IPC shape macro

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

Intra-Particle Components shape macro for ImageJ

Features

  • 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.

Requirements

  • 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.

Warning

  • 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.