In conventional x-ray radiography, information is provided in only two dimensions, (x and y), Information relating to the third or depth (z) direction (corresponding to the direction of propagation of the incident x-rays) is lost as the three-dimensional object is collapsed into a two-dimensional image projected onto film or a detector. In CT imaging, this third dimension is preserved. This is achieved by obtaining a large number of observations at different viewing angles, which allows a cross sectional image to be produced by tomographic reconstruction.
CT image versus a conventional radiograph
Computed tomography (CT) is an advanced radiological imaging technique that provides superior spatial information as compared to standard x-ray techniques.
In conventional x-ray radiography, information is provided in only two dimensions, (x and y), Information relating to the third or depth (z) direction (corresponding to the direction of propagation of the incident x-rays) is lost as the three-dimensional object is collapsed into a two-dimensional image projected onto film or a detector. In CT imaging this third dimension is preserved.
This is achieved by obtaining a large number of observations at different viewing angles, which allows a cross sectional image to be produced by tomographic reconstruction.
Schematic illustrations of back projection
Tomographic reconstruction may be thought of as an advanced form of triangulation.
Features buried within a sample detected by conventional projection radiography can be localized in two dimensions but not in three: the position along the path travelled by the x-ray beam from the source to the detector cannot be determined. However, if we make two measurements at different viewing angles, we can use the process of triangulation to begin to estimate the position of the object within the sample.
Figure a: If we acquire and image though a section of a sample containing two discrete objects, we obtain a profile of the attenuation of the x-ray beam by the objects.
Figure b: If we project the data back along a line corresponding to the direction in which the data was acquired, we obtain a shadow image representing attenuation at this viewing angle. We can then repeat this process at 90 degrees to the first measurement and calculate a second back projection.
Figure c: Combining these two back projections allows us to localize the objects in our sample.
Positional accuracy is even further enhanced by making additional radiographs from more viewing angles and triangulating viewing angles.
Example: CT images of an extracted human tooth
Densely mineralized materials such as teeth and bones are excellent candidates for study by CT imaging due to their strong attenuation of x-rays.
Figure a. Transaxial section from a CT scan of an extracted human tooth. The heavily mineralized outer layer of enamel is clearly distinguishable from the inner dentin layer. Microscopic cracks in the dentin are also clearly visible.
Figure b. Reconstruction of the transaxial slices to produce a 3-D representation of the tooth.
Figure c. 3-D reconstruction with mineralized material set to be opaque to allow visualization of the root canal structures, shown in pink.
Scanning parameters: resolution: =35 um, frame averaging=3, rotation per scan 0.7o, scanned over 360o
Example: Micro CT scan of a rat mandible
In this example, a rat mandible was scanned to assess bone mineral density. Two subscans were acquired and fused to generate the image. Total imaging time was 30 minutes.
Figure a. 3-D reconstruction
Figure b. Sagittal cross section
Figure c. Transaxial cross section
Scanning parameters: resolution: =18 um, frame averaging=3, rotation per scan 0.7o, scanned over 180o
Example: CT image of a mouse knee
Shown here is a three-dimensional reconstruction of a mouse knee from an in vivo scan of mouse. The image was generated by adjusting the attenuation threshold to display only mineralized tissue.
Scanning parameters: resolution= 9 um, filter = 0.5mm Al rotation 0.8o, scanned over 180o. Data was reconstructed using a ring artefact reduction correction=factor of 7, and a beam hardening correction of 30%
Example: Mouse embryo
This scan shows a three-dimensional image of a mouse embryo. Due to the limited mineralization of bone in the embryo, the sample was fixed in osmium tetroxide prior to scanning. It also reflects the same mouse with image clipped to show internal structures.
CT images are acquired with a high performance SkyScan 1176 x-ray microtomography system equipped with a large format 11-megapixel x-ray camera.
An image field width of up to 68 mm allows whole body scanning of rats and mice, with a scanning length of 20 to 200 mm possible.
Selectable image resolutions of 9, 18 and 35 um are available.
Variable x-ray applied voltage (20 to 90kV) and filters allow imaging of a wide range of samples in vivo from lung tissue to bone with titanium implants. The SkyScan 1176 is also well suited to study non-biological materials.
Image acquisition for a standard single field of view (22 mm by 38 mm) at 35 um resolution is seven minutes.
Typically, three fields of view are required to scan a whole mouse, giving a total acquisition time for a whole mouse scan at 35 um of 21 minutes.
