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Cx3D (Cortex simulation in 3D) is a tool for simulating the growth of cortex in 3D initially developed at theInstitute of Neuroinformatics of theUniversity of Zürich andETH Zürich. It was released in2009 under theGNU General Public License version 3.

This repository hosts theSciView version of Cx3D, making Cx3D compatible with the ImageJ and Fiji ecosystem. This includes using SciView for 3D visualization, allowing Cx3D to grow neuronal processes with SciView’s data structures, and support for image-based modeling.

1. Clone the repository (use the greencode button above the list of files)
2. Import the project into an IDE such asEclipse/IntelliJ/NetBeans:
   • In Eclipse: RunImport> Existing Maven Projects and specify the path to the downloadedcx3d folder inRoot Directory
   • In IntelliJ: In theWelcome Prompt, chooseOpen or Import and specify the path to the downloadedcx3d folder
   • In NetBeans: RunFile> Open Project..., select the downloadedSNT directory, and click onOpen Project
3. Wait for all the dependencies to be downloaded, and runsc.iview.cx3d.commands.RandomBranchingDemo
4. Do you want to write your own plugin based on Cx3D? Use thetemplate project!

1. Compile (assuming you have installed git and maven):

git clone git@github.com:morphonets/cx3d.gitcd cx3d-mvnmvn package

2. cd to target directory:

cd target

3. To run an example fromthe tutorial:

jar ufe cx3d-mvn-0.0.4-SNAPSHOT.jar DividingCelljava -jar cx3d-mvn-0.0.4-SNAPSHOT.jar

4. Or, to reproduce a figure fromthe 2009 Frontiers paper:

jar ufe cx3d-mvn-0.0.4-SNAPSHOT.jar Figure_3_Gjava -jar cx3d-mvn-0.0.4-SNAPSHOT.jar

NB: For other examples/figures, replace "DividingCell/Figure_3_G" above with others from thetutorial orfrontiers folders.

This remains the most active fork of Cx3D. The originalCx3D Subversion repository is stalled.

Want to contribute? Please, please do! We welcomeissues andpull requests any time.

This version of Cx3D derived from @tferr'smavenized fork

• Official Cx3D website (for convenience, some of the Cx3D tutorials are also mirrored in themisc directory)
• Parallelized version of Cx3D (abandoned project)
• C++ port of Cx3D