MicroCT Core

  • Dear current and prospective users,
    We hope you are all in good health and safe as we go through these unprecedented times. The MicroCT Core has reopened and started providing services to our users by following NYU's guidelines in order to keep everyone safe and healthy. We accept samples by appointment only due to Covid-19. Please email us at gy10@nyu.edu for any questions and sample inquiries.


MicroCT uses X-RAYS to create cross sections of samples which allows for high resolution 3D imaging and quantification of tissue and bio-materials. It is a non-destructive method that often requires no tissue staining or sectioning of the sample. Conventional optical or electron microscopy allows visualizing 2D images of a specimen surface or thin slices while X-ray (radiography) produces 2D shadow images of 3D structures. In a single 2D shadow projection the depth information is mixed. In contrast, CT allows for visualization and morphometric measurement of complete 3D structure without sample preparation, chemical fixation, or sample destruction. Another factor to note is the micro CT is slightly different than the medical CT. The spatial resolution of conventional medical CT-scanners is in the range of 1 - 2.5 mm, which corresponds to a 1^ - 10 cubic mm voxel (volume element) size. In comparison, the MicroCT reaches a spatial resolution of 5 microns (0.005 mm) corresponding to near 1x10-7 cubic mm voxel size.

Adaptable geometry gives variable resolution choices & variable specimen placement from source

Skyscan Object (specimen) rotates between a static x-ray source and the detector

skyscan object rotating
Category Description

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


0    to   100 kv


No filter,   Al0.5mm,   1 mm AlCu

Sample Size

27mm in diameter (single scan) or 50mm in diameter (offset scan)


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

Category Description
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
Tadpole Head
Materials Plastic; Ceramics
Microorganisms Bacteria

Imaging Process using Mct

Category Description

  -  Consultation, communication, and confirmation


  -  Machine pre-warm and stabilization; flat field correction/calibration

  -  Prepare samples


  -  Use NRecon

  -  Choose optimal parameters


  -  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.

In addition to our other primarily used image analysis software, the microCT core recently added a new computer station that has the Amira 3D Software for Life Sciences from FEI (XImagePAQ Extension for Amira- node locked application license). Please see the following links below that will demonstrate how you can use Amira to do analysis on various types of bones/samples.

Common Morphometric Parameters Calculated by MicroCT

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

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.