NeuroMorph analysis software


NeuroMorph is a toolset designed to import, visualize and analyze mesh models. It has been made specifically for the morphological analysis of objects derived from serial electron microscopy images of brain tissue, but much of its functionality can be applied to any 3D mesh.​​​​​​ These mesh objects can be generated by any 3D image segmentation software, such as Ilastik ( and FIJI (

Visit the NeuroMorph project website for more information


A. Jorstad, B. Nigro, C. Cali, M. Wawrzyniak, P. Fua, G. Knott.  “NeuroMorph: A Toolset for the Morphometric Analysis and Visualization of 3D Models Derived from Electron Microscopy Image Stacks.” Neuroinformatics, 2014. (infoscience link)


Download the latest version of NeuroMorph and the Synaptic Vesicle Density Measure add-on from the NeuroMorph GitHub page.

For more information about the use of these tools, please contact:

Graham KnottAnne Jorstad