Small ANimal Tomographic Analysis (SANTA) Core




Overview of Services

The Small ANimal Tomographic Analysis (SANTATM) Facility was established by Prof Timothy Cox at the University of Washington in 2008 with the support of the Murdoch Charitable Trust that enabled purchase of two high-resolution tomographic scanners: a Skyscan 1076 in vivo low energy micro-Computed Tomograph (microCT) and a Bioptonics 3001M Optical Projection Tomograph (OPT). In 2009, the Facility was relocated to the Center for Developmental Biology & Regenerative Medicine at SCRI. In its 9 years of operation, the Facility has grown to service the high-resolution 3D imaging needs of biomedical researchers throughout the vibrant Seattle translational sciences community, and at other Institutions across the country and internationally. The Facility performs contract imaging and collaborative projects, as well as offering technical assistance and full training in operation of the scanners and software to users who wish to do their own analyses. It is the only service facility in the US offering both OPT and microCT modalities.


The Skyscan microCT (X-ray-based imaging) is ideal for hard tissues such as bone, teeth and fossils, without any special specimen preparation. The scanner is also designed for live imaging of small animals such as mice and rats, and an anesthesia set up and full physiological monitoring is possible during the scanning. It is also useful for non-biological inanimate objects such as bioengineered materials, moulded plastics, cables, or other materials. In recent years the use of contrast agents has enabled the microCT to be used for imaging soft tissues. In this regard, we have experience with a variety of different contrasting procedures for soft tissue imaging in embryos, perinatal specimens and adult animals. Contrasting procedures for which SANTA staff members are experienced include the use of casts, injectable fillers, and metal/heavy element-based stains, such as phosphotungstic acid or iodine, which can each give superb results. Three isotropic resolutions are possible on this scanner - 9, 18 and 35 microns - with data size increasing exponentially with the resolution.


The OPT differs from the microCT in that instead of X-rays it utilizes white, infrared and UV light options and provides exceptional soft tissue anatomical detail in small samples (<2cm width). It also has the ability to detect whole mount protein and gene expression stains (eg. immunohistochemistry and in situ hybridization) and common colorimetric tissue stains (such as alcian blue for cartilage) in 3D at isotropic resolutions up to 3 microns. This system is unique in its flexibility of operation mode although it is ideally suited to model organism embryonic phenotyping, developmental biology and birth defects research in mouse models because the diameter and tissue density of the ‘morphogenetic’ and midgestational stages of embryogenesis permit simple and efficient chemical clearing of such specimens that is required to minimize light diffraction.


The facility has seven high-end Dell workstations running 64-bit Windows 7. Each of these computers has dual quad core CPUs, latest generation Nvidia Quadro GPUs, 8-16GB of RAM, and up to 4 SSDs configured in RAID0 for extreme file read/write performance and realistic 3D volume rendering. All SANTA computers are clustered through a dedicated gigabit network, independent of the campus infrastructure, and share a common network file system for rapid reconstruction of raw data, post-processing and analysis of the large image datasets. Data storage and backup capabilities provided by the SCRI include a high-end HP rack-mount server with multiple gigabit connections to increase the available server bandwidth for the SANTA network. The new server resides in a physically secure limited access equipment room at the Institute, where all data is backed up incrementally on tape, and then periodically sent to Iron Mountain for off-site storage. All generated image data is also mirrored to a 16Tb RAID-5 DroboPro External Backup System on site. The facility has licenses for various commercial 2D and 3D image analysis software packages including Analyze (Mayo Clinic), RapidForm XOR and XOV, and Skyscan’s own suite (CTan, CTvox, and DataViewer), as well as various freeware image analysis and visualization software, including Drishti, ImageJ, Landmark, Dragonfly and 3D Slicer.