Small Animal Imaging Facility

The goal of the Markey Cancer Center Small Animal Imaging Facility is to provide state-of-the-art small animal imaging services to researchers in the Markey Cancer Center of University of Kentucky.

These services include multi-modality imaging, advanced statistical data analysis and a satellite animal facility for longitudinal studies.

The MCCSAIF provides comprehensive imaging support services for MCC investigators, including:

  • Assistance in experimental design
  • Preparing animals for studies, inducing and maintaining appropriate anesthesia and immobilization of animals during imaging
  • Assistance in harvesting and marking appropriate tissues for correlation of macroscopic, microscopic and imaging characteristics of the tissue or organ
  • Processing and interpreting data for publication or grant preparation

The technology provided by major instruments at the facility is applicable to a wide range of cancer research areas that include tumor biology, metastasis and signal transduction. The facility is also equipped to develop animal models and perform surgical procedures to support in vivo imaging studies with these instruments.

Contact Information

Small Animal Imaging Facility Contacts

Piotr Rychahou, M.D. 
Assistant Professor, 
Markey Cancer Center and Department of Surgery 
University of Kentucky 
741 S. Limestone, B336 BBSRB 
Lexington KY 40506-0509


Biostatistics Shared Resource Facility Contacts

Heidi L. Weiss, Ph.D. 
Biostatistics Shared Resource Facility 
Markey Cancer Center 
University of Kentucky 
Roach Building, CC448 
800 Rose Street 
Lexington, KY 40536



The MCCSAIF has teamed up with MCC Core Information Systems to provide a computer-based method of reserving procedure rooms and equipment. This scheduling system allows researchers to check room availability and/or schedule procedure rooms via the internet.

Scheduling utilizes University of Kentucky email through Outlook for reservations. Scheduling can be done via the Office 365 online portal or Outlook desktop client. Download instructions on how to reserve below.

The following resources can be reserved online:

Immunodeficient mice facility:
Surgery station N1 (room 060A1)
Surgery station N2 (room 060A1)
Necropsy station (room 060E)
Xenogen IVIS 50 (room 060E)
GFP/RFP Panoramic Imaging System (room 060E)

Regular/transgenic mice facility:
Surgery station (room 040D1)
Necropsy station (room 040D1)
Xenogen IVIS Spectrum (room 040D1)

Data Repository

The MCCSAIF has teamed up with the Biostatistics Shared Resource Facility (BSRF) and Markey Cancer Center Informatics to provide a new method of data collection and management through LabKey Server. LabKey Server is open-source software that solves many of the data management challenges of modern biomedical research. Research data can be organized and managed in a secure, web-accessible environment, and then analyzed by using R, Excel, FlowJo, and SAS.

The Markey Cancer Center LabKey server can be found at the following URL: 

The Markey Cancer Center LabKey server has been modified to provide the following features specifically for animal studies:

  • Automatically upload bioluminescence intensity data from IVIS 50 or IVIS   Spectrum
  • Manually enter caliper measurements and bioluminescent data
  • Display pre-defined line plots and box plots instantly from entered data for preliminary data visualization
  • Easy access of well-designed database from researcher to statistician for timely statistical analysis

To request login ID and password for LabKey system contact us at


Optical imaging is a proven low-cost, high-throughput way to observe tumor growth and treatment effect in living animals. Oncology models can be used to assess anti-cancer therapies over the course of treatment in vivo. Non-invasive, bioluminescent imaging of tumor growth and metastasis allows longitudinal evaluation of tumor development before, during and after treatment, offering an excellent preclinical strategy to assess tumor response and recurrence.


(Regular mice facility; Room 040D1) 

The IVIS Spectrum is the newest imaging system available from Caliper Life Sciences. It is capable of detecting both luminescent and fluorescent light sources ranging from blue to near-infrared wavelengths using 10 excitation and 18 emission filters. 

NOTE: GFP is not recommended for most fluorescent imaging applications; alternatively, plan to use a red shifted fluorescent protein such as cherry, tomato, or katushka.

It offers both a planar view (the light source is registered on the animal’s surface) and a single-view 3-D reconstruction of both fluorescent and luminescent reporters.

The IVIS Spectrum is connected to the XGI-8 Anesthesia System that allows continuous administration of isoflurane gas for anesthetizing animals during imaging.

The Living Image Acquisition/Analysis Software Package that is included with the system provides advanced quantification and analysis of all data acquired in 3 dimensions from each animal. 


xenogenXenogen IVIS 50

(Immunodeficient mice facility; room 060E) 

Xenogen’s IVIS 50 imaging system includes a highly sensitive camera, a dark imaging chamber to minimize incident light, and software to quantify the results. A CCD camera (cryogenically cooled to -105°C) minimizes system noise while maximizing sensitivity. The system is ideal for bioluminescent and fluorescent in vivo and in vitro imaging.

