3D objects counter



Fabrice CordeliŤres, 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: When this option is selected the behaviour is identical to the original. When unselected, the ImageJ "Results" table is used, which allows the commands "Summarize" and "Distribution" from the Analyze menu to be used on the output data.
  • Used static fields and the IJ.register method: This is to remember chosen options from one execution of the plugin to the next.
  • Split the run() method into run() setupGUI() and analyze(): This makes no difference, it just makes it easier to call this plugin from another plugin.
  • Added implements Runnable, Thread thread, and runThread(), getParticles() etc methods: This is to run the plugin from another plugin, and be able to pass the ImagePlus from one to the other.
  • Moved class variables x,y,z etc into the analyze() method: This is supposed to provide faster access than class variables.
  • Created temporary variables offset and tagvois, to temporarily store the results of the offset(x,y,z) and getTag(voisX...) methods: this increases the plugin speed.






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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