lines on the movement detection from video signals can be
moved by dragging any one. Different top and bottom thresholds for movement detection provide
immunity against small signal variation on the images. For all other channels single threshold
generates time marks when signal crosses selected value. The dotted line in the temperature
monitoring adjusts temperature set point for heating animal body by warm air flow. During
adjustment the set point will be shown in the bottom of the same plot area.
First four plots contain round checkbox in the top left corner, which allows selection of signals, which
will be used to save time marks. Every signal can be selected or deselected by left mouse click to this
checkbox. When signal is crossing thresholds in selected signals, sound beeps will be generated. The
sound indication can be switched ON or OFF by left mouse click to the “speaker” sign under the gain
sliders. Next “disk” sign indicates time mark saving process, which is activated from the main control

program during scanning for time-resolved reconstruction. The bottom sign with thermometer icon
allows control of animal heating. By left mouse click to this sign you can prevent animal heating if
detected temperature is under selected threshold, but heating is not necessary.
Several additional controls for acquisition of physiological monitoring parameters can be tuned in the
SkyScanVisual.ini file located in the same folder as SkyScanVisual.exe file and main control program
of the scanner. In this file one can find additional gain values for ECG and breathing detection.
Recommended value for ECG gain is 1...3 and for breathing detection is 10-60. In the case of using
enforced breathing with external ventilator, breathing channel gain can be even low.

8 CONTROL PROGRAM FUNCTIONS2
8.1 General layout
The control program contains a central image area, a main menu at the top, a toolbar for quick
access to the most useful functions, and a status bar at the bottom. The main menu gives access to
all system functions.
There are three submenus available: Actions menu, Options menu and Help menu.
The title bar at the top of the control program window contains several buttons:
The title bar contains the name of control program and [during scanning] data filename prefix, which
is acquiring or was acquired last. To move control program window, drag the title bar. You can also
move dialog boxes by dragging their title bars. In the next start the control program window and
most dialog windows will be positioned at the places and with the sizes like they have been used last
time.
A title bar may contain the following elements (the colors can be different dependent on used color
scheme):
Control menu accessed by right mouse click to title bar:
Minimize button:
Maximize or Restore button:
Close button:
2
Description based on v1.0 of the control program. If new functions will be implemented in following versions,
the explanations will be included to 1278.txt file supplied inside zip-file with updates.

You can also maximize program window by dragging title bar to the top of the screen and restore
window size by dragging it out. Docking window to the side of the screen will resize it to fit vertical
screen dimension.
8.2 Toolbar
The toolbar is displayed on the top of the SkyScan1278 control software window, below the menu
bar. The toolbar provides quick mouse access to frequently used commands in the SkyScan1278
control software.
 This control in the tool bar is to start/stop the x-ray source. In the first start of the
day the source may require slow rising voltage and current: this “aging” process will be
displayed in X-ray Console window. Following starts will take several seconds. This button
executes the same commands as the Actions -> X-Ray Start/Stop command in the menu.
 The next button in the tool bar is to start/stop the live imaging (Grab Image). In this
imaging mode, the images are continuously acquired and displayed on the screen. Similar
function can be found in menu Actions -> Grab Image. This command will start the x-ray
source if it is not started yet in the case of selected “Start X-ray for imaging modes” at
Options -> Preferences.
 The next control in the tool bar is to take a single image (Snap Image) and show it on
the screen. The acquired image may accumulate several frames like it defined in Options->
Acquisition. Similar function can be found in menu Actions -> Snap Image. This command will
start the x-ray source if it is not started yet in the case of selected “Start X-ray for imaging
modes” at Options -> Preferences.
 This toolbar button open or close image from visual camera with physiological
monitoring information. It starts or close separate program SkyScanVisual, described in
previous chapter of this manual and switch ON or OFF LED illumination for visual camera.
 The next control in the tool bar allows setting up the scanning parameters and start
scanning procedure. The same function can be called from menu Actions -> Start Scanning.

 This control in the toolbar sends last acquired dataset to NRecon program for
reconstruction. See also Actions -> Start Reconstruction in the menu.
 This button in the toolbar starts the volume rendering program CTvox. The same
program can be started from menu Actions -> Start Volume Rendering.
 This button in the tool bar starts the viewing program DataViewer. The same
program can be started from menu Actions -> Start DataViewer.
 By pressing this button the 2D/3D analysis program CTAn will start. The same
program can be started from menu Actions -> Start 2D/3D Analysis.
 This button opens About Box with information about program version and links to
information resources.
 Small downarrow in the right bottom corner of the toolbar allows toolbar customization.
Original order of toolbar buttons can be restored by selecting Add or Remove Buttons ->
Standard -> Reset Toolbar.

8.3 Status bar
The Status bar is displayed at the bottom of the control software. It contains number of control fields
and indicators:
 The first control in the status bar contains blue slider and numerical indicator of current
gantry rotational position. To change angular position click by mouse (don’t drag) to specific
point of the slider. Full range corresponds to [0,360] degree rotation. By moving mouse
cursor over slider without clicking you will see tooltip with expected angular position.
Clicking to the angular value in the right side of the slider allows selecting exact rotational
position by numerical value.
 The second control in the status bar allows moving animal in and out by pressing to
corresponding small buttons with green arrows. The movement will continue as long as
corresponding button has been pushed. Alternatively, you can move animal bed by dragging
on the image with pressed left mouse button and Ctrl in keyboard – the movement will be
executed after releasing left mouse button. The position can be also adjusted by introducing
numerical value after clicking to position indication in the right hand side of this pane.
 Next pane in the status bar indicates number of pixels in currently selected image format and
the pixel size on the object plane. Clicking to this will open submenu for selecting different
image formats. The images in different formats may look similar on the screen because all
image sizes will be scaled according to the size of program window, but saved to disk images
will contain selected number of pixels.
 The fourth tab in the status bar indicates current energy filter and allows selecting different
filters by mouse click with following choice in pop-up submenu. Selecting certain filter will
readjust voltage on X-ray source according to settings in Options -> Scanning Modes dialog.
 Next indicator on the right hand side of the status bar shows progress in the current process
or information on exposure time in current mode.