- Non-invasive imaging of animal models of human disease
- Non-invasive imaging of genetically engineered animals
- Assess efficacy of novel pharmacological agents
- Assess novel drug delivery and gene therapy approaches
- Develop new contrast agents for diagnostic imaging
The following Skyscan Application Notes are available to University of Manitoba staff and may be found on the data analysis workstations in BMSB 75 and 322:
3D visualization of open and closed porosity
3D volume analysis
Adipose tissue measurement in vivo
Adjacency CTAn 1
Adjacency CTAn 2
Advanced image co-registration in dataviewer
Advanced porosity analysis
Air bubbles in glass
Analysis of low-density material in a high-density container
Anisotropy, MIL and stereology
Ant surface rendering for diamond
Automated trabecular and cortical bone selection
Basic 3D surface rendering
BMD calibration in CTAn
Bone micro-CT analysis general
Bone micro-CT analysis mouse
Bone micro-CT analysis rat
Bone sample scanning and analysis
Color coded 3D size distribution CTVol
Color coded 3D size distribution CTVox
Dual energy measurements
Embryo staining with PTA for ex vivo micro-CT imaging
Extracting open and closed pore networks for analysis and visualization
Heart ejection fraction analysis in vivo after synchronized scanning
How to set up a scan
Hu method note CTAn
Image and dataset registration in dataviewer
Image and dataset registration in dataviewer - expanded clay
Image and dataset registration in dataviewer - tooth
Image ROI for edited multi-part ROI
Impact of ROI on the analysis
Linear attenuation coefficients
Lung analysis in vivo after synchronized scanning
Minimal intensity projection in CTVox
MIP and minimal intensity projection of steel reinforced concrete
Orientation analysis in 2D
Orthopedic micro-CT methods
Osteocyte and blood vessel analysis in cortical bone
Oversize reconstruction advanced
Rodent hind limb positioning for in vivo scan
Root canal treatment evaluation
Set binary selection as ROI
Setting pixel size
Sweep operation in 3D
Where are left and right up and down in my images?
Bruker Micro-CT Academy
The materials listed here are available for investigators by request.
Bruker Micro-CT Academy 2014 Issue 1
Bruker Micro-CT Academy 2014 Issue 2
Bruker Micro-CT Academy 2014 Issue 3
Bruker Micro-CT Academy 2014 Issue 4
Bruker Micro-CT Academy 2014 Issue 5
Bruker Micro-CT Academy 2014 Issue 6
Bruker Micro-CT Academy 2014 Issue 7
Bruker Micro-CT Academy 2014 Issue 8
Bruker Micro-CT Academy 2014 Issue 9
Bruker Micro-CT Academy 2015 Issue 1
Bruker Micro-CT Academy 2015 Issue 2
Bruker Micro-CT Academy 2015 Issue 3
Bruker Micro-CT Academy 2015 Issue 4
Bruker Micro-CT Academy 2015 Issue 5
Bruker Micro-CT Academy 2015 Issue 6
Bruker Micro-CT Academy 2015 Issue 7
Bruker Micro-CT Academy 2015 Issue 8
Bruker Micro-CT Academy 2015 Issue 9
Bruker Micro-CT Academy 2014 Issue 10
The materials listed here are available for investigators by request.
CTVol user manual
CTVox quick start guide
NRecon user manual
Skyscan 1176 user manual
The following Skyscan training videos are available to University of Manitoba staff and may be found on the data analysis workstations in BMSB 75 and 322.
Adaptive thresholding of trabecular bone
BMD-TMD calibration for trabecular and cortical bone
Cortical bone 1 peri-endosteal volumes
Cortical bone 2 porosity
Cortical bone 3 peri-endosteal diameters
CTAn volume model viewing
New features CTAn 1-11
Setting the cortical VOI for mouse femur
Setting the trabecular VOI for mouse femur
Setting VOIs for rodent vertebra
Tooth part 1 pulp canal
Tooth part 2 enamel/dentine
Dataviewer training videos
Introduction to dataviewer
Re-orient a dataset in 3D with dataviewer
View cardiac gated scan in dataviewer
NRecon training videos
Adjusting xy ratio for oversize scan reconstruction
Resize projections in NRecon
Larvae of paddlefish (Tetraodon) stained with phospho-tungstic acid
Maxilla and teeth of Saxon child, 1500 old archaeological specimen
Mouse maxilla and molar teeth, software auto-separation
Osteocyte lacunae and blood vessels in bone
Titanium implant in a pig rib, delineation of bone rings around implant surface
Tooth containing titanium implant
Central Animal Core Imaging and Transgenic Facilities
23 Basic Medical Sciences Building
745 Bannatyne Avenue
University of Manitoba
Winnipeg, MB R3E 0J9 Canada
Transgenic services: firstname.lastname@example.org
Imaging services: SAMICF@umanitoba.ca