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.
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.
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. 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
) into Blender.
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.