Oncology Precision Therapeutics and Imaging Core (OPTIC)

The BioSpec series is designed for preclinical and molecular MR imaging and MRI research. State-of-the- art MRI CryoProbe™ technology combined with ultra-high field USR magnets deliver high spatial resolution in-vivo, enabling users to achieve the molecular and cellular level research they desire.

• zero-boil-off and Nitrogen free magnet technology
• AVANCE III HD MRI RF architecture incorporating up to 16 receiver, 4 independent and 8 parallel transmitter channels
• imaging (GRAPPA) for almost all applications including EPI Multiple transmit imaging applications
• Motorized and software controlled animal positioning system for routine handling and increased throughput
• self-gated, steady-state cardiac imaging (no external sensor hardware and triggering devices required)
• RF coil technology for maximum sensitivity and minimum scan times

BioSpec 94/20 USR

• strength: 9.4 T
• of clear bore: 200 mm
• (5 Gauss): +/- 3 m axial, +/- 2 m radial

The BioSpec high-field magnetic resonance imager allows for images of your research of the highest caliber possible. Extremely low voxel size and high detail allow for crystal clear imaging of the organs of interest for your research needs. Whether it’s looking for sites of cancer growth in the abdomen, to glioblastoma growth, the MRI allows for consequence free longitudinal imaging throughout your studies. T1 and T2 weighted images allow for multiple methods of high quality morphological imaging and contrast to help identify your regions of interest. 

​Accelerated acquisition allows high temporal resolution applications such as first pass myocardial perfusion. Self-gating methods or real-time physiological triggering enables free breathing functional cardiac investigations on your research animals here at Columbia University.

The Bruker BioSpec 9.4 tesla MR has the ability to provide high-resolution images of the blood system within the animals of your research. Magnetic Resonance Angiography (MRA) can find problems within the vasculature of the animal that may be causing issues in blood flow and vessel wall condition. Research into aneurysms, and stenosis of blood vessels are common uses for this imaging type.​

The contrast in Diffusion Weighted Imaging (DWI) originates from the difference in amount of diffusion. Regions that have pathologically disturbed diffusion, such as found when multiple sclerosis, epilepsy, and schizophrenia, stroke, or tumors are present, are easily visible. The greatest sensitivity is achieved with higher b values, which can only be realized with extremely strong gradients. The Bruker BioSpec 9.4 Tesla high-field magnet allows Columbia University Researchers to obtain critical information about:

• Infiltration
• Cardiac Infarction
• Connectivity
• Stroke

• Brain, liver, and muscles contain more than just water, and MR spectroscopy makes non- invasive studies of metabolic processes in these tissues possible.
• Metabolic disorders and observe long term changes in metabolic processes even in millimolar concentrations.
• Higher sensitivity and spectral resolution make this the ideal instrument for spectroscopy and spectroscopic imaging of species involving MR-visible nuclei such as 1H, 13C, 19F, 23Na, 31P and others.

Functional MR Imaging requires very high magnet and gradient performance in combination with maximum system stability. The Bruker BioSpec Gradient System allows researchers to collect whole brain image data sets in a single take. Excellent shim performance delivers minimum geometrical Mouse Abdomen distortions even when using echo planar imaging techniques. Unique frequency and phase stability enables even segmented diffusion tensor imaging with EPI.

• neuroimaging procedure
• Brain Activity
• Shows active fibers of the brain, or what has been hindered

• Real-time imaging enables precise animal positioning Enables fast, high throughput workflow.
• Purpose-built for small animal imaging
  • Integrated animal handling animal transfer bed for IVIS Spectrum

The Quantum FX is the first stand-alone micro-CT to deliver high quality images at an X-Ray doses low enough to enable TRUE longitudinal micro-CT in preclinical studies. An investigator can monitor and characterize disease progression throughout their complete study with ease. By thresholding for different signal intensities, it is possible to visualize different types of tissues, and create surface maps of various anatomical structures.

