Surface fraction

In BoneJ1 the volume fraction plugin offered two methods of calculating the fraction: voxels and surface mesh. In BoneJ the voxel method was generalised to work in 2D and 3D, so the plugin was split into two tools. The surface method only works with 3D images, and it would be quite confusing to have both under one menu.

Surface fraction calculates the fraction of bone in an image by comparing surface meshes created from the bone voxels (i.e. foreground voxels) and all the voxels. The bone and total voxels are sent to a marching cubes ops, which creates surface meshes from them. Finally the fraction of bone in the image is determined by comparing the volumes of these meshes.

SurfaceFractionWrapper

• Menu path: Plugins>BoneJ>Fraction>Surface fraction
• Inputs
  • ImgPlus<T> inputImage (T extends RealType<T> & NativeType<T>)
• Outputs
  • Table<DefaultColumn<String>, String> resultsTable

Setup dialog

• No setup dialog

Messages

• If no image is open
  • Show an error dialog
  • Abort the run
• If image is not binary
  • Show an error dialog
  • Abort the run
• If the input image doesn't have three spatial dimensions
  • Show an error dialog
  • Abort the run

Results

• Shows "Bone volume", "Total volume" and "Volume ratio" for each 3D subspace in the Shared table
  • Shows the results calibrated
  • The results have the unit of the calibration, e.g. mm^3. If axes have different units, calibrations are converted into the unit of the first spatial axis (x-axis).

Differences from BoneJ1

• Supports hyper stacks
• Only supports binary images
• Results differ, because marching cubes and mesh volume implementations are different