Some options are already publicly available to approach different tasks of the challenge. For example:

• To perform pixel classification of the 2D slices, you can use the Advanced Weka Segmentation plugin available in Fiji: http://fiji.sc/wiki/index.php/Advanced_Weka_Segmentation
• To interactively train a classifier for 3D segmentation, you may use Ilastik: http://www.ilastik.org/

Please, feel free to post any other tool that you think may help the other participants.

Thanks!

If your segmentation method produces a 3D affinity graph as output. You can use the following Matlab code by Aleksandar Zlateski to run connected components using a specific threshold value and extract the corresponding 3D objects:

• ZiConnectedComponents.mexa64: add this file into your Matlab path and you will be able to run connected components on 3D affinities.
  Usage: 
  >> R = ZiConnectedComponents(AffinityGraph, Threshold [, MinSize = 0] )
    Affinity - 4D Affinity graph of type float or double
    Threshold - float or double (edges below Threshold are ignored)
    MinSize - float or double or Integer (components smaller than MinSize will be ignored)
• ZiConnectedComponents.cpp: corresponding C++ source code (GPL license).

For more information about using affinity graphs and image segmentation you can read the following paper, for example.
Check out Fig. 3: http://hebb.mit.edu/people/seung/papers/Turaga%20et%20al_NeuralComp_2010...

If you have any quesiton, just write it on this thread!

ignacio