Overview

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.

Examples

Instrumentation

SkyScan 1176

CT images are acquired with a high performance SkyScan 1176 x-ray microtomography system equipped with a large format 11-megapixel x-ray camera.

Additional information

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.

Applications

Applications include:

  • 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

Resources

Application notes

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

Adaptive thresholding

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

Angular resampling

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

NRecon overview

Orientation analysis in 2D

Orthopedic micro-CT methods

Osteocyte and blood vessel analysis in cortical bone

Oversize reconstruction

Oversize reconstruction advanced

Porosity analysis

Rodent hind limb positioning for in vivo scan

Root canal treatment evaluation

Set binary selection as ROI

Setting pixel size

Sweep operation in 3D

Trajectory calibration

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

Manuals

The materials listed here are available for investigators by request. 

CTVol user manual

CTVox quick start guide

NRecon user manual

Skyscan 1176 user manual

Training videos

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 shrink-wrap

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

Contact us

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: transgenicservice@umanitoba.ca

Imaging services: SAMICF@umanitoba.ca