Element fraction

In BoneJ1 the volume fraction plugin offered two methods of calculating the fraction: voxels and surface mesh. In BoneJ the voxel method is 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. The voxel tool was also renamed to element fraction.

Element fraction counts the number of foreground and total elements in a binary image, and calculates their ratio.

ElementFractionWrapper

• Menu path: Plugins>BoneJ>Fraction>Area/Volume fraction
• Inputs
  • ImgPlus<T> inputImage (T extends RealType<T> & NativeType<T>)
• Outputs
  • Table<DefaultColumn<String>, String> resultsTable
• Calls
  • ElementFraction in org.bonej.ops

Setup dialog

• No setup dialog

Messages

• If no image is open
  • show an error message
  • abort the run
• If image is not binary
  • show an error message
  • abort the run
• If image has less than two or more than three spatial dimensions
  • show an error message
  • abort the run

Results

• Prints "Bone volume", "Total volume" and "Volume ratio" into the Shared table. "Volume" is "area" if the image is 2D.
  • The results are calibrated
  • The results are shown in the unit of calibration, e.g. mm^2 for a 2D image. If axes have different units, calibrations are converted into the unit of the first spatial axis (x-axis).
• The column headers in the results table must show units

Differences from BoneJ1

• Can handle 2D images and hyper stacks
• Accepts only binary images