Application Steps

1. Submit a scan request form to viscenter@nyit.edu

2. The lab manager approves the request
-under certain circumstances the full committee may review or approve a request

3. Contact viscenter@nyit.edu to schedule scan time

4. Sign a user agreement form
-only required for first time users or after 5 years of use


If you are interested in scanning and have any questions, please check the FAQs or contact the committee:

Kelsi Hurdle, Lab Manager, Anatomy, NYIT*
khurdle@nyit.edu

Simone Hoffmann, Associate Professor, Anatomy, NYIT
shoff04@nyit.edu

Olga Savinova, Associate Professor, Biomedical Sciences, NYIT
osavinov@nyit.edu

Andrew (Drew) Moore, Assistant Professor, Anatomical Sciences, Stony Brook University
andrew.j.moore@stonybrook.edu


*indicates MicroCT Committee chair

Fees

Scanning service is FREE of charge for all users

Specimen Preparation

Packaging

We recommend the following tips and tricks to prepare your specimen for scanning. You can also download a copy of these guidelines here (temporarily unavailable).

Specimen containers: Specimen containers should be low density to minimize X-ray attenuation. We recommend: polyethylene bags, plastic bottles or boxes, Styrofoam cups, Eppendorf’s, and syringes. Specimen containers should only be slightly larger than the specimen itself, in order to allow for best placement of the container within the scan volume. Please keep in mind that the specimen and container should not be larger than 140mm diameter and 200mm length.

Positioning: To maximize resolution, specimens should be placed in the center of the container and oriented as straight as possible with the long axis perpendicular to the ground.

Stuffing (packing) materials: After selecting a container and positioning, specimens should be fully cushioned (stuffed or “packed”) to prevent movement during scanning. Packing materials should be low density and deformable, such as cotton, bubble wrap, packing peanuts, Styrofoam, etc.

Packing Recommendations for Specific Types of Specimens

Wet specimens: Specimens with soft tissue and/or that are typically stored in liquid should be transported in a liquid-filled container. We recommend using a snug-fitting vial or tube. Alternatively, wet specimens may be placed in a vacuum-sealed container or be double-bagged.

For specimens transported in a liquid-filled container: please bring your specimen to the visualization center for packaging.

For vacuum-sealed or double-bagged specimens: wrap the excess plastic around the specimen and place it inside a snug-fitting container. Add cotton, packing peanuts, or any other low density material to the tube to ensure it will not move during scanning.


Two examples of proper packing

Soft Tissue/Bone Specimens

Cotton was placed between each rodent femur to both cushion and prevent movement; alternatively, the femurs could have been completely wrapped in cotton (since only the bones will be visible via the microCT!)
(see image)


Wet Specimen

A wet cotton ball (dipped in the transportation liquid) was placed below and above the lizard inside the container. The cotton is preventing the specimen from moving and from drying out during scanning. Note: only a small amount of liquid is necessary to prevent dessication. Too much will be visible to the microCT
(see image)

Staining

The Visualization Center highly recommends staining for projects that require detailed images of soft tissue. Without staining, little to no detail can be seen of the internal morphology (besides bone) due to the low density of the tissue. Staining increases the radiodensity of the tissue, rendering it visible to the x-ray and producing high-quality CT images.

We recommend staining soft tissue specimens that are as "fresh" as possible and using a fixative prior to staining. Our guidelines provide a general protocol with a %6 Iodine solution. Specimen-based information as well as references detailing alternative solutions are also listed.

If you are interested in having a professional stain your specimens, New York Tech has a staining lab. Please contact Meredith (Merri) Taylor (mtaylo10@nyit.edu) for more information.

Scan Data

Acquisition

Phantoms: The Visualization Center has six different phantoms available for use. The phantoms include: a CT dose phantom, water phantom, point spread function PSF phantom, multi-layer phantom, HA phantom, and a low contrast phantom. For more information about the phantoms and how they can benefit your microCT project, email us at viscenter@nyit.edu.


Post-Processing/Analysis

Post-Scan Reconstruction: We use Bruker's proprietary software NRecon to transform projection images into image stacks. Our default approach is to enhance contrasts of structures while minimizing noise and potential visualization artifacts. We can also follow a set protocol of reconstruction parameters if this is requested by the user.

Data output: Our standard data output type is 16-bit TIFF images paired with a metadata file and the original projection images. We can also save data as jpg, bmp, or png.

The following are programs that are compatible with microCT scan data (for segmentation, 3D visualization, etc.):

Also, make sure that your computer has a mid to high-end graphics card, sufficient RAM and hard drive space or you will not be able to download and view the data. The system will either continuously lag or completely crash. If you require the use of a high-powered computer, you may book time on one of our machines in the visualization center (free of charge).


Storage

An account will be created for you on our Viscenter Data Storage System. Your individual account is password protected and is only accessible to you.* Once your scan has finished and been reconstructed, the data will be uploaded to your account which you can access anywhere with an internet connection. Please download your data within 30 days. After this point, the data will be deleted and irretrievable.

Note that NYIT’s Visualization Center stores information on imaging requests, scanning parameters, type of specimen, and data reconstruction. This information may be visible to the MicroCT committee. It is our policy not to distribute scans, contact information, or logistical details outside of the MicroCT committee unless a request is made in writing to the primary user. The Visualization Center makes no claim to the data of your specimen(s). Ownership of the data resides with the primary user. We will not share, publish, or otherwise distribute your data. For advice on long-term storage, please contact us at viscenter@nyit.edu

*Viscenter Storage System Admins also will have access to your account for maintenance and data transfer purposes.


Sharing

The following websites will allow you to upload and share your data as well as discover and download data others have uploaded to the site:

The following websites allow you to view and download their data, but do not allow you to upload your own onto their database:

(note: some may allow contribution when contacted; see each website for details)

The websites below only allow you to visually view their data; no uploading or downloading:

Please note that, although the Visualization Center encourages data sharing and distribution, it is not our policy to share, publish, or otherwise distribute your data. Ownership of the data (and the right to distribute that data) resides with the primary user only.


Contact information: Please direct additional inquires to viscenter@nyit.edu