The Columbia University OPTIC is proud to provide detailed vascular and contrast imaging via micro CT. Iodinated and nanoparticle contrast agents can provide detailed 3D representation of tissues of interest as well as provide great clarity to the vascularity of any area of interest. Please contact us to see how these contrast agents can help the imaging of your research.

In addition to high contrast vascular imaging, Exitron 6000 nanoparticles by Miltenyi Biosciences can be used to longitudinally show the growth of tumor metastases throughout the length of a study.

Please contact us at cd2758@cumc.columbia.edu to discuss how we can assist in the identification and size of liver metastases in your research.

The Columbia University OPTIC is proud to provide detailed vascular and contrast imaging via micro CT. Iodinated and nanoparticle contrast agents can provide detailed 3D representation of tissues of interest as well as provide great clarity to the vascularity of any area of interest.  Feel free to contact us to see how these contrast agents can help the imaging of your research. In addition to high contrast vascular imaging, Exitron 6000 nanoparticles by Miltenyi Biosciences can be used to longitudinally show the growth of tumor metastases throughout the length of a study.

Please contact us at cd2758@cumc.columbia.edu to discuss how we can assist in the identification and size of liver metastases in your research.

OPTIC can provide automatic and user-guided isolation of bone from non-bone tissue by means of threshold-based segmentation and a novel segmentation algorithm that separately identifies the cortical and trabecular bone in whole-bone specimens. Our analysis suite uses the segmented regions to automatically drive the calculation of common bone morphometric indices that provide researchers with a quantitative description of bone microarchitecture.

The Quantum FX micro CT allows for the quantification and characterization of lung pneumonitis and fibrosis, as well as lung capacity longitudinally using our custom built lung imaging platform to allow for repeated accurate measurements of small animal lungs. Our analysis program allows for lung volumes to be quantified throughout the course of a study.

Columbia University OPTIC is also pleased to offer to its investigators' research teams the ability to perform longitudinal quantitative imaging of visceral and subcutaneous fat volumes as well as the lean whole body muscle mass of small animals using our sensitive micro-CT imager.

The Living Image software system provides the ability to co-register images with both our Quantum FX micro-CT and the IVIS Spectrum to allow for anatomical localization of optical image data.

B-Mode is a two-dimensional ultrasound image. The brightness of each pixel is determined by the amplitude of the returned echo signal from that location. These images allow for visualization and quantification of anatomical structures, as well as for the visualization of diagnostic and therapeutic procedures. Lesions such as tumors and atherosclerotic plaques can be identified and the extent of disease burden can be quantified.

In addition, B-Mode can be used for image guided injections by enabling real-time imaging of needle placement of an injection or aspiration procedure. Example procedures include injection of chemicals, DNA or other biochemical compounds/materials into tissue regions that can be clearly seen within the image area; extraction of fluids and/or cells under image guidance for biopsy, bio-assays and analysis is also possible.

M-Mode imaging provides very high temporal resolution (1000 fps) of tissue motion along a single ultrasound beam and is generally used in cardiovascular research to study the movement of the myocardium and valves, quantify cavity dimensions or to study the movement of vessel walls.

Software analysis tools allow for quantification of key cardiac function parameters including ejection fraction, fractional shortening and cardiac output while M-Mode for visualization and quantification of wall motion in cardiovascular research, single line acquisition allows for the very high- temporal (1000 fps) resolution necessary for analysis of LV function. It is widely used by many researchers here at Columbia University Medical Center for assessing mouse cardiac structure and function.

Color Doppler Mode provides a visual overview of flow within the vessel or cardiac structure of interest. Flow direction and velocity can be delineated by red and blue color spectrums and is used for guidance when placing pulsed wave velocity sample volumes. This technique provides rapid identification of vessels, valves of interest and their corresponding flow rates. The ability to quantify flow direction and velocity greatly improves user confidence in vessel identification. Color flow sensitivity can be automatically pre-set by the user for various flow rates such as heart, carotid, kidney or small vessels such as femoral and arcuate arteries.

