3D Object Counter

Authors: Fabrice Cordelires (Fabrice.Cordelieres at curie.u-psud.fr)
Institut Curie, Orsay, France
Jonathan Jackson (j.jackson at ion.ucl.ac.uk)
UCL Institute of Neurology, London, UK

Source: Object_Counter3D.java

Installation: Download Object_Counter3D.class to the plugins folder, or subfolder, restart ImageJ, and there will be a new " 3D objects counter" command in the Plugins menu, or submenu.

Description: 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).
Thanks to Gabriel Landini for major feedbacks and suggestions.

History: 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 (v1.3): (Jonathan Jackson, j.jackson at ucl.ac.uk)

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 (v1.4): (Jonathan Jackson, j.jackson at ucl.ac.uk)

Plugin remembers user selected options
Fixed bug causing particles to wrap-around image boarders
2007/06/18 (v1.5): (Jonathan Jackson, j.jackson at ucl.ac.uk)

Measurements now spatially calibrated
Volume and Centre of Mass/Centroid 'Surface' value is now expressed as the fraction of voxels on the object surface
2007/06/25 (v1.5.1): (Jonathan Jackson, j.jackson at ucl.ac.uk)

Fixes bug introduced in version 1.5 causing 'draw particles' to fail for particles centered in the first slice

To Do:

An algorithm to estimate the 'Surface Area', rather than the fraction of surface voxels
Contributions welcome!

Authors:	Fabrice Cordelires (Fabrice.Cordelieres at curie.u-psud.fr) Institut Curie, Orsay, France Jonathan Jackson (j.jackson at ion.ucl.ac.uk) UCL Institute of Neurology, London, UK
Source:	Object_Counter3D.java
Installation:	Download Object_Counter3D.class to the plugins folder, or subfolder, restart ImageJ, and there will be a new " 3D objects counter" command in the Plugins menu, or submenu.
Description:	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). Thanks to Gabriel Landini for major feedbacks and suggestions.
History:	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 (v1.3): (Jonathan Jackson, j.jackson at ucl.ac.uk) 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 (v1.4): (Jonathan Jackson, j.jackson at ucl.ac.uk) Plugin remembers user selected options Fixed bug causing particles to wrap-around image boarders 2007/06/18 (v1.5): (Jonathan Jackson, j.jackson at ucl.ac.uk) Measurements now spatially calibrated Volume and Centre of Mass/Centroid 'Surface' value is now expressed as the fraction of voxels on the object surface 2007/06/25 (v1.5.1): (Jonathan Jackson, j.jackson at ucl.ac.uk) Fixes bug introduced in version 1.5 causing 'draw particles' to fail for particles centered in the first slice
To Do:	An algorithm to estimate the 'Surface Area', rather than the fraction of surface voxels Contributions welcome!