Object Counter3D

Revision as of 09:51, 13 November 2009 by White (talk | contribs) (removed categories as this is not the version now in use of this plugin, see 3D object counter plugin)
Object Counter3D (ImageJ)
Author Jonathan Jackson
Maintainer Daniel White
File Object_Counter3D.class (13,353 Bytes)
Source Object_Counter3D.java (23,913 Bytes)
Initial release 31 May 2006
Latest version 14 June 2006
Development status unknown
Category Particle analysis
Website [1]


The Object_Counter3D.java linked in the info box here is by Jonathan Jackson. It is a follow-up of Fabrice Cordelières's _3D_objects_counter.class, _3D_objects_counter.java and its changelog is located on the same website (see infobox).

Newest version (v2.0 - 2007?) of Fabrice's _3D_Objects_Counter.java is available from here: 3d-oc_.jar which if unzipped contains the source code .java files.

Testing of both versions in fiji showed them both to work. Now need to figure out which one to include: The older Jackson version was pushed to contrib branch late june 2009 (how ironic). Pushing both versions doesn't make sense. Both seem to have advantages, but both are about the same speed as tested with small and large z stacks. The Fabrice V2.0 plugin might be a little faster in some of my tests.

They are indeed slightly different, and do give different results for a 4 slice smoothed random image z stack, using the same threshold and max/min no of voxels. The v2.0 plugin excludes particles on edges of image, which is a good thing. Both allow dot size and font size to be set. v2.0 has centroid in pixels not calibrated (others measurements are calibrated). Jackson version centroid is calibrated.

Small bug in v2.0. typing threshold into the box in the gui, if you type in a number lower than 50 , it makes it fifty something! You have to use the arrows to change the threshold to less than 50.

V2.0 plugin is now contained in Fiji; just use Help>Update Fiji to get it.


The original plugin was published here: Journal of Microscopy, Vol. 224, Pt 3 December 2006, pp. 213–232 Received 13 April 2006; accepted 28 June 2006 Blackwell Publishing Ltd TUTORIAL REVIEW A guided tour into subcellular colocalization analysis in lightmicroscopy S. BOLTE & F. P. CORDELIÈRES