8.4 Actions menu
The “Actions” menu offers the following commands.
X-Ray Start/Stop Switches ON or OFF power for x-ray source and locks/unlocks animal
transport system door.
Grab Image Starts / stops taking images continuously
Snap Image Takes one single image.
Open Image... Opens and displays an image from a file on disk.
Save Image... Saves image to disk.
Delete Dataset Deletes full dataset with selected file prefix from the disk
Start Scanning Opens scanning parameters dialog with following scanning start
Start Connected Scanning Starts multiple scans for long object with automatic connection to
single set of results in reconstruction. This option becomes available
after selecting top and bottom of scanning interval by mouse double
right clicks to corresponding positions and in the case if difference in
selected positions cannot be covered by a single scan.
Start Reconstruction Sends acquired dataset to reconstruction.
Start Volume Rendering Sends reconstructed dataset to CTvox for volume rendering.
Start DataViewer Sends reconstructed dataset for viewing by DataViewer.
Start 2D/3D Image Analysis Sends reconstructed dataset to CTan for 2D/3D analysis.
Exit Exits the SkyScan1278 control software.

8.4.1 X-Ray Start/Stop
The Actions -> X-Ray Start/Stop menu gives the option to start or to stop the X-ray source. When X-
ray source is activated, the animal transport system door will be locked. Once the source is powered
an X-ray sign is displayed on the screen.
Double click the X-ray sign to open the X-ray Tube window. The same X-ray Tube dialog can be called
from Options -> X-Ray Source menu. The X-ray sign will disappear when executing the Actions->X-Ray
Start/Stop menu command again after completing voltage and current decreasing to zeros.
The X-ray Tube window has several controls:
Left part of this dialog indicates type of X-ray source and elapsed time of its usage. The right part
contains blue bars with pre-set values, red bars with current values and sliders to change the values.
The checkbox in the bottom can be used to maximize source power for selected voltage.
If main program window will be clicked by mouse or another window will be activated, the X0ray
Tube dialog may be hidden behind main program window. Use Windows taskbar in the bottom of
the screen to get this dialog back to the top of the main window.

8.4.2 Grab Image
The Actions -> Grab Image menu command starts or stops continuous acquiring and displaying on
the screen the images from the x-ray camera. During image acquisition and displaying, one can
measure the linear dimensions of the objects by dragging with left mouse button pressed on the
imaging area or one can display a horizontal intensity profile through the line, where mouse cursor
currently located, by the right click.
8.4.3 Snap Image
The Actions -> Snap Image menu acquires a single image and displays it in the imaging window. In
this mode the image will be acquired using averaging of several frames if such averaging selected in
Scanning Options dialog, which can be called by Options -> Acquisition menu.
8.4.4 Open Image…

Ctrl-O
The Actions -> Open Image gives the option to open/load an image file from the disk or a network
shared location.
You can select the location of the file using the left hand side of the "Open" dialog, the file format in
the right bottom part and then choose the file which you want to open by typing the filename in the
bottom area or by double clicking to the file in the list of names. The loaded image will be displayed
in the imaging area of the SkyScan1278 control program.

8.4.5 Save Image…
Ctrl+S
The Actions -> Save Image menu gives the option to save an image file to disk or to a network shared
location.
One can select a location for the file using the left hand side of the "Save Image" dialog, choose the
file format in the bottom part and choose the file name, which you want to use by typing it in the
corresponding editable area. Click to existing in the list file if you want to overwrite it.
The image can be saved in one of the two supported formats: 8-bit bitmap (*.bmp) or 16-bit TIFF
(*.tif).
8.4.6 Delete Dataset

The Actions -> Delete Dataset menu firstly opens submenu to define type of dataset to be deleted:
After selecting type of dataset, the program will show full list of file prefixes of datasets with selected
type in current data folder. The data folder can be adjusted in Options -> Data Folder...
To delete dataset from the disk, select file prefix and press Ok or double click to file prefix, which you
want to delete.

8.4.7 Start Scanning
The Actions -> Start Scanning menu firstly opens dialog to define scanning parameters. The Scanning
option dialog can be seen in several variations dependent on last selection of scanning parameters.
First type of this dialog corresponds to step and shoot scanning:
 Filename prefix: The acquired images will be saved to the files with selected prefix name
extended by 8-digit index for angular position indication and .tif extension as a 16-bit TIFF
files.
 Data directory: The Data directory defines location on the local disk or on the shared
network location where acquired dataset will be saved. Use “Browse” button to select
different location or to create new folder.
 Scanning mode defines type of gantry movement during acquisition. It can be scan and shoot
for detailed scanning or continuous rotation for fast scanning
 Rotation step (deg): the Rotation step in degrees, which will be used for gantry rotation
during collecting angular views for tomographic reconstruction. By changing the rotation
step, the time of the acquisition cycle and disk space required to save dataset will increase or
decrease, which can be seen at the bottom of the dialog at Estimated scanning time and
Dataset size.
 Averaging (frames): if this checkbox selected, at each angular gantry position the specified
on the right field number of frames will acquired and averaged before saving angular
projection to the disk. By increasing the number of frames, the noise can be reduced but the
time of acquisition will increase.

