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README.md

NeuronBuild

NeuronBuild_Pyramid-IIIC-2-5M-10_CU

Scripts to import neuron morphology data (from neuromorpho.org) into Cinema 4D and ZBrush.

NeuronBuild C4D

https://github.com/NWoolridge/NeuronBuild

Watch a video on using this script: https://vimeo.com/207323665

Watch a video on the new features: https://vimeo.com/391015129

The current working version is 1.8. (Note: Version 1.6 was experimental, and not fully functional.)

NeuronBuild C4D | Nick Woolridge | 2013-2020 | n.woolridge@utoronto.ca Version date: February 2020

A script to import swc files downloaded from neuromorpho.org, and create accurate spline-based and/or polygonal models of neuronal structure. To download structure files, and to find out more about neuromorpho and its file format, please go to:

www.neuromorpho.org

Ascoli GA, Donohue DE, Halavi M. (2007) NeuroMorpho.Org: a central resource for neuronal morphologies.J Neurosci., 27(35):9247-51

Many thanks to the thousands of researchers and students who have populated the neuromorpho repository.

Notes on using NeuronBuild

The reconstruction units are μm (micrometers). In C4D these correspond to the world units defined in your project settings.

Note: soma (cell body) definitions vary from file to file; this script assumes a three point spline (which is very common). The soma object is disabled by default, since they rarely produce acceptable geometry; the soma can be re-enabled by digging into the hierarchy. Note: use of neuromorpho files comes with an obligation to cite neuromorpho.org and the original publication; see here.

How to use:

  • add to your C4D Scripts folder (find the user prefs folder via C4D's Preferences dialog; the Scripts folder is within the Library folder)
  • Browse and download a .swc or .swc.txt file from http://neuromorpho.org/
  • Open the Script Manager in C4D, the script should be in the pop-up menu at the top of the window.
  • In the Script Manager in C4D load the NeuronBuild script and click "Execute".
  • An import options dialog should appear; choose options for imported geometry, and click "Import File".
  • In the open file dialog, choose the swc file and click "OK".
  • A neuron should appear in your viewport.
  • If all the geometry options are chosen, the geometry consists of a HyperNURBs object, which contains a Connect object, which contains a null object, which contains the sweep objects that define the axons and dendrites. Since the Soma (cell body) definition in the swc files is so rudimentary, you may want to delete or hide it, and let the soma be defined by the merging dendrite roots.

Within the sweep objects are n-sided splines (named "Profile") set to 6-sides; you could search for these objects and change the number of sides to 4 to simplify the geometry. Also in the SweepNURBs objects are the splines that define the dendrite paths, and rail splines that define their radius.

The new volume builder and volume mesher objects allow for the creation of a single, optimized mesh. The resolution of the mesh is set by the Voxel Size setting in the volume builder object. If the default resolution is too low (which it almost ceratinly will be), gradually lower the Voxel Size until you have an acceptable result. BE CAREFUL: jumping immediately to a very low voxel size may generate an enormous number of polygons, which could potentially exhaust your system resources.

Version History

  • 1.8: Added options (disabled by default) to insert the model hierarchy in a Volume builder and Volume mesher object, yeilding a single mesh. Adjust the Voxel dimension in the volume builder to adjust resolution. Be careful not to make the resolution too low, since this can potentially generate large poly counts. Added support for other SWC entities. Removed R12, R13 compatibility.
  • 1.7: Added support for glial processes (ID 7 in neuromorpho's version of the SWC file format). This means that astrocytes are now supported (unreleased)
  • 1.6: Incomplete conversion to Upy framework; do not use.
  • 1.5: Stable version for C4D R13-R21
  • 1.4: Modifications made by Graham Johnson on March 11, 2013 – support for Cinema 4D r12 and r13 (Oconnect and AddMultiLineEditText compatibility – convert right handed .swc data to Cinema 4D left-handed with coordSystem test – added safety test if user hits cancel button while in the system browser. Reports as 'Cancelled in Browser.'

This software is open-source under the MIT License.

NeuronBuild ZBrush

https://github.com/NWoolridge/NeuronBuild

The current version is 1.2.

NeuronBuild ZBrush | 2017 Nicholas Woolridge & Marcus Burgess | n.woolridge@utoronto.ca

Many thanks to Marcus Burgess, moderator at the ZBrush ZScipting Help Forum, who was extremely helpful in understanding how to do just about everything this script does!

Watch a video on using this script: https://vimeo.com/207323832

Version date: March 2017

How to use:

  • Obtaining neuron morphology files: go to http://neuromorpho.org and find and download a neuron file you are interested in. These will usually have the ".swc" or ".txt" file extension; either is fine.
  • In ZBrush, use Menus > ZScript > Load; navigate your file system to find the script file, select it, and click on "Open"
  • A button called "Import_Neuromorpho_SWC_File" will appear in the tutorial palette; the tutorial palette is just below the viewport. Drag the divider up to see the button.
  • Click on the "Import_Neuromorpho_SWC_File" button, and choose the neuron morphology file you downloaded earlier.
  • Depending upon the complexity and size of the file, parsing the file can take some time; a note will appear indicating the number of lines in the file, then the zsphere construction will occur. It may appear that ZBrush has frozen, but be patient.
  • PLEASE NOTE: to generate a mesh from a zsphere model, one would normally use the adaptive skin function. We have found that users should choose the "Use Classic Skinning" option in the Adaptive skin settings, otherwise ZBrush may crash.
  • ALSO NOTE: the scale of the models produced in Neuronbuild ZBrush is currently set to 1/50 the size of the models produced by the NeuronBuild C4D script. This is due to scale limitations within ZBrush. To have the models from each script match in terms of relative dimensions, scale a model produced by Neuronbuild ZBrush by 50x in C4D or other apps.

If you use this script, please consider posting the results of your work in the ZBrush forums at: http://www.zbrushcentral.com/zbcinfinite.php

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A script to import neuron morphology data into 3D apps

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