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Other Tools
Other helpful addons for use with NeuroMorph
UI location View3D » Other Tools
Version 1.0.0 Author(s) Anne Jorstad, Biagio Nigro, Diego Marcos, Tom Boissonnet
Blender 2.78 License GPL


Executable information
File name NeuroMorph_Parent_Child_Tools.py
Current version download https://github.com/ajorstad/NeuroMorph/tree/master/NeuroMorph_Other_Tools




NeuroMorph Links

Blender Wiki Home
Code on GitHub
For more information please visit the NeuroMorph project website.


Overview

Generate 3D Image Stacks

Macro for Fiji to creates image stacks in the X and Y dimensions, given an original image stack.


NeuroMorph Parent-Child Tools

An easy interface to show/hide/delete all children of an object and assign the parent of selected objects.


NeuroMorph Import Objects

Import object models from .obj files obtained through 3D image segmentation software into Blender.


NeuroMorph Naming

An interface for naming objects according to a naming convention developed for neural structures.


Generate 3D Image Stacks: Description

Macro for Fiji that creates image stacks in the X and Y dimensions, given an original image stack (which we define to be stacked in the Z dimension).

To use:

  • Open the original image stack in Fiji (File - Import - Image Sequence)
  • Open the Generate_3D_image_stacks.ijm macro file in Fiji
  • Click "Run"
  • Choose the desired location of the new image stack folders
  • Confirm the voxel dimensions from the original imaging procedure


(Macro courtesy of Tom Boissonnet.)


Parent-Child Tools: Description

Parentchildtools.png

An easy interface to show/hide/delete all children of an object and assign the parent of selected objects.

Show Children: Make visible all children of active object.

Hide Children: Make invisible all children of active object.

Select Children: Select all children of active object.

Delete Children: Delete all children of active object. Note: parent object must be visible.

Assign Parent Object: Assigns all selected objects to be children of the object chosen from the drop-down menu.


Import Objects: Description

Import object models from .obj files obtained through 3D image segmentation software (e.g. ilastik or TrakEM2) into Blender. Allows the objects to be remeshed and rescaled according to user needs.

See full instructions here.


NeuroMorph Naming: Description

Naming.png

Previously part of the deprecated NeuroMorph Measurement Tools, provides an optional interface for naming objects according to a naming convention developed for neural structures that depends on the object type and numerical index. The object type options are:

  • "other": gives the user the option to assign a custom name to the mesh by entering it in the box provided.
  • "Axon": has a numerical index and a type (excitatory, inhibitory, unknown, N/A).
  • "Dendrite": has a numerical index.
  • "Spine": has a numerical index.
  • "Bouton": has a numerical index.
  • "Synapse": depends on the identity of the dendrite and the axon it connects, and also the identity of the dendritic spine and axonal bouton. For example, the name of an inhibitory synapse connecting spine 4 of dendrite 14 and bouton 2 of axon 23 will be syn_d14s4a23b2_I.
  • Update Object Name: Changes name of currently selected object to abide by the naming convention.