 360 deg scanning: by selecting this option, the CT scan will take images over the complete
turn of the gantry while in the case of unchecked this option the angular projections will be
collected over a little more than 180 degrees, which is enough for tomographical
reconstruction. Using 360 deg. scanning option may slightly reduce artifacts in the places
with big density gradients, but requires near twice longer scanning time.
 X-ray off after scanning: this option allows switching OFF the X-ray source after completing
data acquisition cycle. In case of multiple connected scans for long object (described in next
chapter), the X-ray source will be switched OFF after finalizing the last scan.
 Time-resolve scan option is available after opening Physiological Monitoring window by
Options -> Visual Camera ON/OFF and allows collecting selected number of images in every
angular gantry position for following sorting according to physiological monitoring time
marks to create time-resolved (4D) reconstructions. More details on time-resolve
reconstruction can be found in Chapter 9 of this Manual. The Physiological Monitoring
subsystem described in details in Chapter 7 of this Manual.
 Send e-mail after scanning to address: This option activates sending an e-mail after finishing
the scan to the selected e-mail address. This option is available if e-mail service is properly
activated in Options -> Scanner Settings. To test proper receiving of e-mails, automatically
sent by SkyScan1278 system, one can use the send test e-mail now button. After successful
finalizing the scan, you will receive e-mail with direct link to acquired dataset. Clicking to this
link you can open remote or local folder where all results are collected and start to process
them remotely. If scan will be interrupted by operator or by any problem, the e-mail with
corresponding information will be also send to selected address.
 Partial width: Partial width selection allows saving disk space when the object takes only part
of the width of the image. During the adjustment of the partial width, the selected part will
be marked on the image. Be sure that the object will always stay inside selected partial field
of view during a full rotation when scanning.
 The bottom part of the dialog window contains indications of estimated scanning time as
well as required and available disk space.
After selecting necessary parameters, pushing Scan button will start the scanning process, Close
button allows exit this dialog without starting scan, but with stored selected settings and Cancel will
exit without saving settings.
During scanning process the progress dialog will be displayed on the screen, which will show run-
time estimation of remaining scanning time (will be shown after completing several angular
positions) and allows interrupting the scan:
The checkboxes in the bottom of progress dialog allows closing scanner control program after
finalizing the scan and if necessary, shutdown SkyScan1278 system including internal workstation.

In the case of selecting Scanning Mode as a, the Scanning Options dialog will be shown with slightly
different layout:
In this case you can select one of two available gantry rotation speeds instead of rotation step for
image acquisitions. The highest speed allows shortest scanning time, which is in combination with
unchecked 360 deg scanning will allow getting scanning time around 7 sec. Lowest speed will provide
better quality, but longer scanning time, which is in the case of selected 360 deg scanning will be just
under one minute.
In the case of continuous gantry rotation, the image on the screen will not be updated because
image updating may increase scan duration. All angular images will be collected to computer
memory and will be saved to the disk files during gantry return to original position after completing
the scanning process.
8.4.8 Start Connected Scanning

The Actions -> Start Connected Scanning menu allows scanning objects/animals longer than single
field of view using multiple partial scans automatically connected during reconstruction to one final
set of results. To define top and bottom of scanning area the operator should move animal bed to
the position where top of the expected scanning volume can be seen on the image and by using
double right mouse click define first limit of scanning volume. Afterwards the animal bed should be
moved to get final scanning position inside the image and by right double click second limit of the
scanning volume can be defined. If you wish to modify the limits, similar marking by mouse right
double click can be repeated. Only last two selected positions will be taken into account. If distance
between selected positions cannot be scanned in one standard scan, this option in the menu
becomes available and selecting this option will start scanning procedure similar to described above,

but it will contain several partial scans with automatic animal bed movement in between of partial
scans. The partial scans contain all necessary information (in *.log file) to get properly connected
during reconstruction. The filename prefix for projection files in all partial scans will contain
extension “~NN” where NN is a two-digit index of partial scan.
8.4.9 Start Reconstruction
The Actions -> Start Reconstruction menu starts the NRecon reconstruction program. This command
expects a valid acquisition result in the current data folder (data folder can be defined in Options ->
Data Folder...). In the case of presence of several datasets in the current data folder, the operator
can choose one for reconstruction in the dialog, which will appear after calling Start Reconstruction
function. Afterwards control program will link acquired dataset with reconstruction program NRecon
and will start this program. The User Manual for the NRecon reconstruction program
NRecon User Guide: http://www.bruker-microct.com/next/NReconUserGuide.pdf
8.4.10 Start Volume Rendering
This command starts the external program CTvox, which performs volume rendering of
reconstructed results. The User Manual for CTVox program can be downloaded from Bruker microCT
website:
CTvox Quick Start Guide: http://www.bruker-microct.com/next/CTvox_QuickStartGuide.pdf
8.4.11 Start DataViewer
This command starts the external program DataViewer, which shows reconstruction results saved in
BMP or JPG format as a slice-by-slice movie or in the form of three orthogonal virtual slices crossed in
any point of the reconstructed volume. It also allows distance measuring in 3D, rotating and reslicing
a dataset in any alternative orientation.

