What is the difference between in vivo micro-CT and ex vivo micro-CT scanning?

What is the difference between an in vivo micro-CT and ex vivo micro-CT instrument?

What does in vivo and ex vivo mean?

Simply put, in vivo (latin for within life) is the scanning of live specimens and ex vivo (Latin for out of living) typically refers to things that used to be alive or samples excised from something that was living.  For micro-CT, in vivo typically refers to systems that scan mice and rats and in some cases rabbits, while ex vivo systems typically handle the remainder of the applications.

What are the typical applications for invivo and exvivo micro-CT scanners?

In vivo micro-CT instruments, since the animal remains alive, longitudinal studies can be performed to measure the affects of drug, diet, hormonal, and other treatments on tumors, bone growth and quality, body mass, and other applications on the same subject.  This can reduce the number of animals needed for a study.  In vivo scanners are ideal for measuring fat content, analyzing COPD where breathing monitoring is required, and many regenerative models.  In vivo micro-CT data has been used as a reference for registration with micro-PET or micro-SPECT scans.  Due to the scanning geometry, in vivo scanner can also be utilized to scan longer objects despite the tradeoff in resolution compared to ex vivo systems.

Ex vivo micro-CT instruments typically handle the remaining applications.  These include end point studies of specific regions of an animal that get excised (lungs, bone, tumors, implants, grafts etc), biomaterial studies, implants in large animals, materials studies, compression studies and more.

Ex vivo micro-CT instruments allow for higher spatial resolution, longer scan times (since dose to the sample isn’t of concern), better signal to noise ratios and therefore better images.  Ex vivo systems have typically been used for most applications outside of a living animal.  Some common ex vivo applications are imaging fine trabecular bone of mice and rats for osteoporosis; vascular diseases in the brain, lung, and other organs; cartilage wear models that are commonly performed with stain tissue to enhance the contrast, and fine structures like alveoli in the lung.  Other applications include biomaterials, implants from larger animals, materials studies, compression studies, the study of food and seeds, anthropological studies, rock core samples,  and more.

Related: How much does a micro-CT cost?

What is the difference in the design of an in vivo and an ex vivo micro-CT system?

micro-CT rotation principle
Micro-CT Setup

In order to produce a micro-CT scan, a series of 2D x-ray images have to be collected while the sample or the x-ray source / detector pair rotate through 180 or 360 degrees.  In vivo and ex vivo systems approach this in two different ways.

SkyScan 1176 In Vivo MicroCT
In Vivo Micro-CT Design

For in vivo systems, it is best to have the living animal remain stationary during the scan to minimize and movement of the animal and for its own welfare.  This requires its vital signs be measured using an EKG, that anesthesia tubes can enter into the system to keep the animal sedated, and that there is a heater to keep the animal warm during the procedure. For lung studies there is typically a breathing monitor as well.  This is most easily achieved by rotating the source and the camera around the animal similar to medical CT systems.

In ex vivo micro-CT scanners you do not have to be concerned about any physiological monitoring, dose to the animal, and you can more securely mount the sample to avoid movement.  This means that the sample stage can rotate while the heavy x-ray source and camera remain stationary.  Rotating a small sample and stage in an ex vivo scanner has two advantages; First, a higher degree of rotational accuracy can be achieved which translates into a better 3D resolution in the reconstructed image, the second benefit is the ability to change the distance between the source and sample by translating the rotational stage (and in some systems the distance between the source and the detector) giving you control of the geometric magnification.  In systems such as the SkyScan 1172, SkyScan 1173, SkyScan 1272, and SkyScan 2211 there is continuous travel of the stage so that any magnification can be selected.  This allows you to put the sample right next to the x-ray source so that you can achieve much finer resolutions ex vivo than you can in vivo, and to move the sample closer to the detector to get larger fields of view.

Scanning speed, image quality, and dose considerations

SkyScan 1172 MicroCT
SkyScan 1172 MicroCT

In ex vivo micro-CT systems you don’t have to worry about x-ray dose that the sample absorbs.  This allows you the freedom to scan longer than you would with an in vivo micro-CT system.  These means that you can use any combination of more steps, a higher frame average, more pixels, more connected scans to improve the quality of the image.  The full pixel density of the detector can be utilized in ex vivo scans versus either binning the pixels or reducing the field of view when scanning in vivo.

For in vivo scanners it is critical to have large field of view detectors versus a line detector.  This allows you to capture a significant length of the animal without having to scan multiple times which would greatly increase the x-ray dose to the animal.  Consider how much area you will need to acquire in order to get a meaningful volume for analysis (distal end of a femur including the trabecular  end and mid shaft for example).  Large area detectors also allow you to get small enough pixel sizes (9 micron) for fine detail while keeping the dose to a minimum.

Additional stages

Mechanical or thermal stages can also be added to ex vivo scanners to test samples under different environmental conditions.  Samples can be tested under different compression or tension loads to see deformation.  A thermal stage can be used to either heat or cool samples such as ice, frozen food products, etc.

Some ex vivo scanners allow you to add a sample carousal.  This can load samples automatically into the scanner, perform the scan, remove it, load the next one and repeat the process for the remaining samples.


There are advantages to both in vivo and ex vivo micro-CT systems and they can be used as complimentary systems.  The ability to follow a treatment on a single test animal is an invaluable resource, while the fine resolution and longer scan times of ex vivo systems may be the correct path for your research.

For more information on Ex Vivo systems visit:

SkyScan 1272 Programmable Ex Vivo Micro-CT

SkyScan 1173 High Energy Desktop Ex Vivo Micro-CT

SkyScan 1174 Compact Ex Vivo Micro-CT

Skyscan 2211 Multi-scale Nano-CT

For more information on In Vivo systems visit:

SkyScan 1176 High Resolution In Vivo Micro-CT

SkyScan 1278 Ultra Low Dose, High Throughput Micro-CT

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