All software can be downloaded from our GitHub page.
All documentation can be found at our GitHub wiki page.

Measure surface areas, volumes, and lengths of user-defined regions of meshes. Measurements can be exported for analysis.


Video Tutorial (outdated, but still relevant for this tool)

Scroll through image stacks in 3D. Place spherical markers (eg vesicles) on images, and draw lines that can be constructed into both open surfaces (eg synapses) and closed surfaces (eg mitochondria) in 3D. Open surfaces with holes are handled. Closed surfaces that branch are not handled.


Create centerlines of tubular structures (eg axons), and perform analyses using these centerlines. Includes tools to generate cross-sectional surface areas, and project objects (eg vesicles, synapses) onto the centerline for distribution analysis. Experimental tools are provided for detecting bouton swellings. Also includes tools to clean meshes, and import/export meshes with VMTK. Data can be exported for analysis.


Calculate the regions of two surfaces that are within a given distance of each other. Provides meshes and outputs surface area data for analysis.

Also includes the Sphere to Surface Distances tool, which computes the closest distance from each vesicle sphere to a synapse mesh. Provides meshes and outputs surface area data for analysis.


Generate 3D Image Stacks
Macro for Fiji, creates image stacks in the X and Y dimensions, given an image stack in Z.

NeuroMorph Parent-Child Tools
Allows the user to easily to show/hide all children of an object, delete all children of an object, and assign the parent of all selected objects.

NeuroMorph Import Objects
Import object models from .obj files obtained through 3D image segmentation software (e.g. ilastik or TrakEM2) into Blender.

NeuroMorph Naming
Previously part of the deprecated NeuroMorph Measurement Tools, allows objects to be named according to a naming convention developed for neural structures.

IMOD to Blender (correct Y mirroring)
Tool to correct IMOD-exported meshes by rotating in the Y dimension, so that they can be processed correctly in Blender.


These tools are deprecated. They are provided for legacy purposes as they were released with the 2014 NeuroMorph Neuroinformatics paper.

NeuroMorph Measurement Tools
See updated NeuroMorph Measurement Tools.

NeuroMorph Image Stack Interactions
See NeuroMorph 3D Drawing and NeuroMorph Retrieve Object from Image.

NeuroMorph Import Objects
Now found in Other Tools.

Video Tutorial