IPC shape macro

2020-01-03T13:43:22Z (GMT) by Hornby, A.J.

Intra-Particle Components shape macro for ImageJ


  • Multiple components are supported using image stacks and identified by slice number
  • Components are linked to host particle by ROI number
  • Binary and non-binary image inputs accepted
  • Particles with 0 internal components generate "nothing to measure" message within results table
  • Size thresholds are defined as number of pixels
  • Holes in particles and components are not included in area measurements
  • The macro runs in batch mode by default. Edit the setBatchMode() argument in line 40 to disable.


  • An 'original' image file containing particles.
  • A (sub)folder containing one or more 'component' image files that have been thresholded or segmented from the original image
  • The Shape Filter plugin (add the Biomedgroup update site to ImageJ/Fiji)

Known issues

  • Convexity values can exceed one for small particles or components. This appears to be a resolution issue, possibly involving rendering of the convex hull in the Shape Filter plugin.


  • The macro uses the clipboard to copy from the results table during measurements


v1.0.1. Minor edits

v1.0.2. Minor edits to notes and readme to bring everything in line. Notes removed from macro.