8.4.12 Start 2D/3D Image Analysis
Selection of Actions -> Start 2D/3D Image Analysis sends reconstructed results to the external
program CTan, which can e.g. perform 2D and 3D numerical image analysis and build triangulated
surface rendering. These surface rendered models can be viewed in the connected CTvol program.
Complete user manuals in pdf-format are available for downloading from Bruker microCT website:
CTan User Manual: http://www.bruker-microct.com/next/CTan_UserManual.pdf
CTvol User Manual: http://www.bruker-microct.com/next/CTvol_UserManual.pdf
8.4.13 Exit
Use this command to end your session. You can also use the Close command on the Title Bar. Double
click on the small icon in the left corner of the title bar is the same as the Exit command.

8.5 Options Menu
The Options menu offers the following commands:
Acquisition... Opens the acquisition dialog to setup the scanning parameters.
Data Folder... Browse to change the data directory for the scanning results.
X-ray Source… Opens the X-ray Source Console window.
Filters Gives the option to choose between different energy filters.
Visual Camera ON/OFF Starts /Stops physiological monitoring and imaging from visual
camera.
Dose Meter SHOW/HIDE Shows or hides Dose Meter window
Preferences… Opens the preferences window.
Configurations Opens submenu to save or load all scanner settings
View Gives options to modify program appearance.
Annotation Allows add study and animal description to log-file
Update Current Flat-Field Refreshes flat-field references for current imaging mode.
Recover log-file from Encrypted Copy Restores log-file using automatically saved encrypted copy
Scanner Settings... Opens dialog to adjust scanner parameters.
Scanning Modes... Opens dialog to adjust exposures and other scanning settings.

Some functions in Options menu may be greyed to prevent unauthorised access to important
settings. To get access to such settings use Ctrl+Alt+Shift+S keyboard combination. Next click to the
same combination of keys will restore protection for functions with important settings.
8.5.1 Acquisition
The Options -> Acquisition command opens the Scanning Options dialog described above in the
chapter 8.4.7, but without Scan button. All settings can be stored by selecting Close button or
discharged by selecting Cancel button.
8.5.2 Data Folder...

The menu Options -> Data Folder... gives the option to select the destination folder/directory for the
scanning results via the windows standard folder browsing dialog. The selected directory can be on
the local drive or can be located on the network storage:
Use Make New Folder button to create subfolder under currently selected.
8.5.3 X-ray source…

The Options -> X-ray Source… menu opens the X-ray Tube window described above in the chapter
8.4.1.
8.5.4 Filters
The Options -> Filters menu offers the user to choose between 4 different energy filters.

The same options can also be selected from the status bar control. The currently selected filter is
greyed out. Selecting different filter will automatically modify setting for X-ray source, such as
voltage and current, according to selected in Options -> Scanning Modes.
8.5.5 Visual Camera ON/OFF
This function starts or stops the SkyScanVisual program and illumination for visual camera. The
physiological monitoring functions provided by SkyScanVisual program described above in the
chapter 7 of this Manual. This function should be selected to get time-resolve acquisition available.
8.5.6 Dose Meter SHOW/HIDE

The Options -> Dose Meter SHOW/HIDE menu shows or hides following Dose Meter window:
The dose measurement based on absorption calculation from acquired X-ray images. The dose meter
should be calibrated with all three animal cassettes. For calibration, install empty animal cassette,
switch on live acquisition by toolbar button or Actions->Grab Image menu, select installed animal
cassette in the top left part of Dose Meter dialog and press calibration button. In the case of using
ECG electrodes or/and temperature probe, all such parts should be installed in cassette before
calibration.
Dependent on selection in the middle part of the dialog, the accumulated dose or dose rate will be
shown in the bottom part. The accumulated dose can be set to 0 by pressing reset button. It will be
also set to 0 when animal transport system will be open for animal exchange. In the case of dose
meter window is shown on the screen, the accumulated during particular scan dose will be saved
with dataset into associated log-file. Switching between accumulated dose and dose rate does not
interrupt accumulated dose counting.
The Dose Meter window can be closed by close button or by second click to the Options -> Dose
Meter SHOW/HIDE menu.

8.5.7 Preferences...
The Options -> Preferences... menu opens following Preferences dialog:
 Fit the window checkbox allows scaling any image format to the size of imaging area inside
program window.
 Start X-Ray for imaging modes switches X-ray source ON if any imaging mode selected
without additional clicks to X-Ray ON/OFF menu function or corresponding toolbar button.
 Sound notifications checkbox switch ON or OFF playing short soundtracks for indication of
beginning or ending some functions and for attention to error messages.
 Show dosemeter in the start automatically opens Dose Meter window during initialization of
control software.
 Flat-field correction checkbox allows switching intensity correction across the images ON and
OFF. Flat-field correction can be also toggled by double mouse click to the text indication in
the left top corner of the imaging area in the program window with text indication ff or flat-
field correction OFF. Typical position of this switch is ON.
 Add automatically incremented suffix allows saving datasets with additional incremental
numbering added to selected filename prefix in every scan started from touchscreen. It
allows avoiding typing new dataset filename prefixes in corresponding dialog on the screen
of computer every time before next scan will be started from the touchscreen.
 Create new folder with incremented name distributes every new dataset started for scanning
from the touchscreen to separate subfolder with incrementally updated numerical index in
the folder name.
 Current index shows and allows modifying current index for last two listed options.
 After Scanning: start reconstruction allows automatic start of reconstruction program after
the end of the scan using reconstruction settings from predefined protocol or previously
used settings

