MICRO offers both drop-off and unassisted scanning (for trained users only). All users are required to read and agree to the MICRO User Agreement before any scanning can take place. If you are interested in having materials scanned at MICRO please contact us at micro@uark.edu or submit a scanning request form.

Scanning services are offered on a first-come first-serve basis and will depend on the equipment configuration and your scanning needs. MICRO also offers users the ability to reserve time on our analysis computer, where we offer a full suite of Avizo/Amira products, 256 GB of RAM, a 2x Quad-Core Intel Xeon processors, and a PNY Quadro video card. As with scanning, scheduling for the analysis computer is on a first-come first-serve basis. Please submit a scan request form or email micro@uark.edu to schedule time on the equipment, or you can refer to our scanning and analysis calendars for availability.

Below you can find details about scanning fees, scheduling, specimen mounting, and information about how to optimize the scan parameters for your objects (also see Scanning FAQs). 

MICRO Scanning Fees

Fees are charged for scanning on an hourly basis and depend on your affiliation with the University of Arkansas as well as your scanning needs. These fees include active scan time on the machine and scan reconstruction time. Interested users can submit an object to generate a sample scan so that we can optimize scan parameters according to the object properties and analytical needs. NSF-sponsored research will be billed at a reduced rate.

Internal UniversityExternal University/ Non-ProfitIndustry
Drop-off$80/hour$120/hour$175/hour
Unassisted*$60/hour ($1,500 monthly cap)$100/hour ($2,500 monthly cap)not available

*Offered to high-volume trained users only. To find out if your scanning needs qualify for this, please contact us at micro@uark.edu or refer to the User Training page.

Estimating Scan Length

The length of a scan primarily depends on the desired effective pixel size (~resolution) of the scan and the level of detail you are interested in obtaining (i.e., how little noise or other scan artifacts).

Parameters that can be adjusted and optimized during scan set-up include: beam energy (kV), beam current (µA), effective pixel size, gain, exposure length, pixel binning, frame-averaging, number of projections, and a feature to minimize ring artifacts (i.e., detector shifts during scanning). During the initial test scans of your objects, we will work with you to optimize these parameters according to your scan needs.

Specimen Preparation

We recommend the following packing and mounting practices to maximize imaging (you can also download these guidelines here).

Wet specimens: Specimens with soft tissue or that are typically stored in liquid should be packaged by the user prior to delivery to MICRO. Please note that we do not have facilities for wet specimen preparation in MICRO

Specimen container: Specimen containers should be low density to minimize X-ray attenuation. Polyethylene bags (e.g., for wet specimens) and plastic bottles or boxes (with labeling removed) work well. (Wet specimens should be double-bagged to prevent dehydration during scanning and/or transport.) Specimen containers should be only slightly larger than the specimen itself, in order to allow for best placement of the container within the scan volume.

Packing materials: Specimens should be packed within containers to prevent movement during scanning. Packing materials should be low density and deformable, such as cotton, bubble wrap, or foam.

Positioning: The scan volume is a 2000 x 2000 x 2000 voxel cube. Positioning your specimen within its container optimally may differ depending on how your scan will be performed. Thus, considering the type of scan should inform how specimens are packaged:

 

  • Single-volume scans: If your specimen is to be scanned as a single volume, then orienting it so that the long axis passes diagonally through the middle of the volume (i.e., 45º from horizontal) will facilitate higher-magnification scans
  • Multi-volume scans: Specimens that are too tall for a single volume at the preferred resolution can be imaged as “tall scans” wherein multiple volumes are imaged sequentially and digitally fused as a post-processing step. For these scans, specimens should be oriented with the long axis perpendicular to the ground

Adhesion: We have several beds, platforms, and mounting pins of various sizes. We typically adhere specimen containers to the CT scanner for the duration of the scan using soft wax or hot melt adhesive.

Data Handling

To ensure user satisfaction MICRO Pledges the following:

Reconstruction: We are capable of reconstructing CT data using a series of optimization steps. Our default approach to data reconstruction is to utilize the scanning and reconstruction settings for each specimen that contrasts multiple structures clearly while minimizing noise and potential visualization artifacts. We also recognize that users may wish to have datasets that are reconstructed to specific parameters with ease of automated segmentation methods in mind (e.g., in Avizo, VG Studio, etc.), and we will honor such requests.

Data output: Our standard data output type is a 16-bit TIFF image stack paired with one or more metadata files. TIFF is a lossless image format, which can result in datasets that are several gigabytes in volume. TIFF stacks are not inherently spatial, but the *.XtekCT metadata file included with your datasets contains the voxel dimension in X, Y, and Z orientations for input into 3D modeling software. We are also equipped to output *.VGL volume files that open directly into VG Studio Max.  You can analyze your data using a free program called Fiji – ImageJ.  Dr. Paul Gignac has shared some info about how to work with your data in this program.  You can find it here: https://micro.uark.edu/micro-instructions-for-working-with-image-stacks-in-fiji-fiji-is-just-imagej/

Your specimen: As researchers ourselves, we appreciate the delicate, rare, and invaluable nature of research specimens. We treat all specimens with care, and we may elect not to scan material if it appears too delicate to handle or if packaging has been damaged prior to arriving at MICRO. We return all specimens to the individual(s) or entity, who contracted the scanning (i.e., “the primary user”). MICRO will not ship specimens to addresses or personnel other than the primary user.

Your specimen data: Please include an empty, USB-capable hard drive or thumb drive with any specimens shipped to MICRO. The hard drive must be compatible with Windows 7 (e.g., FAT32, NTFS, or exFAT) and have sufficient storage space for all scan data. Data will be returned on the included hard drive with the specimen. Visitors to MICRO should bring their own portable storage device(s) along with their specimen(s). MICRO is not responsible for data integrity on non-MICRO hardware.

MICRO 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 outside of MICRO to anyone but you without express, written permission.

Storage lifetime: MICRO will store all primary scan data for 90 days. Within this period, reconstructed image stacks or VGL files may be deleted to allocate additional space, but they can be reconstituted from the original scan data. Unless a written request has been received and approved by MICRO, all scan data will be deleted following this 90-day period. *.XtekCT metadata files may be retained as templates upon request for users planning for extended periods of CT scanning. Data may be deleted with a written request from the primary user at any time.

Backup: Unforeseen issues with data management or physical infrastructure can occur from time to time. MICRO systems are backed up regularly to allow for full restoration from backups as needed.

Security: We secure our systems with antivirus protections to prevent malware from spreading. It is our policy to move data onto users’ portable hard drives but not to move files onto our systems. We regret any inconvenience this might cause.

Documentation: We generate a digital “paper trail” for all inquiries, imaging requests, data reconstruction, analytical work, and data deletion to facilitate an efficient workflow. This information may be visible to the MICRO Advisory Board and relevant staff at the Center for Advanced Spatial Technologies. It is our policy not to distribute scans, contact information, or logistical details outside of the MICRO team unless a request is made in writing by the primary user.

Contact information: Please direct additional inquires to micro@uark.edu with “MICRO Policies” in the subject line.

If you would like to download these policies as a pdf please click refer to the MICRO User Agreement.