Color Doppler Imaging is a powerful tool for visualizing the blood flow and vascular health of certain tissues. It is also vitally important when surgical techniques involve areas of high vascular density.

Pulsed-Wave (PW) Doppler Mode is used primarily for the hemodynamic assessment of blood flow through the arteries and veins; it provides quantifiable information about the direction and velocity of blood through the specified vessel. PW Doppler can measure both direction and velocity of blood flow; abnormal flow is represented by an increase or decrease in velocity, a change in direction or flow, or the presence of turbulent flow. PW Doppler also provides information on the relationship between velocities in a cycle. For example, the ratio of systolic peak velocity to end-diastolic velocity in the renal artery relates to the health of the kidney vasculature in diabetic conditions.

Power Doppler Mode can provide a visual overview and general quantification of flow velocity and spatial vascular profile. This is a particularly useful tool in the assessment of vascularity. Measurement tools in the Power Doppler Mode can calculate percent vascularity which is an index of relative vascular density. Small changes in organ vascularity can be detected with Power Doppler imaging and monitored with progression and regression of pathology or as a response to therapy. Power Doppler imaging can be done in conjunction with 3D-Mode to provide volumetric information.

The CUMC OPTIC can help you assess the blood flow of tissues of interest. Investigators interested in hemodynamic research would find this technique extremely valuable to any preclinical research.

Contrast Agents allow untargeted and targeted contrast to be used with the VEVO 2100 high- resolution in vivo micro-imaging systems. The contrast agents and protocols have been optimized specifically for high-frequency micro-ultrasound and for preclinical applications.

Ultrasound-based contrast agents are typically small micron sized micro-bubbles that may be air or gas filled. Tissue typically reacts linearly to ultrasound energy while micro-bubbles react in a non- linear fashion to the same energy. Using proprietary filtering the VEVO system removes virtually all the linear response of tissue signal from the quantification process, allowing researchers to quantify only   the micro-bubble response. As these microbubbles are intravascular, they are easily introduced intravenously and pass through the vascular stream mimicking red blood cell movement.

Untargeted VEVO MicroMarker Contrast Agents provide image enhancement of the blood pool such as imaging and quantification of tumor and organ perfusion (including myocardial perfusion). The study and quantification of relative perfusion in vivo is an important metric for both cardiovascular studies (i.e. myocardial perfusion) as well as cancer research and tumorigenesis study (i.e. tumor perfusion) and general organ perfusion. Vascular architecture and structures can be visualized in tumor models and relative tumor perfusion can be quantified. For cardiovascular studies, imaging myocardial perfusion is possible along with the VEVO system's capabilities to perform complete cardiovascular assessments.

Contrast Imaging is a specialty here at the Columbia University OPTIC. Our experts can help you with valuable vascular studies for your investigations.

3D-Mode combined with B-Mode, Power Doppler Mode and Contrast and Photoacoustic Imaging Functionality allow for advanced data acquisition and analysis in various application areas. Semi- automated 3-dimensional imaging can be performed rapidly and reproducibly. Following 3D acquisition, the VEVO software constructs the scans into a 3D image.

This powerful software enables investigators numerous functions, such as:

• sections in all directions, x-, y-, z- and any other plane variation
• 3D volume measurement

3D imaging can be performed in B-Mode, Power Doppler Mode and Contrast Mode providing higher throughput when compared to other imaging modalities.

B-Mode high-frequency ultrasound imaging can be used for guided injections by enabling real- time imaging of needle placement of an injection or aspiration procedure. Example procedures include injection of chemicals, DNA or other biochemical compounds/materials into tissue regions that can be clearly seen within the image area; extraction of fluids and/or cells under image guidance for biopsy, bio-assays and analysis is also possible.

