We encourage scientists using MorphoGraphX to develop their own plugins to address specific questions. If you develop a plugin you think would be of general use, please contact Richard Smith so that we can host the plugin on this page and/or include it in the next release of MorphoGraphX.


MorphoGraphX can be extended with plugins that can be compiled separately and loaded at runtime.

Please let us know about the plugins you have developed and we can host them here.

You can download our sample plugins to get started.


AddOns are groups of plugins that are developed around a theme and are built along with MorphoGraphX with the CMake build system, and can be distributed as separate packages or included with MorphoGraphX.

The following AddOn adds processes for neural network voxel prediction with 3D U-Nets to improve the segmentation of cell wall markers.

Already in MorphoGraphX!

The following contributions are now incorporated into MorphoGraphX and are available in the latest version:

Fibril Orientation – Adapted from  the ImageJ plug-in FibrilTool (see Boudaoud et al. (2014)) this tool now works on curved surfaces and uses a segmented mesh (less clicking!).

CellAtlas – A tool to annotate and analyze 3D segmentations of radially symmetric plant organs, such as roots, hypocotyls, or mature embryos. See Montenegro-Johnson et al. 2015.

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