3 Dimensional models instead of 1D

[RABuijse]

Hello,

A couple of weeks ago i asked if it was possible to export files from Neugen to .ugx, which using the .txt export function worked out well. Now i wanted to know if there is any way in NeuGen to create 3 Dimensional Neurons like this one:

instead of the One Dimensional networks one gets from exporting the files:

Is there an option to do this or does this afford too much computing etc.?

Thanks in advance!

[stephanmg]

NeuGen does not generate/export 3D networks.

[bsumirak]

As @stephanmg has already pointed out, this is not part of NeuGen's functionality.
There are at least two reasons for this:

• Creating 3D neuron geometries from 1D is not an easy task (especially if you want them to be adequate for HPC).
• There is no functionality on the UG4 side to properly process the network's synaptic connectivity.

However, there have been efforts to automate the creation of individual 3D cells from 1D. One of them is AnaMorph (produced meshes are nice-looking, but very fine and probably require an AMG solver for simulation purposes). The UG4 neuro_collection plugin also offers some experimental functionality for 1D->3D conversion (e.g., in grid_generation/neurites_from_swc.*), which is intended to produce coarse grids for GMG solvers by leveraging the inherent anisotropic structure of neurons.
There also is a utility function save_neuron_to_swc in the UG4 cable_neuron plugin that can be used to extract specific neurons from a NeuGen-generated network.
Do note though that NeuGen pays no attention to the 3d spatial structure of the neurons it creates. They typically contain a number of self-intersections, especially in the vicinity of branching points. Problematic areas can be manually corrected in the 1D geometry. For the generation of more than one 3D geometry, I recommend automating this process.

[stephanmg]

I second @bsumirak comments. If you want to mesh cells from NeuroMorpho.org I might have an automatisation tool you might find usefull.

[RABuijse]

I will definitely check out AnaMorph. Downbloading Neurons from NeuroMorpho.org was one of my options anyway, so i'm very interested in the automatisation tool!

[stephanmg]

@RABuijse then check this out: https://github.com/NeuroBox3D/AnaMorph and https://github.com/NeuroBox3D/neuromorpho