Image Processing - What happens after scanning?

  1. When the scan is complete, the file is automatically saved in .txrm format. 
  2. This file is opened into the image reconstructor software, where the raw images are "put together" into 3D form. The file is saved as an image stack in a variety of possible output formats including: dicom, bin, or tiff.
  3. The reconstructed file is opened in an appropriate image processing software for the desired purpose. Our workstation has the following softwares which are accessible to all users: Amira 5.4.2, Avizo, ImageJ, Matlab. Once the data set is uploaded, both 2D image slices and a 3D rendering is automatically attainable with a viewer. Quantitative results may also be found through image thresholding and segmentation techniques, and allows for acquiring differences in intensity (grayscale changes) or mineral density changes. Volumes of specific features can also be determined, for example the volume of a specific mineralized tissue (enamel, dentin, bone), volume of vasculature networks, volume of osteocyte/lacunae, or even soft tissue. *Note- for imaging soft tissue, an appropriate staining/contrast agent must be used.