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MicroCT Core - NYU

26 Orders Completed
New York, New York, US

About MicroCT Core - NYU

The overall goal of the mCT Core is to facilitate extraordinary transnational research performed by NYU PIs. Our investigators are dedicated to elucidation of new knowledge regarding skeletal acquisition and integrity and to the translation of fundamental advances into clinical practice. Specifically, our mission is to provide high quality and cost effective skeletal phenotyping of animal models of musculoskeletal disease, to optimize image processing, and to train investigators to design and interpret mCT data.

NYU College of Dentistry (NYU Dentistry) core research facilities and equipment offer a broad range of instrumentation and capabilities not often found in academic dental centers. Designed to be shared by investigators both on campus and externally, and to foster collaborative research, these state-of-the-art technologies are playing an important role in the growth of basic, clinical and translational research to improve human health. We invite you to take advantage of NYU Dentistry core scientific resources that are contributing not only to the quality and productivity of research conducted at NYU Dentistry, but also beyond our walls.

Recent Publications

  • Basu-Roy U, Han E, Rattanakorn K, Gadi A, Verma N, Maurizi G, Gunaratne PH, Coarfa C, Kennedy OD, Garabedian MJ, Basilico C, Mansukhani A. PPARγ agonists promote differentiation of cancer stem cells by restraining YAP transcriptional activity. Oncotarget. 2016 Aug 12. doi: 10.18632/oncotarget.11273. [Epub ahead of print]
  • Mediero A, Wilder T, Reddy VS, Cheng Q, Tovar N, Coelho PG, Witek L, Whatling C, Cronstein BN. Ticagrelor regulates osteoblast and osteoclast function and promotes bone formation in vivo via an adenosine-dependent mechanism. FASEB J. 2016 Nov;30(11):3887-3900. Epub 2016 Aug 10.
  • Nakatani T, Chen T, Partridge NC. MMP-13 is one of the critical mediators of the effect of HDAC4 deletion on the skeleton. Bone. 2016 Sep;90:142-51. doi: 10.1016/j.bone.2016.06.010. Epub 2016 Jun 16.
  • Ramme AJ, Lendhey M, Raya JG, Kirsch T, Kennedy OD. A novel rat model for subchondral microdamage in acute knee injury: a potential mechanism in post-traumatic osteoarthritis. Osteoarthritis Cartilage. 2016 Oct;24(10):1776-85. doi: 10.1016/j.joca.2016.05.017. Epub 2016 May 31.
  • Liu Z, Kennedy OD, Cardoso L, Basta-Pljakic J, Partridge NC, Schaffler MB, Rosen CJ, Yakar S. DMP-1-mediated Ghr gene recombination compromises skeletal development and impairs skeletal response to intermittent PTH. FASEB J. 2016 Feb;30(2):635-52. doi: 10.1096/fj.15-275859. Epub 2015 Oct 19.

Our Services (4)



X-ray microtomography
Price on request
  • Pixel Size (microns): isotropic; 0.5 to 27 microns (diameter of a blood cells is 6-8)
  • Matrix Size: 1k x 0.5k, 2k x 1k, 4K x 2K
  • Voltage: 0 to 100 kv
  • Filters: No filter, Al0.5mm, 1 mm AlCu
  • Sample Size: 27mm in diameter (single scan) or 50mm in diameter (offset scan)
  • Optimization: Sample holders constructed to allow for 6 adult mouse; femurs/tibia’s to be run at one time (approx. 1h 19m for 6 bones)
  • Scan Duration: Depends on resolution and sample size

Types of Samples Imaged

  • Mouse: Femur; Tibia; Whole leg/knee joint; Vertebra/ribs; Skull cap; Head; Teeth; Jaw; Pup; Limb/paws/tails
  • Rat: Knee joint; Jaw; Skull
  • Rabbit: Femur; Joint
  • Bovine: Teeth
  • Human: Tibia; Teeth
  • Bird: Bone
  • Tadpole: Head
  • Materials: Plastic; Ceramics
  • Microorganisms: Bacteria