This is a widely used technique here at the Irving Cancer Research Center for the orthotopic implantation of tumor cells into organs of interest to better recreate the disease model compared to subcutaneous tumor xenografts. It is also possible to carry out image-guided injections of embryos in utero as early as mid-gestation.

• in vivo imaging of fluorescence, bioluminescence, and Cherenkov Radiation
• throughput (5 mice at a time) with 23 cm field of view
• resolution (to 20 microns) with 3.9 cm field of view
• eight high efficiency filters spanning 430 – 850 nm
• spectral unmixing applications (enhanced fluorescent imaging ability)
• for distinguishing multiple bioluminescent and fluorescent reporters
• switch in the fluorescence illumination path allows reflection-mode or transmission-mode illumination
• 3Dforand
• import and automatically co-register CT or MRI images yielding a functional and anatomical context for your scientific data.
• traceable absolute calibrations

Bioluminescence imaging measures light emission resulting from an enzymatic reaction catalyzed by one of several different luciferase enzymes. The luciferase gene may be incorporated into cells that are implanted in mice, or directly into mouse tissues through genetic engineering or viral transduction. Expression may be driven from general promoters as an indirect measure of tumor volume, or from gene- specific promoters to functionally visualize pathway activity.

Firefly luciferase requires D-luciferin to be injected into the subject prior to imaging. The peak emission wavelength is about 560 nm. Due to the attenuation of blue-green light in tissues, the red-shift of this emission makes detection of firefly luciferase much more sensitive in vivo (compared to the other systems).

Renilla luciferase requires its substrate, coelenterazine, to be injected. As opposed to luciferin, coelenterazine has a lower bioavailability. Additionally, the peak emission wavelength is about 480 nm, a wavelength at which tissue attenuation is greater.

Bacterial luciferase has an advantage in that the lux operon used to express it also encodes the enzymes required for substrate biosynthesis. Although originally believed to be functional only in prokaryotic organisms, where it is widely used for developing bioluminescent pathogens, it has been genetically engineered to work in mammalian expression systems as well. This luciferase reaction has a peak wavelength of about 490 nm.

While the total amount of light emitted from bioluminescence is comparatively low (not detectable by the human eye), the fact that there is no background light emission makes it extremely specific. The ultra- sensitive CCD camera within the IVIS Spectrum can image bioluminescence with great sensitivity. Common applications of BLI include in vivo studies of infection (with bioluminescent pathogens), cancer progression (using a bioluminescent cancer cell line), and reconstitution kinetics (using bioluminescent stem cells).

The IVIS Spectrum can image and quantify all commonly used fluorophores, including fluorescent proteins, dyes and conjugates. Our IVIS Spectrum achieves superior spectral unmixing through a wide range of high resolution, short cut-off filters and advanced spectral unmixing algorithms.

Spectral unmixing not only allows detection and separation of multiple reporters, but greatly reduces   the effects of tissue auto-fluorescence. The IVIS Spectrum is the most sensitive system to visualize these fluorescent agents in various in vivo research needs for Principal Investigators here at Columbia University Medical Center.

The IVIS Spectrum optical imaging system:

• sensitivity and flexibility
• and epi-illumination imaging
• light from the excitation filter wheel feeds through a fiber optic bundle to illuminate the specimen from either the top, in epi-illumination (reflectance) mode, or from underneath the stage, by means of an automated bundle switch. Trans illuminating the subject from below at precise x, y-locations allows for transmission imaging, enabling more sensitive detection and accurate quantification of deep sources. Transmission fluorescence imaging also reduces the effects of auto fluorescence.
• designed to simplify advanced and complex biological models by intuitively guiding the user through experiential setup and analysis. The imaging wizard with the newly added probe library will help design imaging settings and select the right filter pair for fluorescence studies. The software also offers a step by step guide for spectrally unmixing multiple fluorescent signals from the same animal. Advanced spectral-unmixing algorithms and a broad range of high spectral resolution filter sets minimize auto fluorescence and provides the opportunity to image a wide variety of targeted and activatable fluorescent probes and reporters.

