NeuronBuild 1.8


#1

Hi all,

I just wanted to let you know that I have released a new version of my free python script for C4D: NeuronBuild. This script allows a C4D user (there is also a separate version for ZBrush) to import neuron morphology data from NeuroMorpho.org. It creates realistic, accurate models that you can use in your illustrations and animations, either directly or as the basis for further modelling. There are more than 100,000 entries in the NeuroMorpho repository, across numerous species and cell types.

You can learn more, and download the script at: https://github.com/NWoolridge/NeuronBuild

A video on the new features is available at: https://vimeo.com/391015129

New in this Version:
• I added options to put the model into a volume builder and volume mesher. This will simply create a single mesh that can be used for further modelling or to get better shaded results when rendering. NOTE: the resolution is set deliberately low, since the volume mesher could create many millions of polygons and potentially crash C4D if you are not careful. So, once the model is created, adjust the Voxel Size attribute of the Volume Builder object downward in increments until you are happy…
• I added the ability to create a single spline object from all the dendrites, axons, etc. (and a single rail spline as well). This can be used as a proxy for the full model, or as a path for animations of signal impulses, or in a mospline object to create growth, etc. Right now these are created outside the main hierarchy, but I may want to change this…
• I fixed an issue where astrocytes and other glia wouldn’t make a model.
• I fixed some bugs where odd combinations of the options might create weird results

Things to keep in mind:
• The detail and dimensionality of NeuroMorpho entries varies significantly, depending upon the techniques used to collect the data. Some entries result in a relatively flat, or only minimally 3-dimensional, model; this may be because the neuron itself is largely planar in structure, or because the data was collected from a single view. If you are unhappy with the morphology of a cell you downloaded, try another!

Please let me know if you have any issues, or would like things to work differently. Since it is open source, you can also contribute changes if you want!

Best,

Nick


#2

Fan-friggin tastic. Thanks Nick! Image looks amazing.

its been a while since I worked with accurate neuron data (and those neuro morpho files). Hoping to get some time soon to play. Thanks again


#3

For those lowly souls still on R19 and don’t have Fields, your magical script works perfectly with the xpOVDB mesher of X Particles.
Thanks SO much!


#4

Sweet! Thanks Nick!


#5

Thanks, Nick! Appreciate your efforts.
So cool! I want to do another neuron project and use this tool!

Nick is there, just out of curiosity, a database you know of that will have neuronal data as well as maybe neighoring data like an astrocyte or other glial cell together in a single dataset?

Arik


#6

Hi Arik,

I don’t know of a database that shows those kinds of interactions, but the work that Eyewire is doing segmenting dense blocks of neural tissue shows some amazing interactions. Once I’m at the office I’ll send some links…


#7

Someone on the c4d science animation google group had recently asked about astrocyte data. If I remember correctly there might have been a solution. I build those and microglia by hand which as a result end up slightly stylised. It would be cool to have the actual data files.


#8

Thanks Joel.
I tried to get into that Google group but couldn’t get in for some reason.
Something for glial cells could come in handy, though. I built this astrocyte by hand from ortho images. Fun but not that fun. Journal of Neuron cover.


#9

Very cool image there Arik! Thanks for sharing.


#10

Great image, Arik!

Here are some of the resources I was thinking of. These were passed on to me by Amy Robinson of Eyewire.

Neuroglancer is a project by Google to provide an interface for volumetric visualization in the browser. There are some very cool demo datasets on the github page worth exploring.

Museum with retinal cell meshes: http://museum.eyewire.org/?neurons=26065,20117,26051,17212

A number of great dense multi neuron datasets here in the gallery, and you can download the meshes…


#11

Hey thanks, guys.
Nick, very cool links! Definitely going to spend some time looking through these.
Incredible what can be done nowadays.


#12

Nick, Thanks for that link! Gorgeous
When I download the meshes I get only single neurons which seem no better than NeuronBuild.

How can I create actual multi-neuron meshes from the data sets? (besides making fake ones with cloning)


#13

https://neuroml-db.org/gallery

The Neural Open Markup Language project, NeuroML, is an international, collaborative initiative to develop a language for describing and sharing complex, multiscale neuron and neuronal network models. The project focuses on the key objects that need to be exchanged among software applications used by computational neuroscientists.

Examples of these objects include descriptions of neuronal morphology, the dynamics of ion channels and synaptic mechanisms, and the connectivity patterns of networks of model neurons. This modular approach brings additional benefits: not only can entire models be published and exchanged in this format, but each individual object or component, such as a specific calcium channel or excitatory synapse, can be shared and re-implemented in a different model.

The NeuroML Database is a relational database that provides a means for exchanging these NeuroML model descriptions and their components. One of our goals is to contribute to an efficient tool chain for model development using NeuroML. This emphasis allows the database design and subsequent searching to take advantage of this specific format. In particular, the NeuroML database allows for efficient searches over the components of models and metadata that are associated with a hierarchical NeuroML model description.

But they have Blender models. So i think you have to use Blender to convert for C4D

http://blenderneuron.org/docs/introduction.html#overview

Edited: to get simulate voltage potential propagation in Blender instead of just mesh you have to install Neuron

https://neuron.yale.edu/neuron/ maybe someone can make an exporter for C4D


#14

There are also models in Sketchfab


#15

Thanks for the pointer to NeuroML; it would be great to be able to add simulated signal propagation and other aspects of neurophysiology to C4D…


#16

IMHO NeuronBuild is fun and NeuroML is enough to give anyone a migraine! If anyone thinks NeuroML is fun I would love tp hear about it and be converted.


#17

Seeing your Vimeo tutorial my eye caught a plugin called autoPACK…
I’ve downloaded it but I really don’t understand anything … The site was claiming the plugin can pack anything not just proteins … Am I missing something ? Could you upload a simple scene <=R20 of objects packed together using this plugin so I can understand how it works ?

I was looking for a tool that clutters/stacks objects together. Can autoPACK do the job ?


#18

Any chance for a Blender version of NeuronBuild?


#19

https://neuromorph.epfl.ch

cheers

celke


#20

Thanks for yet another great link!