Micro-CT Principles, Strengths, and Weaknesses

Computed tomography (CT) is a non-invasive imaging tool that provides 3-dimensional (3D) images of the internal organs. CT offers very good contrast of bone to soft tissue and thus can have novel applications in bone research.

Micro-CT is an advancement which enables imaging in three dimensions on a small scale with very high resolution. It does not require any sample preparation or histological slicing. Using a micro-CT scanner, the internal structure of a tissue can be visualized without destroying the sample tissue.

Micro-CT systems were first built by Feldkamp et al for the analysis of 3D trabecular bone micro-structure. The first micro-CT scanner was commercially available in the year 1994 and soon became a standard imaging tool in the field of bone research.

These days, micro-CT scanners having varying resolutions are offered by many manufacturers to fit a range of applications that enable bone tissue analysis and in vivo measurements. New algorithms for image processing and data analysis techniques have emerged in recent times, which have opened up micro-CT techniques in several new uses.

Principles of micro-CT

Micro-CT works with the help of a micro-focus X-ray source that illuminates the sample. By rotating the sample, several views can be acquired from different angles. These multiple angular images are reconstructed to create a high resolution 3D image of the structure.

In micro-CT systems, X-rays are passed through various types of target tissues in the human body. Tissues absorb or deflect the X-rays to varying degrees. The CT system measures the intensity of X-rays transmitted by different tissues at different angles. Micro-CT systems use low‐energy, micro-focus X‐ray source and offer high resolution images in experiments using small animals. Several 2D images obtained using a micro-CT imaging can be combined with the help of a computer to form 3D images.

Strengths of micro-CT technique

  • Rapid technique that gives results within 40 min to 12 h
  • Highly sensitive to bone and lung tissue
  • Provides high resolution images, and allows the resolution to be further enhanced by using contrast agents
  • Not destructive to target tissues
  • Reconstruction and analysis of images is easy
  • Easy to interpret results in 2D and 3D formats
  • Micro-CT scanners are inexpensive compared to other systems using similar imaging tools

Biological applications of micro-CT

Micro-CT has been successfully applied to biological imaging in the following areas:

  • In vivo imaging of head / knee
  • Bone analysis
  • Lung tumor detection in vivo and ex vivo
  • Imaging and quantification of tumors
  • Ex vivo imaging of the rabbit brain
  • Phenotyping of the mouse kidney
  • Imaging of mouse heart calcification and chest of live animals using contrast agents in vivo
  • Imaging of tooth and jaw bone in mice

The micro-CT technique has also been used for imaging inflammatory bowel disease in mice and other zoological applications.

Applications of MicroCT

Weaknesses of micro-CT technique

  • Use of radiation which can be harmful to animals at high dosages
  • Exposure to radiation can manipulate the size of tumors and hence alter results
  • Stains are unavailable for some type of tissues
  • Requires good IT infrastructure and data pipelines
  • Not suitable for distinguishing similar types of tissues


  1. https://physicsworld.com/
  2. https://b-cube.ai/en
  3. https://www.ncku.edu.tw/
  4. http://www.sciencedirect.com/science/article/pii/S1002007108000658
  5. https://www.bruker.com/en.html

Further Reading

Last Updated: Jul 24, 2023

Susha Cheriyedath

Written by

Susha Cheriyedath

Susha has a Bachelor of Science (B.Sc.) degree in Chemistry and Master of Science (M.Sc) degree in Biochemistry from the University of Calicut, India. She always had a keen interest in medical and health science. As part of her masters degree, she specialized in Biochemistry, with an emphasis on Microbiology, Physiology, Biotechnology, and Nutrition. In her spare time, she loves to cook up a storm in the kitchen with her super-messy baking experiments.


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