Surface area

Surface area creates a surface mesh from the given 3D binary image, and then calculates its area. First it selects all the foreground voxels, and feeds them to a marching cubes op. The marching cubes op outputs a mesh, whose area is calculated with another op. Isosurface wrapper also offers to option to save this mesh as an STL file.

SurfaceAreaWrapper

• Menu path: Plugins>BoneJ>Surface area
• Inputs
  • ImgPlus<T extends RealType<T> & NativeType<T>> inputImage
  • boolean exportSTL
• Outputs
  • Table<DefaultColumn<String>, String> resultsTable

Setup dialog

• Options
  • exportSTL (boolean)
    • Label: Export STL file(s)
    • Tool tip: Create a binary STL file from the surface mesh
    • Widget: Check box
    • Optional (required = false)

Messages

• If there's no image open
  • Show an error dialog
  • Abort the run
• If the input image doesn't have three spatial dimensions
  • Show an error dialog
  • Abort the run
• If the input image is not binary colour
  • Show an error dialog
  • Abort the run
• If image calibration is anisotropic
  • Show a warning about incorrect results (surface area incorrectly scaled)
• If user chooses to export STL files
  • Show a file dialog
  • Cancelling file dialog must stop plugin
• If the writing of one or more STL files fails
  • Show an error dialog which lists each failure

Results

• Prints Surface area for each 3D subspace in the Shared table
  • Shows the unit of the area, e.g. mm^2 (pixel for uncalibrated). If axes have different units, calibrations are converted into the unit of the first spatial axis (x-axis).
• STL-files

• Saves the mesh of each 3D subspace in binary .stl format if option chosen
• Files are saved in little endian order

Differences from BoneJ1

• Supports hyper stacks, i.e. 3D images with channels and/or time frames
• Results differ because of different implementations of marching cubes and mesh surface area
• Supports only binary images