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 amarching 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.

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

• 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)

• 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

• PrintsSurface area for each 3D subspace in theShared 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

• 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