How to convert, reduce, and load micro CT scans

August 6, 2018

Checkpoint can help you convert those large micro CT scans into files that are more manageable. The following explains how to load a stack of TIF image files from a micro CT scanner and convert them into a NifTi (.nii) file type which Checkpoint can load. During this process you'll also have a chance to shrink (or down sample) the large micro CT scan into a smaller size.

  1. First, click on the "Image Stack" button (far right side) from the Specimen tab when Checkpoint starts up.

     
  2. This will show the Image Stack importing workflow as shown here:

     
  3. Click on the "Select Image Files" button and navigate to the folder that contains the TIF image files for your micro CT image stack. Choose all of the TIF files that represent your scan and you should see them populate the window as follows:

     
  4. Validate that the order of the image files is correct. These are sorted alphabetically by default, but if the files are not numbered consistently, you can move individual files up/down in the list with the bottons on the right-hand side.
     
  5. Enter a name for the scan and also the pixel and slice spacing. You will need to obtain this from the CT scanner software or proprietary files that came with the scan, for example:

     
  6. Choose what you want to do with the scan. Choosing the "Checkpoint Files (*.ckpt)" option creates a .ckpt file in the same folder as the TIF image files with a list of the files so that you can load the image stack in the future by just opening the .ckpt file. If you want to shrink or down sample the micro CT scan, you can choose one of the "Convert to NifTi XMB [] (*.nii)" options. This allows you to reduce the size of the micro CT, scan while maintaining as much quality as possible, and saves it as a NifTi (.nii) file that you can load in the future. Click on the "Save Stack" when ready to save the results. In this example, we are reducing an 11GB micro CT scan down to 178MB.

     
  7. When the reduction is complete, you will be asked where to save the NifTi file.
     
  8. You can then load the newly created NifTi (.nii) file as you would normally load any scan from the Specimen screen:

     
  9. Clicking on the "Open Specimen" button loads the smaller version of the micro CT scan:

For more information about Checkpoint, please click here: Checkpoint Software

David F. Wiley, PhD

President & CTO

Leave a Reply

Your email address will not be published

Log in or register to post comments