 After reconstruction start ... selects program, which will be automatically start after
reconstruction. The reconstructed set of results will be automatically send to selected
program
8.5.8 Configurations
This command opens following submenu:
A configuration contains all scanner settings and all flat-field references. You can save, load or delete
existing configurations. The Preset option allows loading factory predefined settings and flat-field
references. Get Settings from *.log File allows repeating scanning with settings saved in the log-file
with one of previously made scans. In this particular case, flat-field references will not be updated.
8.5.9 View
This command allows modifying program window and dialog windows appearance according to
selection from the number of available layouts and colour schemes used in most popular Windows
applications.
8.5.10 Annotation
This command opens following window:
The fields in this dialog can be filled by essential information about scanned animal and study
purposes as well as information about the operator and study date. All information from Scan
Annotation window will be saved in the log file associated with acquired dataset.

8.5.11 Update Current Flat-Field
This Option allows collecting flat-field reference maps for current camera image format and energy
filter. Before acquiring flat-field reference remove animal cassette from the scanner. Acquired flat-
field references will be saved automatically and will be used in following scanning.
8.5.12 Recover log-file from Encrypted Copy

The control software saves all scanning parameters and associated information in *.log file with
filename identical to selected filename prefix in the same location where all acquired images are
placed. The *.log file is a text file, which can be open and modified by any text editing program.
To avoid possible manipulations with valuable information on scanning settings, the control software
always saves encrypted copy of the original log-file. The Recovery log-file from Encrypted Copy
function allows restoring original information from the encrypted copy back to the text-form log-file.
It keeps encrypted copy untouched for possible next recovery.
8.5.13 Scanner Settings…

The Options -> Scanner Settings… menu gives access to all settings of your system. The settings are
listed in the following Scanner Settings dialog:
 Scanner S / N: serial number of the scanner, which will be included in all *.log files saved with
datasets.
 Pixel size for largest image format (um) is a scanner calibration for proper distance
measurements and reconstruction geometry. This parameter corresponds to pixel size in the
object plane for largest image format. To verify this parameter one can scan a cylindrical
object with well-known diameter, reconstruct central section, measure in CTan “area
equivalent object diameter” and modify (if necessary) existing setting according to
proportion between measured object diameter and calculated by CTan.
 Image rotation (deg): is an angular misalignment between rotation axis and vertical direction
of the pixels in the camera, which will be automatically compensated in every image
acquisition. This parameter can be calculated in Engineering Mode of NRecon by comparison
of misalignment in the top and in the bottom of the object.
 Image centering (pix): is a positional misalignment between rotation axis and central column
of detector measured in pixels at largest image format. This parameter can be taken from
Image Misalignment calculation in NRecon from the scan using this parameter as a 0.
 Server to send e-mail messages specifies server connection used for e-mailing (contact your
local IT staff if you don’t know this name)
 From and Subject specify the information, which will be included in corresponding fields of e-
mail, which will be send to you. Some local security settings can prevent receiving e-mails
with unknown sender name. Subject name may violate spam detection rules. In this case you
can modify information in From and Subject fields for e-mails, which the system will
automatically send to you, to comply local security rules.
 Save events to log-file checkbox activates saving reports on scanner activities to
SkyScan1278.log file, located in the same folder as the control program. It is strongly
recommended to keep this option selected for possibility to trace down the origin of the
problem if any occur.
8.5.14 Scanning Modes...

The Options -> Scanning Modes allows modifying camera exposure, adjusting X-ray source voltage
and current used for every energy filters, changing names for energy filters, acquiring flat-field
references for selected or all filter / image format combinations, automatically adjust camera
exposures, etc.
 Filter Name: defines the names of the energy filters how they will be shown on the screen.
As a factory pre-set, the software uses materials and thickness of the filters. For particular
application such technical description can be replaced by application specific name according
to practical usage.
 X-Ray Source – Voltage (kV): this line of the table allows editing X-ray source accelerating
voltage for every energy filter. The accelerating voltage defines peak energy of X-ray
spectrum, emitted by X-ray source. Selected value of tube voltage will be automatically
adjusted during filter changing.
 X-Ray Source – Current (uA): the currents for X-ray source for every filter. The current defines
intensity of radiation emitted by X-ray source and limited by maximum power of X-ray
source.
 Camera exposures (ms): The values of camera exposures for all possible filter / image format
combinations. The screenshot above shows typical values. The exact values can be selected
using automated procedure during flat-field updating process described below.
 Rot. Step (deg): pre-sets for rotation steps between gantry’s angular positions, which will be
suggested in Scanning Options dialog in the beginning of the scan. Every doubling in number
of pixels in horizontal direction of the image format requires twice smaller rotation steps.
 Flat-Field reference map(s) updating can be selected by switching for one of three possible
options: Do not update flat-field references selection will store all modified parameters
shown in the tables in this dialog, but will not update any flat-field reference. Update Flat-
field for marked modes and modes with modified exposure can be used for selective update
of flat-field reference in the case of changing exposure of manual selection for modes.
Selected modes shown with blue rectangle around the exposure time. The selection can be
added or removed by mouse click to editable area of any exposure indicator. Update flat-
field references for all listed modes allows updating all flat-fields for the system.
 Update bright reference only will update only flat-field references using X-ray radiation
(bright-field references) and keep previously saved flat-field references without X-rays (dark-
field references). The dark-field references are relatively stable and shouldn’t be updated
periodically unless big changes in exposure time.
 Adjust exposure automatically allows automatic adjustment of optimal exposure time for
every mode, which will be updated, before acquiring flat-field references.