Imaging Process using Mct

  • Scheduling: Consultation, communication, and confirmation
  • Scanning: Machine pre-warm and stabilization; flat field correction/calibration; Prepare samples
  • Reconstruct: Use NRecon; Choose optimal parameters
  • Analysis: Use DataViewer, CTAn, CTvox; Quantify morphometric parameters


  • Images can be reconstructed using one, several, or all cross sections obtained.
  • The core optimizes software corrections (beam hardening, ringing artifacts, smoothing, thermal, and post alignment) for each study to allow for maximum reconstructed image quality.
  • After the serial reconstruction, one can display realistic 3D-images with the possibility to rotate and cut through the object model.
  • From the axial 2D data set and/or from the 3D volumetric images one can calculate a variety of internal morphological parameters.
  • Standards are also used to allow for the calibration of the signal attenuation to density, thereby allowing for determination of bone mineral density on any given data set if desired.
  • For presentation and publication purposes, the core can also construct surface maps, renderings of specific areas (such as bone trabecular), attenuation images (cross-sectional, coronal and sagittal views), and movies where the object rotates in 3D space.

Analysis and Software

All results are reported to the investigator in Excel and summaries can be made if requested. For investigators that would like to quantify on their own, the facility provides access to the software (CTAn) free of charge. However, it is strongly recommended that a training session be scheduled, as the choice of VOIs, drawing of ROIs, and analysis requires some experience in order to provide accurate and consistent data.

Common Morphometric Parameters Calculated by MicroCT

  • Tissue Volume: TV, mm3
  • Bone Volume: BV, mm3
  • % Bone Volume: BV/TV, %
  • Bone Surface/Volume Ratio: BS/BV mm-1.
  • Bone Surface Density: BS/TV mm-1.
  • Trabecular Thickness: Tb.Th mm.
  • Trabecular Number: Tb.N mm-1.
  • Trabecular Separation: Tb.Sp mm.
  • Degree of Anisotropy: DA. Measure of 3D symmetry
  • Fractal Dimension: FD. Indicator of surface complexity.
  • Total Porosity (percent): PO(tot), %.
  • Bone Mineral Density: BMD/TMD, g/cm3.

Pilot Scans and Consulting

The core offers free initial imaging consolation and pilot scans if necessary. Here the core will try to optimize the imaging parameters (pixel and matrix) so that the research goals are met while keeping the scan time costs as low as possible. The core has custom designed sample holders to allow for the maximum number of samples to be scanned at one time, while maintaining desired resolution and accuracy. For complex issues related to murine bone collection, storage, and/or study design Dr. Yakar is available on a limited basis. Please contact her directly to set up an appointment.

Data Storage

Data Storage and Backup Policy: Starting July of 2015, the facility is using a Globus server to store/backup ALL raw data up to seven years; however, we are backing up reconstructed data for ONLY six months. Please note, after six months of delivering you the reconstructed data, we will be deleting it permanently. For inquiries regarding raw data before 2015, please contact the operator personally.

Example of a Typical Scanning Protocol

The distal end and mid-shaft of six adult mouse femurs can be scanned at one time in 58 minutes using a pixel size of 9.7 um and a matrix of 2000x1000. If the entire bone needs to be scanned, then an oversized scan with 2 segments is required, thereby increasing the scan time of the six bones to 2 hours. Reconstruction of the six bones takes one hour, regardless of the image size, As a result, imaging and reconstructing of six adult mouse femurs takes 2-3 hours ($150-$225), depending upon whether or not the entire bone needs to be scanned. Based on previous work, analysis of mouse femur takes approximately 45 minutes per bone sample for full Tb and cortical analysis. Construction of cool 2D and/or 3D images takes approximately 15 minutes per bone sample.



Price on request
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Imaging & Spectroscopy

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Tomography Services

Computed tomography services
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Gina Yildirim

micro CT Core Technician(M.S.)

Shoshana Yokar

Associate professor, Micro-CT core director

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