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Small Animal Tomographic Analysis Facility (SANTA)

Data Analysis and Management

Scanning Your Sample

The higher the scan resolution and larger the area being scanned, the larger your file size will be and the longer your scan and subsequent reconstruction will take. Operation manuals (in PDF format) can be downloaded from the forms page and are also available on the facility's computers.

Analyzing Your Data

Following scanning of samples, data reconstructions can be done on your own local machine or using our in-house computer cluster. However, for high-resolution scans it is recommended that the in-house cluster be used because of the computing power required.

SANTA holds an institutional-wide license for Skyscan's CTan software, which offers a range of operations for the analysis of tomographic data. This license can be provided to users if they wish to analyze their datasets on their computer of choice and in the comfort of their own space, but is also available of the facility's workstations.

We also have other licensed and open-source software for data analysis and segmentation, including Analyze, 3D Slicer and RapidForm, as well as various software and freeware options for multi-dimensional visualization (Drishti, Dataviewer, CTvol, CTvox, Bioptonics Viewer, Photoshop, ImageJ, etc.). Users are welcome to book our workstations to use these resources.

Please note: Users must send an email request for a copy of the CTan license file if they wish to run the full version of CTan on their own computer. The Skyscan visualization software (CTvol, DataViewer etc.) does not require a license. The latest versions of this software can be downloaded from Skyscan.

Data Storage and Backup

Users are responsible for storing and backing up their own data. However, each user will be provided up to 50 gigabytes of storage space on SANTA's networked computers.

Users should be aware that each raw dataset and reconstruction dataset together may use anywhere from a few gigabytes to 20 gigabytes or more depending on the scanned sample's resolution and size. It is therefore recommended that frequent users have their own portable external hard drive (typically of at least 0.5-1.0 terabytes) to store their data. These external hard drives are available from any store selling computers, including the University Book Store, and can cost anywhere from under $100 to a few hundred dollars, depending on the storage capacity.

DVD burners are also available in each computer for a backup alternative, although please be aware that some scan datasets may need multiple DVDs.

Software We Use

NRecon/NRecon Server

For reconstruction of raw datasets generated by the scanner.


For analysis of scan data (e.g., optimization and clean-up of datasets, density and volume measurements, segementation and data reduction) and exporting data to 3D file formats.


For visualization of 3-D models – typically meshes.


For visualization of 3-D models – typically voxel-based.


A multi-platform, open-source volume exploration and presentation tool.

3D Slicer

A multi-platform, open-source program for visualization, segmentation and analysis.

Analyze v9.0 and v10

For visualization, segementation and complex analysis of datasets.

RapidForm XOR and XOV

CAD-capable visualization and quantitative analysis of 3-D mesh-based images.

Note: The same software can be used for data acquired on both the microCT and OPT scanners.


Seattle Children’s complies with applicable federal and other civil rights laws and does not discriminate, exclude people or treat them differently based on race, color, religion (creed), sex, gender identity or expression, sexual orientation, national origin (ancestry), age, disability, or any other status protected by applicable federal, state or local law. Financial assistance for medically necessary services is based on family income and hospital resources and is provided to children under age 21 whose primary residence is in Washington, Alaska, Montana or Idaho.