8.6 Help Menu
The Help menu contains only access to About Box with information for your SkyScan1278 system:
8.6.1 About SkyScan1278…

About SkyScan1278... displays the version number of the control software, the versions and status of
hardware parts connected to the system and the contact details of the Bruker microCT:
Shown on the above screenshot information about the X-Ray tube temperature is taken in the
moment of opening About box.
By clicking on the underlined items you can send an e-mail to Bruker microCT headquarters or open
the Bruker microCT website.

9 4D (TIME-RESOLVED) ACQUISITION AND RECONSTRUCTION
9.1 Time-resolved method
The Time-resolved tomography or 4D tomography refers to a special scanning mode in which each
event is recorded sequentially with selected properties together with other events happening in the
meanwhile. For example, if we consider the acquisition of one x-ray image as an event, the time of
the acquisition, together with any physiological signals - such as from breathing - that are measured
in the animal being scanned, can be recorded.
The SkyScan in-vivo scanners have enabled time-resolved acquisition together with a physiological
monitoring system to allow users to acquire 4D images. Alternatively, one can use this mode to
reduce motion artifacts (e.g., breathing artifacts). More specifically, at each view, or gantry angular
position, multiple projection images are acquired and the acquisition time of each image is recorded.
These projection images at one angular position are called time frames. In the meanwhile, the time
marks of a specified physiological signal, which may indicate breathing or heart beating or any
periodic movement, are recorded separately by a physiological monitoring over the duration of the
scan.
How to acquire a time-resolved scan?
In the Scanning Options dialog as shown below, frame averaging will be disabled when Time-resolved
scan is selected. Instead, multiple frames at one angular position will be acquired. All acquired
images will be saved individually, and time marks corresponding to the exact acquisition time of each
image will be recorded in a separate text file. The number of frames per angular position can be
given in the corresponding edit box (for example – 10).
During acquisition, 10 sequential images will be collected and saved directly into individual files
without any averaging. The exact time marks of each image acquisition will be recorded in a separate

text file as a list. The list of these time marks will be used later for sorting, together with time marks
from physiological monitoring. The following graph illustrates the acquisition of a time-resolved
scan: the red numbers indicate the sequential image frames obtained at each angular position, and
the red marks on the time axis at the bottom are the corresponding time marks for the frames.
Physiological monitoring works independently from acquisition process. Physiological monitoring

subsystem can record movements of the animal using a TV-camera mounted on the object bed,
breathing signals from an airflow sensor or heart beat through integrated ECG amplifier. One or
several of available signals can be selected to create synchronization time marks. In most cases, the
breathing signals are used. The graph below illustrates the combination of a time-resolved scanning
with monitoring on breathing (shown in blue curve). The exact time marks of each breathing cycle
recorded by the physiological monitoring subsystem (blue marks) are also saved to a separate text
file as a list.
At the end of a time-resolved acquisition, we will get a set of projection images and two 2 text files
with time marks. Please note that slightly different name convention is used for time-resolved data.
If a time-resolved scan is given prefix MyListModeData, and there are in total 300 angular views and
10 time frames per view, the following items form a complete dataset:
MyListmodeData.log the normal log file, which contains a few more entries related to the time-
resolved acquisition
MyListmodeData_pm.lst contains a list of physiological time marks in text format
MyListmodeData_aq.lst contains a list of acquisition time marks in text format
MyListmodeData~dddd~dddddddd.tif the projection files: the first 4 digits (~dddd~) is the time
frame index starting from 0; the last 8 digits (dddddddd) is the normal sequence number starting
from 0. For example, MyListmodeData~0008~00000255.tif is the 9-th frame at 256-th angular
position. In total, there will be 300 x 10 = 3000 projection files.
9.2 Sorting time-resolved data

A time-resolved scan has to be sorted offline before any further processing. This can be done with
TSort, a standalone SkyScan program. For detailed and up-to-date information on how to use the
TSort, please refer to online document coming with this program. The screenshot below shows that a
raw time-resolved scan with 168 angular views and 8 time frames per view is loaded and is ready to
be sorted into 4 time bins.

The TSort can be invoked by drag-and-drop, double-click or by other SkyScan programs. Multiple
instances are allowed: care should be taken when one works on the same dataset with multiple
instances of TSort. The original dataset will not be modified in any way by Tsort. The sorted datasets,
or the bins, are stored in the same directory as the input time-resolved data. They are ready for
reconstruction and further processing. These sorted datasets have a fixed name convention as well:
MyListModeData ~#dddd~dddddddd.tif, where the 4 digits in ~#dddd~ contains two numbers:

the first 2-digit number is the bin index starting with 0, and the last 2-digit number is the total
number of bins; the second 8 digits dddddddd is the view index as usual. For example,
MyListModeData~#0204~00000255.tif is the 256-th projection image in the 3rd time bin with 4 time
bins in total.
When opening a time-resolved dataset, time information is retrieved from the two lst files. On the
main window, a table at the upper part shows a few relevant acquisition parameters: number of time
frames, number of views, the average time interval between two time frames at one angular
position, and the average synchronization signal interval. It is generally assumed that the mean sync
signal interval is the mean time period of a physiological signal, e.g., a breathing cycle, and should be
at least a few times longer than the average time interval between two time frames.
Sorting consists of dividing a cycle evenly in time into a few segments (virtual division), also called
time bins. This is performed for each physiological monitoring time cycle. Each bin is then filled with
images obtained within the corresponding time interval. Irregularity of the physiological signals are
tolerated, as each cycle is divided individually, and variation in number of images per bin is taken into
account: a bin with multiple frame images is filled with the mean of the images, a bin with 0 frame
image, also called a “hole”, is replaced by its nearest neighbour.
The number of bins can be given interactively. In TSort, the bin number is limited to a maximum of
16. To minimize sorting error, it is not desirable to have more bins than the number of time frames
per angular view. Whatever the number of bins per cycle is given, sorting statistics will be shown in a

table at the lower part of TSort window: number of empty views and its percentage in the total
number of views, and number of time frames per view for the majority of views. Note that you may
switch a bin on/off by double-click on the row. This is handy if you are only interested in a particular
phase of the cycle, for example, only when the lung of the animal is at its fullest. You may sum up all
the time frames at one angular position. This is equivalent to the situation when a normal scan is
done with frame averaging.
9.3 Data sorting process

To further illustrate how a time-resolved scan is sorted. Let’s divide every breathing cycle into 4 time
bins: A, B, C and D as depicted in the graph below. For time bin A at angular position 0, TSort
searches for all images acquired inside the time interval: frame 2, 7 and 8 are found, which are
averaged to form the first projection image A0 in a new sorted projection dataset . This binning
procedure is then performed for all angular positions to form A1, A2, … . Together with these new
projection images, a log file is created based on the original one to form a complete scan which is
ready for reconstruction.
TSort performs the same procedure for all four time bins and finally creates four new sets of angular
projections: A0,A1,A2,….; B0,B1,B2,….; C0,C1,C2,…; D0,D1,D2,… as shown in the following picture:

9.4 Reconstruction of time-resolved data
The sorted time-resolved scans (time bins) can be reconstructed in the normal way in NRecon. No
special setting required.
9.5 Visualization of time-resolved results

Raw time-resolved projection images, sorted time-resolved projection scans and reconstructed time-
resolved scans can be viewed with DataViewer.
All scans can be viewed either in 2D or 3D with the time axis (labelled “T” in DataViewer). An
“animated” view can be obtained by either scrolling on the T-axis or using the animation button
(select “Time” as the animation parameter in Options->Preferences at viewing). A typical screenshot
is shown below.

10 GLP (GOOD LABORATORY PRACTICE) MODULE
10.1 Access rights

The GLP module is a separate program, which allows management of user’s rights for access to
different functions of control program when activated. There are three levels of access: user,
operator and supervisor. Following table summarizes access rights to all functions in control
software:
FUNCTION user operator supervisor

X-Ray ON / OFF yes yes yes
Grab / Snap Image yes yes yes
Open Image yes yes yes
Save Image yes yes yes
Delete Dataset no yes yes
Overwrite Existing Image no yes yes
Start Scanning yes yes yes
Scanning with Overwriting no yes yes
Start Reconstruction yes yes yes
Start Volume Rendering yes yes yes
Start DataViewer yes yes yes
Start 2D/3D Analysis yes yes yes
Options->Acquisition yes yes yes
Options->Data Folder yes yes yes
Physiological Monitoring ON/OFF yes yes yes
Dose Meter Show/Hide yes yes yes
Preferences: Switch Flat Field OFF no yes yes
Configurations: Save yes yes yes
Configurations: Load no yes yes
Configurations: Delete no no yes
Configurations: Load Preset no yes yes
Configurations: Load from log-file no yes yes
Update Flat-Field for Current Mode no yes yes
Recover log from Encrypted Copy no no yes
Scanner Settings no no yes
Scanning Modes no no yes

10.2 Installation
1. Find the UsrMan.exe application in the home directory of the SkyScan1278 control software.
2. On the first start of the UsrMan.exe, the following dialog will be shown.
3. Please send this serial number to Bruker microCT, to get a license file necessary to use the
User Management module.
4. Once we receive your request with serial number, a license file and administrator password
will be sent back to you.
5. Copy received license file into directory where the SkyScan1278 control software is located
and where UsrMan.exe application is.
6. By starting the UsrMan.exe application now, you will be prompted to provide credentials for
the application as shown in the following dialog.
7. Once successfully started, you will see the main dialog of the UsrMan.exe application.

10.3 Adding New User
1. Click Add user.. button to add a new user to control SkyScan1278 scanner.
2. Type a user name and a password and press OK button. Application will ask you for the
password once more
3. Repeat the procedure 1 and 2 to add more users.
10.4 Managing user rights

1. There are three types of the user accounts possible with UsrMan.exe application. A
supervisor with full access to all the functionality of the SkyScan1278 control software. Also
user and operator with limited access.
2. To adjust user access rights use selection next to the user name, if not selected, user account
will have the operator rights for the SkyScan1278 control program.
10.5 Required user management to run control software

1. If you run SkyScan1278 control software without creating any user you will see the error
message “There are no registered users for the application”.
2. To run SkyScan1278 control software without access by particular user, you can disable the
accounts from UsrMan.exe application. You need at least one user account already created
to disable the account.
10.6 Deleting user account

1. Select the name of the user account you want to delete ,
2. Press delete button.
10.7 Change password for the user account

1. Select user account for which you want to change the password.
2. Click Change password button
3. Enter new password. You will need to re-enter password once more for the confirmation
dialog.
4. Administrator password cannot be changed for the UsrMan.exe module.

