Skeletonise wrapper

This page documents the wrapper class of the Skeletonize3D plugin in BoneJ2. The plugin is used trough a wrapper instead of called directly to:

1. Place it under the Plugins>BoneJ menu entry
2. Provide custom functionality

The wrapper will call the Skeletonize3D plugin even though it still is very much in the ImageJ1 world. In the ideal case we would help @iarganda to convert the plugin into an Op, but currently we do not have the resources.

Skeletonize3D creates a topological skeleton of the given image as the name implies. If the image contains more than one separate object, it creates a skeleton of each. A skeleton is thin version of the original shape, which emphasizes geometrical and topological properties.

• BoneJ1 source
• BoneJ1 documentation

Skeletonise wrapper

• Menu path: Plugins>BoneJ>Skeletonise
• Inputs
  • ImagePlus inputImage the image to be skeletonised
• Outputs
  • ImagePlus skeleton the resulting binary skeleton
• Calls
  • Skeletonize3D_ in sc.fiji.skeletonize3D

Setup dialog

• No setup dialog

Messages

• If there is no input image
  • Show an error dialog
  • Abort the run
• If the input image is not 8-bit binary colour
  • Show an error dialog
  • Abort the run

Results

• Creates an ImagePlus output image that shows the skeleton of the input image
• Does not overwrite the input image
• Output image has the same calibration as input image
• The title of the output image is "Skeleton of <title of input image>"
• If input image has an inverted LUT (background white, foreground black), the LUT of the output image must be inverted

Differences from BoneJ1

• Skeletonize3D_ is included via Maven instead of packaging it in org.bonej.*
• Renamed from Skeletonise 3D in BoneJ1, because the plugin can be used for 2D images as well
• Does not auto-invert result image LUT