3D objects counter



Fabrice Cordeli�res, Institut Curie, Orsay (France).

Fabrice.Cordelieres at curie.u-psud.fr


Thanks to Gabriel Landini for major feedbacks and suggestions.


Jonathan Jackson (j.jackson at ion.ucl.ac.uk) proposed a new version of the plugin (Object_Counter3D.java, Object_Counter3D.class) which changes are listed under the history section.



2005/06/15: First version

2005/12/05: Threshold can now be set up using a slider. Modifications in algorithm: first step of ID attribution followed by a second step of ID minimization (regularization)


2006/05/31: Release of Jonathan Jackson�s version of the plugin. Here are the changes:

  • Added "New_Results Window" option: Use to preserve existing data in the main ImageJ "Results Table"
    Unselect this option if you wish to use the commands "Analyze->Summarize" and "Analyze->Distribution"
  • Results are given in floating point precision
  • Works in "Batch Mode"
  • Improved exectution speed
  • Added methods to facilitate calling from another plugin

2006/06/14: Update to Object_Counter3D

  • Plugin remembers user selected options
  • Fixed bug causing particles to wrap-around image boarders






Download _3D_objects_counter.class to the plugins folder and restart ImageJ.



This plug-in counts the number of 3D objects in a stack and displays the volume, the surface, the centre of mass and the centre of intensity for each object. The threshold value can be adjusted using the first slider and user may navigate through the stack using a second slider. Results are presented both as a results table and as new stacks where either the full volume, the edges of each particle, the centre of mass or centre of intensity is represented. On this stack, each structure appears under a different colour. A tick box allows logging a summary of the overall measurement (useful to keep a track of successive counts).

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