Working with the Center for Quantitative Imaging

Procedures and resources for existing clients

New clients that have not worked with the Center for Quantitative Imaging (CQI) before can get started by submitting this form.

We are excited that you are considering utilizing the Center for Quantitative Imaging as part of your research. Please read this information as you prepare your project to ensure that utilizing computed tomography (CT) is feasible and will produce the desired data. We recommend that you consult with CQI staff to discuss your project before you begin designing your experiment or samples to ensure compatibility with this technology. If you are preparing a grant we can provide you with information about the facility and sample costs to use in your submission.

Samples and Resolution

Sample Composition

Dense materials require a high power to penetrate the material. Samples made of these dense materials (i.e. lead, tungsten, etc.) should be as small as possible. Samples will rotate when in the scanner, so the longest dimension that x-rays will need to penetrate should be considered. This includes having multiple samples attached to the same base. While the individual pieces may not have an exceptionally long axis, when combined the x-rays will need to penetrate all the samples together.

Determining Desired Resolution

Computed tomography creates a three-dimensional dataset made up of voxels (3D pixels). Each voxel will be set to the desired resolution. However, to accurately visualize and measure something in three-dimensional space, the voxel size/resolution needs to be 3-5 times smaller than what you are trying to visualize or measure. For example, if you are trying to measure porosity where the pores average 10um in diameter, we recommend scanning at 2-3um.

Sample Mounting

Samples will need to be mounted in such a way that: 

  • they rotate along a vertical axis,
  • there is no collision with the x-ray source,
  • the desired region of interest stays within the field of view,
  • the x-rays penetrate the shortest x and y axes, even if that is not typically how your sample is oriented, and
  • flat surfaces (including internal structures) are not perpendicular to the axis of rotation.

CQI has basic plastic tubes and foam that can be used for mounting. Adhesives such as painter's tape, putty, hot glue, super glue, etc., may be necessary to keep your sample from moving. It is critical that your sample does not shift during scanning. We will work with you based on the needs of your sample. 

However, mounting time is an associated staff cost. If you are scanning samples that are irregular in nature, you may consider 3D printing a mount to provide to CQI for the scanning of your samples. Additionally, if you need to know the alignment or orientation of samples, consider placing a physical mark (indent, notch, etc.) within the FOV. Surface marks such as sharpie lines or tape will not appear on scans and should not be used. 

We recommend you consult with CQI staff to discuss mounting your samples before submission. It is always appreciated when you consider how your samples will be scanned in advance. 

Sample Size and its Relationship to Scanning Resolution

General Electric Micro-Nano CT System

The GE phoenix v|tomex|x L scanner works based on geometric magnification. The achievable resolution is based on the relationship between the distance of the sample and the detector to the x-ray source. We can achieve higher resolution (smaller um) the closer the object is to the source. Therefore, a sample needs a small radius to be able to rotate close to the x-ray source.

However, with increased resolution comes a smaller field of view (FOV). The field of view can be calculated by multiplying the voxel size by 2000. For example, a sample scanned at 7um has a 14mm field of view.

An additional consideration is the size/density relationship and the desired resolution. While we may be able to find a geometric magnification to achieve a high resolution, the power that is required to penetrate your sample should not exceed your desired resolution.

For example, if your desired resolution is 21um, we cannot use more than ~21W of power to penetrate the longest axis, without risk of unsharpness (edge blurriness).

Range of resolution achievable using the GE Scanner: hundreds of microns to single microns.

Zeiss Versa 620

The Zeiss Versa 620 works based on optical magnification. Below is a table provided by Zeiss showing the possibilities and limitations of the Zeiss Versa 620 with respect to sample size, voxel resolution, and field of view.

Objective recommendations for typical user scan conditions

Sample Size


Voxel Size
Bin1 (µm)

Voxel Size
Bin2 (µm)
FPX 15 - 140 (200*) 140 6 - 57 12 - 115
0.4X 6 - 50 (100*) 50 (90) 3 - 30 6 - 60
4X 2 - 20 (50*) 6 (10) 0.7 - 3 0.7 - 6
20X 0.5 - 4.0 (10*) 1.1 0.3 - 0.6 0.5 - 1.2
40X 0.3 - 2.0 (5*) 0.5 0.2 - 0.3 0.3 - 0.6

Range of resolution theoretically achievable using the Versa Scanner: tens of microns to 0.2 microns. 

However, with increased resolution comes a smaller field of view (FOV). The field of view can be calculated by multiplying the voxel size by 2000 (for bin 1) and by 1000 for (bin 2). For example, a sample scanned at 700nm has a 1.4mm FOV at bin 1 and a 0.7mm FOV for bin 2. Most samples scanned on the Versa are scanned using bin 2.

Getting the Results

Estimates of Scanning Time

Clients often want to know how long a sample will take to scan. Unfortunately, we cannot give you an estimate until we have examined the sample and placed it into the scanner. There are several parameters that are set for each scan that depend on the individual sample and research objectives. We will communicate with you each step of the way and get approval for the estimated time prior to beginning scanning. We will also ask that you approve the first scan before we proceed in case any changes need to be made to the procedure.

Working with Your Data

CQI will make your data available to you for 60 days from the date of data delivery. Instructions on accessing and downloading your data are available. At this time, CQI can provide limited assistance with the post-processing of your data. However, we are developing training documents that will be available in the future. 

One important thing to think about is the type of data you wish to receive. We will automatically produce VG Studio projects and 32-bit .vol files. These data are quite large as 32-bit data store a lot of information. This may be more information that you need. Data can be converted to 16-bit or 8-bit data which reduces overall file size. We can produce other data file types upon request with the associated staff time costs. However, some of these file types (i.e. .stl files) require CQI staff to make decisions about thresholding your data. It may be best to learn how to produce these types of files on your own. 

CT data are inherently large datasets and require a lot of memory to read and process. CQI does have a limited number of workstations that Penn State users can remote into to access Avizo and ImageJ, two popular software applications that are utilized by CT users. Please Remote Access to Shared Workstations (ImageJ and Avizo) for more information.

Citing the Center and Staff

If you publish or present data obtained from CQI, please include an acknowledgment of this facility in your publication. At minimum:

The co-authors would like to acknowledge the Energy and Environmental Sustainability Laboratories at Penn State, Center for Quantitative Imaging, [staff member names].

Or, more specifically:

Imaging was performed at the Center for Quantitative Imaging at Penn State. The co-authors would like to thank [staff member names] for their assistance in [description of work].

If specific staff members have assisted you, please include their names in your acknowledgment section. If they made a significant intellectual contribution, please consider making that staff member a co-author of your report. Examples of a significant intellectual contribution include: helping develop new methods, helping to design the experiment, selecting or collecting samples of interest, analyzing or interpreting data, or writing/revising a portion of the paper.