Software

All software can be downloaded below, or from our GitHub page .
All user's guides can be viewed at our Blender Wiki page .



User's Guide Video Tutorial*

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

*Video tutorial is outdated, but still relevant for this tool.


User's Guide

NeuroMorph Centerline Processing
Processes center lines generated by the Vascular Modeling Toolkit (VMTK), perform calculations in Blender using these center lines. Includes tools to clean meshes, export meshes to VMTK, and import center lines generated by VMTK. Also includes tools to generate cross-sectional surfaces, calculate surface areas of the mesh along the center line, and project vesicle objects onto the center line. Tools are also provided for detecting bouton swellings. Data can be exported for analysis.


User's Guide Video Tutorial

These tools have been 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.


User's Guide

NeuroMorph 3D Drawing
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.

NeuroMorph Retrieve Object from Image
Objects existing at any image point can be retrieved (made visible), allowing for easy navigation of object connectivity. Requires the 3D Drawing tool to be loaded.


User's Guide

NeuroMorph Proximity 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.

NeuroMorph Synapse Vesicle Distances
Compute the closest distance from each vesicle sphere to a synapse mesh. Provides meshes and outputs surface area data for analysis.

User's Guide

Generate 3D Image Stacks
Macro for Fiji, creates image stacks in the X and Y dimensions, given an image stack in Z. Open the original image stack in Fiji (File - Import - Image Sequence), open the .ijm macro file in Fiji, click "Run", choose the location of the new image stack folders, and confirm the voxel dimensions from the original imaging procedure.

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. See the User's Guide for a description of the complete pipeline for importing IMOD meshes into Blender.