10.8 Specify number of logon attempts
You can change the number of attempts to login in the user management module by select spin
control in the UsrMan.exe application.
10.9 Uninstalling user management

1. Open a command window in Microsoft Windows System by typing cmd in the Start->Run.
2. Change the directory where UsrMan.exe application resides.
3. Type UsrMan.exe /u to uninstall the application.
4. When prompted, type in the administrator password.

11 SERVICE AND SUPPORT
The SkyScan1278 scanner is designed as a maintenance-free instrument and doesn’t require any
periodical service.
New versions of control software and all associated program packages supplied with your scanner
may be available for download in the “Software Updates” section of the Bruker microCT website:
http://www.bruker-microct.com/products/downloads.htm.
In the case of any problem please contact your local distributor. A list of distributors is available at:
http://www.bruker-microct.com/company/distributors.htm.
For all users of micro-CT instruments Bruker microCT organizes annual User Meetings. Information
on previous Meetings and announcement of forthcoming events can be found at the Bruker microCT
website: http://www.skyscan.be/company/company.htm (=> User Meetings)
If your control computer is connected to internet, you can get access to the Bruker microCT website
by simple click to the corresponding underlined web-address in the “About…” box in the Help part of
the Main Menu. In the same place you can find a link to send e-mail to scanner producer.
: This symbol warns about an ionizing radiation hazard coming from an X-ray source.

12 DOCUMENT VERSION
V1.0 Initial document, released Octiber 2015.


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SkyScan-1278 User Manual V1.

© Bruker microCT 2015

Designed and manufactured by Bruker microCT in Belgium

SkyScan-1278 User Manual V1.0 10/2015 1

1 INTRODUCTION IN X-RAY MICROTOMOGRAPHY .......................................... 6

2 SKYSCAN-1278 SYSTEM OVERVIEW ............................................................ 12

2.1.1 General ............................................................................................... 13

2.1.2 X-Ray Source ...................................................................................... 13

2.1.3 X-ray detector:..................................................................................... 13

2.1.4 Animal handling system ...................................................................... 13

2.1.5 Integrated physiological monitoring ..................................................... 13

2.2 Supplied software ....................................................................................... 13

2.2.1 Scanner control and data acquisition software .................................... 13

2.2.2 Physiological monitoring software “SkyscanVisual” ............................ 14

2.2.3 Reconstruction software “NRecon” with GPU acceleration ................. 14

2.2.4 Software for time –resolved (4D) reconstruction “TSort” ..................... 14

2.2.5 Visualization software “DataViewer” .................................................... 14

2.2.6 Format Converter “TConv” and “DICOM converter” ............................ 15

2.2.7 2D/3D morphological analysis software “CTan” .................................. 15

2.2.8 Realistic visualization by surface rendering “CTvol” ............................ 15

2.2.9 Realistic volume rendering software “CTvox” ...................................... 16

2.2.10 Control and Reconstruction Workstation ............................................. 16

2.2.11 Physical: .............................................................................................. 16

2.3 Installation requirements ............................................................................ 17

3 INSTALLATION PROCEDURE ......................................................................... 18

4 SCANNER’S CONSTRUCTION ........................................................................ 25

5 GETTING STARTED ......................................................................................... 29

6 TOUCHSCREEN FUNCTIONS ......................................................................... 41

8 CONTROL PROGRAM FUNCTIONS................................................................ 47

8.4.1 X-Ray Start/Stop ................................................................................. 52

8.4.2 Grab Image ......................................................................................... 53

8.4.3 Snap Image ......................................................................................... 53

8.4.4 Open Image… ..................................................................................... 53

8.4.5 Save Image… ..................................................................................... 54

8.4.6 Delete Dataset .................................................................................... 54

8.4.7 Start Scanning..................................................................................... 55

8.4.8 Start Connected Scanning .................................................................. 57

SkyScan-1278 User Manual V1.0 10/2015 3

8.4.10 Start Volume Rendering ...................................................................... 58

8.4.11 Start DataViewer ................................................................................. 58

8.4.12 Start 2D/3D Image Analysis ................................................................ 59

8.4.13 Exit ...................................................................................................... 59

8.5 Options Menu ............................................................................................. 60

8.5.1 Acquisition ........................................................................................... 61

8.5.2 Data Folder... ...................................................................................... 61

8.5.3 X-ray source… .................................................................................... 61

8.5.4 Filters .................................................................................................. 61

8.5.5 Visual Camera ON/OFF ...................................................................... 62

8.5.6 Dose Meter SHOW/HIDE .................................................................... 62

8.5.7 Preferences... ...................................................................................... 63

8.5.8 Configurations ..................................................................................... 64

8.5.9 View .................................................................................................... 64

8.5.10 Annotation ........................................................................................... 64

8.5.11 Update Current Flat-Field .................................................................... 65

8.5.12 Recover log-file from Encrypted Copy ................................................. 65

8.5.13 Scanner Settings… ............................................................................. 65

8.5.14 Scanning Modes... .............................................................................. 66

8.6 Help Menu .................................................................................................. 68

8.6.1 About SkyScan1278… ........................................................................ 68