ObjCounter plugin

author: Gherardo Varando, gherardo.varando@gmail.com

What it is?

ObjCounter is an ImageJ plugin to segment connected objects in stack of images. The plugin detects the objects, and it can create stacks with the labelled objects, stacks with centroid or center of masses of the detected objects, and it can exports the results to csv format. Moreover if an overlay (with single dots labelling every objects) is present then it is possible to evaluate the segmentation.

ObjCounter is based partly on _3D_Object_Counter code by Fabrice P. Cordelières (http://imagej.net/3D_Objects_Counter). The algotihm is different, the connection is done in every slice, then based on the intersection between objects in different slices the objects are linked or not (modifying the fraction parameter change the tolerance to connections, e.g. with fraction=0 all the possible connections will be made, similar to _3D_Object_Counter ).

The _3D_OC_Options class is the same as used in _3D_Object_Counter plugin, and should not cause any conflict.

Installation and dependencies

ObjCounter is an ImageJ plugin, thus ImageJ must be installed (see http://fiji.sc/ to install FIJI a "batteries-included" distribution of ImageJ).

To install the plugin just copy the .JAR file into the plugin directory of your ImageJ installation (see imageJ help for more information).

Trying to segment big object could lead to thread stack overflow due to the recursive calls and to the default small thread stack size. To avoid this problem you need to change the Java option relative to the size of the thread stack, Java options are defined in the ImageJ.cfg file in the main directory of your ImageJ installation (see ImageJ help on example of Java configurations for ImageJ ). The thread stack size can be changed with the option -XssSIZE where SIZE is the desired size of the thread stack. Refer to Oracle documentation for a complete explanation of the Java options ( Windows, Linux , Mac OS X ).

In Linux just copy/paste the following line to the ImageJ.cfg config file in your ImageJ installation :
.jre/bin/java -Xss515m -cp ij.jar ij.ImageJ 


This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with this program. If not, see http://www.gnu.org/licenses/.