This is a collection of frequently asked questions about the Segmented Inner Organs of the Visible Human (SIO).
Is this the same as the Visible Human model?
No. The original color images of the Visible Human male published by the U.S. National Library of Medicine were reduced in size and geometrically aligned with the CT images to obtain an isotropic data volume. In a subsequent segmentation procedure, these data were augmented with anatomical object labels.
What is the resolution of the model?
The limiting factor is the voxel spacing, which is given by a voxel size of 1 mm x 1 mm x 1 mm. Structures smaller than that may only be represented as slight changes in color or CT intensity.
How accurate is the segmentation?
The segmentation was done using an advanced 3D algorithm based on the colors of the different organs, which in general could locate the object borders very accurately (see references).
Can I have a look at the data first?
Sure, please download the sample file. This ZIP archive contains a set of 5 consecutive slices, each with color, CT, and label images. An object list is also included, which links the numbers in the label images to their anatomical meanings.
Does the model include the muscles?
Yes, the model includes almost all of the muscle tissue of the torso. However, it is mostly labeled as “unclassified muscles”, only a few muscles of the abdominal region are explicitly labeled. Please have a look at the object list.
Does this model include all parts of the Inner Organs anatomy atlas?
Almost, but some very thin arteries and nerves of the Voxel-Man 3D-Navigator: Inner Organs anatomy atlas which are not visible on the cross-sectional images were modeled with a tube editor and represented as polygonal surface structures. They are not part of this model.
How is the label volume organized?
Just like color and CT data, the label volume comes as a stack of numbered cross-sectional images. Color, CT and label images with the same number represent different properties of the same voxels. Instead of colors or intensity values, a label image contains numbers, indicating the shape of the different anatomical structures, as determined in the segmentation process. To find out which objects are represented by these numbers, have a look at the object list.
I can’t see anything on the label images, what’s wrong?
For technical reasons, these are 16 bit TIFF images, which some programs cannot display properly. Programs which can handle these data include ImageJ (free) or Photoshop, among others. If the image still appears all black, adjust the brightness/contrast or level/window settings, respectively.
How can I create a volume dataset from these images?
The images need to be stacked on top of each other. For example, in ImageJ, use File > Import > Image Sequence … to create image volumes for color, CT, and label data, respectively.
Is this a polygonal surface model?
No, the data comes as a 3D voxel model. If you need a surface model, you can create it for yourself, using methods such as Marching Cubes.
Can I get the model as a Collada, X3D, STL, VRML, 3DS file?
All of these are 3D graphics formats for polygonal surface representations, see the previous question.
How can I obtain the model?
The model is available free of charge, but requires a signed license agreement. Please follow the instructions given on the Segmented Inner Organs page.
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