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Small Animal Tomographic Analysis Facility (SANTA)

Equipment and Uses

SANTA's key equipment includes a Skyscan 1076 micro-computed tomography (MicroCT) scanner and a Bioptonics 3001M optical project tomography (OPT) scanner.

Micro-Computed Tomography

SANTA's model 1076 microCT scanner

SANTA's model 1076 microCT scanner

The facility's micro-computed tomography scanner is set up for both ex vivo (i.e., non-living specimens) scans and in vivo (live/anesthetized animal) scans at isotropic resolutions of between 9 and 35 microns.

Typical applications for microCT imaging are related to analysis of hard tissue, such as bone and dental research, as well as anthropological, paleontological and geological studies. However, other non-biological samples can also be scanned.

Types of analysis include quantitative two-dimensional and three-dimensional analyses, qualitative and quantitative studies of developmental trajectories (four-dimensional analysis), mutant phenotyping, BMD calculations and more. Micro-computed tomography can also be applied to any soft tissues with the use of appropriate contrast agents (such as vasculature imaging) or without contrast (live 4-D lung imaging). We have two stains available that facilitate acquisition of internal soft tissue detail while a number of other agents are commercially available.

To facilitate live imaging, the system has a built-in physiological monitoring system that permits visualization and movement detection, respiratory gating, temperature stabilization and electrocardiography.


  • Model: Skyscan 1076
  • Scanning volume: 68 mm scannable diameter; 200 mm scannable length
  • Isotropic resolution options: 9, 18 and 35 micron
  • Max single scan length: 25 mm
  • Consecutive scans seamlessly stitched
  • Simple batch-scan mode available

For more details on the scanner and extra examples of the types of scans possible, please see the Skyscan website.

Optical Projection Tomography

SANTA's model 3001M OPT scanner

SANTA's model 3001M OPT scanner

Optical projection tomography (OPT) imaging is suited for any type of small soft tissue (e.g., whole mouse or chick embryos, or dissected tissues). Fixed specimens up to roughly 17 mm in diameter (25 mm height) are embedded in low-melting-point agarose, and then made optically clear.

The use of white, infrared and UV light sources enables detection of a range of commonly-used tissue stains including but not limited to beta-galactosidase (for gene expression), fluorescently labeled antibodies, as well as alizarin red and alcian blue stains. However, tissues can be easily imaged without any stain simply using the inherent autofluorescence of tissue under UV light. Three different UV filters allow consecutive imaging of different stains as well as general autofluorescence to enable co-registration of the stain with internal anatomical structures.

For more details on the capabilities of the Bioptonics 3001M OPT scanner and the types of data obtainable, please see the Bioptonics website.


  • Model: Bioptonics 3001M
  • Scanning volume: 1 mm to 17 mm diameter
  • Isotropic resolution options: Adjustable from ~3 micron (1024x1024) through to ~35 micron (512x512)
  • Consecutive scans using different light/filter options

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