The Craniofacial Center’s Small Animal Tomographic Analysis (SANTA) Facility
at the University of Washington School of Medicine
May 2009
Boiler-Plate Language for Animal Protocols
Please copy (or modify as required) the following information into your animal protocol or animal protocol amendment.
Please only use the information that is appropriate to the species that you are using. If you have any questions or
comments, please contact A/Prof Timothy Cox (phone: 206-616-9703; email: tccox@u.washington.edu)
Introductory Paragraph for your Amendment:
The Craniofacial Center’s Small ANimal Tomographic Analysis (SANTA) Facility provides state-of-the-art imaging of
small animals and tissues to CHRMC and UW researchers and their collaborators. The facility is housed within the
Department of Pediatrics, University of Washington School of Medicine, and currently offers in vivo micro-computed
tomography (microCT) and optical projection tomography (OPT) imaging modalities. The former is suitable for ex vivo
studies on a wide variety of small animals or tissues or in vivo studies on appropriately anesthetized mice, rats, and
other small animals. The latter imaging modality is ideal for soft tissue and embryonic studies, including morphology,
tissue composition, and 3D gene and protein expression profiles. The facility also provides high-end workstations for
the analysis of collected data in both two- and three-dimensions.
Description of Imaging Modalities:
Tomographic imaging is a non-invasive technique that involves the collection of defined-thickness planar sections of an
intact object. Individual sections can be analyzed or ‘reconstructed’ by computer algorithms into realistic 2D and 3D
images of the scanned object that permits ‘visualization’ of internal structural detail.
1) Micro-Computed Tomography: Computed tomography is a procedure that is routinely performed on humans.
Micro-Computed Tomography can be performed on intact tissue, deceased whole animals or on anesthetized animals
and only differs from the technique used on humans by the fact that the resolution is ~100-1000x greater (ie. microns
versus millimeters). The available Skyscan 1076 microCT is a low dose in-vivo X-ray scanner for slice imaging and 3D
image reconstruction from small animals (up to 68mm wide and 200mm long) at isotropic resolutions of 9, 18 or 35
microns.
2) Optical Projection Tomography: OPT microscopy is a new technique that allows the 3D imaging of biological
specimens up to 1.5 cm across at resolutions of as high as 3.1 microns. It was initially developed with the hope of
enabling accurate measurement of 3D shapes. However, it has proven to be a fast method for determining the 3D
distributions of gene expression patterns, labeled antibodies and cell-specific stains during embryo development or in
isolated adult organs from small animals. OPT is based on the same principles as micro-computed tomography except
that it employs either white, infra-red or UV light instead of X-rays.
Examples of methods of sedation of small animals
Animals will be anesthetized in accordance with the Principal Investigator’s approved protocol; the table below lists
possible methods.
TYPE OF ANESTHESIA
SIDE EFFECTS
Ketamine/ Xylazine
Isoflurane
Used for anesthesia. No side effects anticipated at the dosage used.
Used for inhalation anesthesia and titrated to effect. No side effects anticipated at the
dosage used.
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The Craniofacial Center’s Small Animal Tomographic Analysis (SANTA) Facility
at the University of Washington School of Medicine
May 2009
Anesthesia Doses:
DRUG/SPECIES
MOUSE
Ketamine / Xylazine
100 mg/kg Ket. / 10 mg/kg Xyl. given intraperitoneally; re-dose ketamine only at ½ dose
Isoflurane
1-3%
RAT
40-60 mg/kg Ket. / 3-5 mg/kg Xyl. mixed
together and given intraperitoneally;
re-dose ketamine only at 1/3 dose
1-3%
Disposition of Animals Following Study:
Any animal euthanized prior to scanning (ex vivo) or after completion of the scan (in vivo) will be conducted according
to the Principal Investigator’s approved protocol.
(Note: All protocols must include a euthanasia plan for each animal species if needed. In time, personnel within the
facility will become available to assist with such procedures, however, this must be arranged with the Facility Director
and will require addition of the person to the PI’s approved protocol.)
Skyscan 1076 MicroCT specifications:
X-Ray Source
X-ray Source
Energy Range
X-ray Filtering
X-ray Exposure to Animal
10W, <5um spot size, >10000h expected lifetime, air cooled sealed type
Continuously variable peak energy 20-100kV
4-position automatic filter changer for energy filtration (no filter, Ti 0.025mm,
Al 0.5mm, Al 1.0mm >99.9%purity)
0.1-0.5 Gy per scan typical
X-Ray Detector
CCD
Number of Pixels
Detectability
12bit cooled digital X-ray camera with fiber-optic coupling to scintillator
10 Megapixel (4000x2300)
9-14um
Maximum Object Size for Reconstruction
Single Scan
Multi- Scan Mode
~25 mm single scan length x 68mm diameter
210mm length x 68mm diameter (~25mm steps)
Scanning System
Source-Detector Pair
Physiological Monitoring Subsystem
Miniature CMOS-camera with LED illumination
Real-time local body movement detection
Air / gas flow sensor
Temperature sensor
Chamber heating
ECG-amplifier with "x-ray invisible"
connections to the animal's body
Software package
Source-detector pair rotation with 0.02 deg. min. step size, 50um object
positioning accuracy with 400mm travel, 50mm camera positioning/alignment
with 1um accuracy, <10 microns overall stability during scanning
Real time visualization of anesthetized animal during scanning
Enables non-contact scanning synchronization with breathing
Facilitates scanning synchronization with breathing
Enables animal temperature measurement
Occurs by airflow on the object bed
For cardiac monitoring during scan
‘Runs’ animal physiological monitoring (temperature measurement and
stabilization, body movement detection, pulse rate measurement in breathing
and heart activitiy, etc.) and supports scanning synchronization with local body
movements / breathing / heart rate.
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The Craniofacial Center’s Small Animal Tomographic Analysis (SANTA) Facility
at the University of Washington School of Medicine
May 2009
Reconstruction Array
1.
2.
3.
Format
Pixel Size
9um
18um
35um
1000x1000 pixel to 8000x8000 pixel cross-section format
Bioptonics 3001M OPT specifications:
Physical characteristics:
Compact desk-top scanner controlled directly from PC without using any additional interface cards
Size:
925W x 270H x 300D
Weight:
24kg
Power:
100-240V AC, 50-60Hz, 300VA
Computer connections:
Scanner control: RS232 port
Image output: IEEE1394 (FireWire)
Magnification range:
Field of view:
4x4 mm….20x20mm
Illumination system:
Automatic filter changer with independent intensity control for transmission light with following illumination options:
White (transmission)
8 x white LEDs
InfraRed (transmission)
8 x IR LEDs
Fluorescence
Metal-halide 120W UV Source with liquid light guide:
› GFP – exciter 425nm/40 nm / emitter LP475 nm
› GFP+ – exciter 480nm/20 nm / emitter LP515 nm
› TXR – exciter 560/40 nm / emitter LP610nm
Camera:
CCD-Camera with high quantum efficiency sensor operated in on-chip integration mode:
Resolution:
1024x1024 or 512x512 square pixels
Dynamic range:
>63dB (>1:1500)
Exposure range:
1 ms - 10sec with 1ms step
Image output:
12-bit digital with IEEE1394 (FireWire) interface
Quantum efficiency:
>70%
Motorization & object manipulator:
6-axis micro-step controller with independent microprocessor
control for each motor:
Motorized zoom
Motorized focus
Motorized filter changer
Object rotation: 0.9 degree full step, 0.1125 degree micro-step
Motorized object alignment system
Motorized object positioning with 50 mm travel
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