Please post in this thread links to publicly available software that can help participants segmenting 3D neurites from EM images.
Thu, 02/07/2013 - 16:30
Some options are already publicly available to approach different tasks of the challenge. For example:
Please, feel free to post any other tool that you think may help the other participants.
Tue, 02/19/2013 - 18:03
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:
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!
Fri, 03/15/2013 - 17:39
There was a small bug on the code. We have just fixed it and uploaded the new files.
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