The OPTIC is pleased to offer a series of Preclinical Experimental Therapeutics options to build these new applications on a collaborative basis. Development projects are initiated through a free initial consultation with a staff member in order to determine the project goals, experimental design, controls, and any technical limitations. If we can complete the design in this time, there is no charge. At the end of the consultation, if more work is required, we will provide a determination of the scale of effort required to build the protocol (Tier 1 – 4). The user then has the option of entering into a collaboration to initiate the project for a substantial discount relative to being billed on an hourly basis.

Tiered projects are entered into with the following understanding:

• If our estimate is severely too high (i.e. a Tier 3 project gets solved in 3 hours), then we will adjust the project to the appropriate Tier.
• If our estimate is severely too low (i.e. a Tier 1 project looks like it could take a full week), you will have the option of either stopping work with no charge, or agreeing to increase the Tier and continue work.
• Once the protocol is developed, you may use it for your experiment at standard hourly rates. The development project does NOT include scanning of experimental mice, except as necessary to develop the protocol.
• Because a new technique is being developed collaboratively, the first publication that emerges from the user’s lab using the technique will include contributing OPTIC personnel as authors.
• Once the protocol is developed, the OPTIC can provide the new application as a service for any other users. You also agree that we may utilize sample images or analysis results in promotional materials to demonstrate the potential of the technique to other users.

Tier 4 projects are those we estimate will take a substantial effort (weeks or months), akin to developing a whole new laboratory technique from scratch. These will be assessed on a case-by-case basis and may include contributions from scientists in the users’ lab working side-by-side with OPTIC personnel over an extended period.

Additional information:

• In addition, the OPTIC will provide a special service for users who are writing or planning a grant that will include funding for imaging studies. We will scan a small number of animals to provide example images or data that may be included in the grant. Generally, these will be using established imaging techniques.
• For each project, OPTIC will provide consultations on experimental design. The project timeline will be determined in advance, since model development takes a significant amount of time. Arrangements for protocol submission are also initiated early on to ensure that the proposed experiments are completed within the expected time frames. ​Examples of the type of studies we can perform are tumor growth measurements, PK/PD studies, monotherapy and combination efficacy and survival studies, Drug toxicity and MTD studies, and more.
• Once the logistical details are finalized, the OPTIC team will implement the study and assist the investigator with data presentation and interpretation.

OPTIC strictly follows SOPs in-house and through the NIH best practices for tissue collection, tumor model generation, and model quality control. The goal is to have standardized methods for generation, maintenance, and analysis of personalized tumor model experiments. This will enhance the clinical relevance of generated models.

• Users must be trained before any access to the instrument is given. 
• After providing documentation of IACUC approval for their work, the user must complete an initial introduction to the instrument administered by the Senior Staff Officer, Christopher Damoci.
• They must then complete an in-depth training program including both theory and practical portions.
• Following these training sessions, the user must complete two imaging sessions in which they operate the instrument under supervision.
• Finally, the user must pass a practical test administered by Mr. Damoci or the technician, demonstrating competency to use the instrument safely without supervision.

A key component of the user training program is a focus on infection control procedures. Shared small animal imaging instruments pose a significant risk of cross contamination in the event of a disease outbreak within the animal facility. To minimize this risk, the users will be trained to disinfect the instruments both before and after use. Failure to adhere to these procedures will result in retraining in the first instance, and suspension of instrument access after repeated infractions.

• Obtain access to the animal facility barrier at the HICCC by completing the requisite training. Access therefore requires an IACUC approved protocol, training in the safe and humane handling of animals, and barrier specific training.

• Complete an introductory demonstration of basic operation and capabilities of the instrument given by an SAISA technician or manager.
• Complete in-depth training on the IVIS provided by an SAISAR technician or manager. The in-depth training will consist of theory section in which the basic principles of ultrasound imaging are taught, followed by a detailed practical teaching session.
• After initial training, the User must complete two imaging sessions in which the user operates the instrument under supervision. Additional imaging sessions will be performed as needed.
• The user must pass a practical test, administered by the OPTIC technician or manager. At this time, access to the scheduling calendar will be granted.