The system is connected to a gas anesthesia unit that allows continuous administration of isoflurane gas for anesthetizing animals during imaging. It has the capacity to monitor and image up to three mice simultaneously,  in addition to imaging cell culture plates.

“Living Image ® 3.0” software allows for absolute quantification (photons/sec/cmsq/sr) of bioluminescent and fluorescent signal, both in vivo and in vitro. Analysis of imaging data is available to all users. 
Analysis software can be purchased from Caliper LifeSciences to allow analysis by users on their own computers.  

rfp-gfpGFP/RFP Panoramic Imaging System with Dual Controllable Excitation

(Immunodeficient mice facility; Room 060E)  

The GFP/RFP Panoramic Imaging System is used for visualizing fluorescent proteins and other fluorescent molecules in mice. Targets such as fluorescent tumors can be viewed from three different angles at the same time with a single camera. A major benefit of this design is that the excitation lighting is comparable over the radius of the animal, allowing targets that would be in shadow (with lighting from above) to be brightly illuminated and clearly imaged. The dual controllable excitation system is the only system that allow for the independent control of two excitation wavelengths while maintaining even illumination on the subject. 

sugery stationSurgery Stations

Each surgery station is set up with a dedicated isoflurane vaporizers (to maintain the animals under anesthesia during procedures), induction chambers, microflex breathers, heated surgical beds and a scavenger system.


meiji microscopeMeiji EMZ8TR

(Regular mice facility; Room 040D1) 

Table-top trinocular surgery microscopy with Zoom Stereo on S4200 Boom Stand. Zoom Range:  7x to 45x. Shown with a Schott ACE fiberoptic ring light.


insofluranePortable Isoflurane Anesthesia System

A precise and consistent and preset flow rate from each outlet offers a highly efficient, precise gas flow that is easy to use.

  • Fixed flow rates are set specifically for mice and rats 
  • Each output is individually controlled with simple on/off switch 
  • Five outputs supply anesthesia to the induction chamber and up to four breathers 
  • Preset flow rates eliminate need for flowmeters and manual adjustments 
  • Flow rate is not impacted by the type or number of accessories connected 
  • Pushbutton oxygen flush purges induction chamber before removing animals 
  • Anesthesia stand facilitates safe, easy transport of the unit


procedure roomCommon Use Necropsy Room and Surgery Station

Each facility has necropsy (Room 033) and surgery stations (Room 051). A common use necropsy room and surgery station can be used during times of high demand.


Experimental Design

The Markey Cancer Center’s (MCC) Biostatistics Shared Resource Facility (BSRF) collaborated with the MCC Small Animal Imaging Facility to provide guidance regarding experimental design, data collection and statistical analysis of xenograft, transgenic and other mouse models of cancer.

The goal is to ensure that studies are designed properly in order to adequately address research hypotheses and collect and store high-quality data.

Basic elements for designing experiments:

  • Research objectives and translation into testable statistical hypothesis.
  • Primary study endpoint. Secondary and exploratory outcomes.
  • Number of groups, choice of control groups
  • Animal model and features/characteristics of animal model
  • Study Design: Two or multiple parallel groups, Factorial design, Longitudinal study, Paired design
  • Sample size (# of animals per group):
    • Effect size: Hypothesized amount of difference between groups and amount of variation in study outcome
    • Statistical power desired (at least 80%) and significance level (usually 5%)
    • Sample size method consistent with study design and analysis plans
  • ID/Coding of Animals
  • Randomization
  • Blinding

Data collection (LabKey):

We recommend that data collected in the MCCSAIF use the database system developed through LabKey. This will facilitate accurate, clean and complete data collection and data entry for timely statistical analysis. 
Please refer to the LabKey link in this website for use of this database system.

Overview video of “Experiment design, data collection and statistical analysis”

Location & Directions

College of Pharmacy Building 
789 S. Limestone 40536-0596 
Building #0596; Code: BPC 

Interactive Campus Map (No. 596) 

Employee parking (E-parking) available at Parking Structure No. 6 

Visitor parking available at Parking Garage No. 8

MCCSAIF is composed of two separate facilities – facility for immunodeficient mice and facility for regular/transgenic mice. Each facility has housing room with a connected procedure room. 

Immunodeficient mice facility
060A – animal housing room 
060A1 – procedure room with two surgery stations 
060E – procedure room with necropsy station and imaging equipment 

Regular/transgenic mice facility
050B – animal housing room 
040D1 – procedure room with surgery station, necropsy station and imaging equipment

NCI Comprehensive Cancer Center - A Cancer Center Designated by the National Cancer Institute

Markey Cancer Center is designated by the National Cancer Institute as a Comprehensive Cancer Center – a distinction that recognizes our commitment to accelerating precision cancer research and care to patients. We are the first and only NCI-Comprehensive Cancer Center in Kentucky, and one of 56 in the nation.