morphonets / cx3d

The Cx3D modeling framework in SciView and SNT

SciView - Cx3D

Image-based modeling using SciView

Cx3D (Cortex simulation in 3D) is a tool for simulating the growth of cortex in 3D initially developed at the Institute of Neuroinformatics of the University of Zürich and ETH Zürich. It was released in 2009 under the GNU General Public License version 3.

This repository hosts the SciView 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.

Quick Start

1. Clone the repository (use the green code button above the list of files)
2. Import the project into an IDE such as Eclipse/IntelliJ/NetBeans:
   • In Eclipse: Run Import> Existing Maven Projects and specify the path to the downloaded cx3d folder in Root Directory
   • In IntelliJ: In the Welcome Prompt, choose Open or Import and specify the path to the downloaded cx3d folder
   • In NetBeans: Run File> Open Project..., select the downloaded SNT directory, and click on Open Project
3. Wait for all the dependencies to be downloaded, and run sc.iview.cx3d.commands.RandomBranchingDemo
4. Do you want to write your own plugin based on Cx3D? Use the template project!

To run the original Cx3D demos and tutorials from the CLI

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

git clone [e-mail]:morphonets/cx3d.git
cd cx3d-mvn
mvn package

2. cd to target directory:

cd target

3. To run an example from the tutorial:

jar ufe cx3d-mvn-0.0.4-SNAPSHOT.jar DividingCell
java -jar cx3d-mvn-0.0.4-SNAPSHOT.jar 

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

jar ufe cx3d-mvn-0.0.4-SNAPSHOT.jar Figure_3_G
java -jar cx3d-mvn-0.0.4-SNAPSHOT.jar

NB: For other examples/figures, replace "DividingCell/Figure_3_G" above with others from the tutorial or frontiers folders.

Development

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

Contributing

Want to contribute? Please, please do! We welcome issues and pull requests any time.

Acknowledgements

This version of Cx3D derived from @tferr's mavenized fork

Resources

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