• Each MRI, ultrasound and/or IVIS spectrum user must provide a Columbia account number for billing.
• User passwords must be obtained prior to using the analyzers. Individuals are required to save their data to a flash drive since computer storage space is limited. Staff routinely delete all files.
• Users who cancel an appointment less than 24-hours in advance are subject to the full charge of the scheduled time.

Spectral Imaging AMI HTX Optical/X-Ray Imaging System  

• Trained Users (Cancer Center Member: $72.00/hr, Internal - Columbia: $80.00/hr, External: $186.69/hr, DLD Member: $64.00/hr, DLD/HICCC Member: $56.00/hr) 
• Assisted Usage Mon-Fri 09:00 AM - 05:00 PM (Cancer Center Member: $144.00/hr, Internal - Columbia: $160.00/hr, External: $373.37/hr, DLD Member: $128.00/hr, DLD/HICCC Member: $112.00/hr)

Bruker BioSpec 9.4 Tesla Small Animal MR Imager  

• Assisted Use/training MRI Mon-Fri 08:00 AM - 05:00 PM (Internal - Columbia: $350.00/hr, External: $816.75/hr, Cancer Center Member: $315.00/hr, DLD Member: $280.00/hr, DLD/HICCC Member: $245.00/hr)
• Trained User MRI (Cancer Center Member: $180.00/hr, Internal - Columbia: $200.00/hr, External: $466.72/hr, DLD Member: $160.00/hr, DLD/HICCC Member: $140.00/hr)

Visulasonics VEVO 3100 High Frequency Ultrasound Imaging System  

• Assisted Use/Training Mon-Fri 09:00 AM - 05:00 PM (Cancer Center Member: $153.00/hr, Internal - Columbia: $170.00/hr, External: $396.71/hr, DLD Member: $136.00/hr, DLD/HICCC Member: $119.00/hr)
• Trained User (Cancer Center Member: $81.00/hr, Internal - Columbia: $90.00/hr, External: $210.02/hr, DLD Member: $72.00/hr, DLD/HICCC Member: $63.00/hr)

Perkin-Elmer Quantum FX micro-CT Imaging System  

• Assisted Use/Training Mon-Fri 09:00 AM - 05:00 PM (Cancer Center Member: $216.00/hr, Internal - Columbia: $240.00/hr, External: $560.06/hr, DLD Member: $192.00/hr, DLD/HICCC Member: $168.00/hr)
• Trained User (Cancer Center Member: $157.50/hr, Internal - Columbia: $175.00/hr, External: $408.38/hr, DLD Member: $140.00/hr, DLD/HICCC Member: $122.50/hr)

IVIS Spectrum Optical Imaging System  

• Assisted Use/Training Mon-Fri 09:00 AM - 05:00 PM (Cancer Center Member: $144.00/hr, Internal - Columbia: $160.00/hr, External: $373.37/hr, DLD Member: $128.00/hr, DLD/HICCC Member: $112.00/hr) 
• Trained User (Cancer Center Member: $72.00/hr, Internal - Columbia: $80.00/hr, External: $186.69/hr, DLD Member: $64.00/hr, DLD/HICCC Member: $56.00/hr)

Imaging Analysis Workstations  

• Assisted Use Mon-Fri 10:00 AM - 05:00 PM (Cancer Center Member: $90.00/hr, Internal - Columbia: $100.00/hr, External: $233.36/hr, DLD Member: $80.00/hr, DLD/HICCC Member: $70.00/hr)
• Unassisted (Internal - Columbia: $20.00/hr, External: $46.67/hr, Cancer Center Member: $18.00/hr, DLD Member: $16.00/hr, DLD/HICCC Member: $14.00/hr)