Grid generation scripts for creating VR-ready Unity mesh bundles in the .vrn format. The .vrn archive will include 1d and 3d meshes and refinements as well as inflations. To retrieve 1D morphologies in the SWC format stored in publicly available database for neuronal morphologies at NeuroMorpho refer to the neuromorpho wrapper.

Attention: Temporarily generated grids are stored here (Comparison of additional points in between branching points or not) and there (Full cell geometries with blown up meshes, HINES ordering and 1d grid hierarchies with spline (sub)-sampling) until a more convenient location in a Cloud storage has been decided by the team.

• Git

• Python

• Bash or Sh, Windows users please see the installation instructions for either WSL (https://docs.microsoft.com/en-us/windows/wsl/install-win10) or Cygwin (https://cygwin.com/install.html)

• ug4, see installation instructions in ughub to install the core software

• neuro_collection plugin for ug4, see instructions in NeuroBox3D

• vr-grids, see vr-grids

• neuromorpho (optional), see neuromorpho

Attention: Windows users need a valid installation of Bash, i.e. either by activatiing WSL on Windows or install the Cygwin environment on Windows! OSX and Linux derivates should come with a preinstalled Bash or Sh variant.

1. Check that Python is installed: Issue in a terminal (Bash or Sh): command -v python. If Python is available it will report the path to the Python binary. Likewise use command -v git to check if Git is available on your system. If you do not meet these prerequisites, install them for your operating system (OS).

2. Clone the ughub repository from the location above: https://github.com/ug4/ughub.git to install ug4:

git clone https://github.com/ug4/ughub.git

After cloning (Or manually downloading the ZIP archive of the repository via Github's website) the repository to your local hard drive, follow precisely the installation instructions detailed in the ug4 repository here in the README.md file on the repository's landing page matching your OS.

3. Install the mesh generation plugin (neuro_collection):

Follow the installation instructions here and install the additional ug4 plugin neuro_collection which is required for mesh generation by: ughub addsource neurobox https://github.com/NeuroBox3D/neurobox-packages.git ughub install neuro_collection

4. Build ug4 with the neuro_collection plugin enabled for mesh generation: cmake -Dneuro_collection=ON -DENABLE_ALL_PLUGINS && make

5. Acquire the VR mesh generation pipeline scripts:

Either clone the vr-grids repository from here or download the pipeline_vr.sh scripts from this repository's Code folder:

git clone https://github.com/stephanmg/vr-grid.git.

Navigate to the folder Code and use the script pipeline_vr.sh. The next step can be skipped if you manually download a SWC file from the NeuroMorpho.org database.

6. (Optional) use the neuromorpho REST API wrapper to download morphologies from the NeuroMorpho.org database.

Clone the repository at https://github.com/NeuroBox3D/neuromorpho

Follow installation instructions in the repository's README.md from above

7. Invoke the VR pipeline script to generate a mesh via:

pipeline_vr.sh -i <INPUT_PATTERN> -o <OUTPUT_FOLDER>

Note that -i <INPUT_PATTERN> specifies a SWC file name or a file glob of SWC files and -o <OUTPUT_FOLDER> is the output folder for generated meshes. In the output folder given by the -o parameter, also the VRN bundle for Unity will be stored with the same name as the input file except for the file extension is changed to .vrn.

1. Either retrieve manually a file from NeuroMorpho.org or use the NeuroMorpho.org REST API wrapper:

python get_swc.py --name 44-4

This will retrieve the file 44-4 from NeuroMorpho.org database which will subsequently be used in mesh generation.

Currently a VRL-Studio project is developed and found here to allow the user to interactively and visually bundle meshes.

2. Use the pipeline_vr.sh scripts to create geometries

pipeline_vr.sh -i <INPUT_PATTERN> -o <OUTPUT_FOLDER> -s1 <SEGMENT_LENGTH_1D> [-c <BUNDLE>] [-s2 <SEGMENT_LENGTH_3D>] [-c1 <CREATE_1D>] [-c3 <CREATE_3D>] [-d <DEBUG>] [-q <QUIET>] [-m1 <METHOD_1D>] [-m2 <METHOD_3D>] [-a <REMOVE_ATTACHMENTS>] [-v <FOR_VR>] [-p <PRE_SMOOTH>] [-r <REFINEMENT>] [-f <FORCE_SPLIT_EDGE>] [-b <INFLATE_MESH>]

Basic usage (Single input file and output to NewCell folder): ./pipeline_vr.sh -i 44-4.CNG_original.swc -o NewCell/

Note, that the option -a false removes the attachments for visualization in ProMesh and writes additional meshes with the suffix _wo_attachments: ./pipeline_vr.sh -i 44-4.CNG_original.swc -o NewCell/ -a false

Note that the option -c true will only bundle the meshes into a .vrn file. ./pipeline_vr.sh -i 44-4.CNG_original.swc -o NewCell/ -c true

Extended usage: ./pipeline_vr.sh -i 37-4a.original.swc -o NewCells/ -s1 "-1" -s2 -1 -c1 true -c3 true -m1 min -m2 identity -a true -p true -r true -f false -b false -v true

This will output the 1d regularization, 1d refinements, blown up meshes in HINES format with and without attachment data to the provided folder NewCells (Folder must not exist before) The regularization will be done with minimum edge length between branching points unless the user specifies an alternative edge length themself for regularization.

Usually it suffices to keep the default parameters (Which are shown above explicitly) and invoke the following to achieve the same as above.

Cells will be packaged into a .vrn file if and only if all geometries pass the automatic geometry consistency checks.

The 1D cells (SWC) respectively the cell topologies from NeuroMorpho.org need to fulfill the following conditions:

1. Cells need to be acyclic, i.e. cycles are neuroanatomically not meaningful and thus disallowed
2. Bifurcations >= 4 branches are not allowed

If any of these conditions are violated the user will be issued an error message during mesh generation.

A temporary folder to put in cells for checking if they fullfill all prerequisites on the mesh quality. If the test cells pass the algorithmic quality checks and the visual quality checks in ProMesh and Unity as well, then these will be moved to the main virtual-reality project repository StreamingAssets folder found over here Defective cells will be stored in the folder Defective Cells as a backup.

Fully working cells can be added to the CI pipeline script test (Travis/Appveyor) to ensure these still work in later revisions of the grid generation.

Currently usable cells (no blowups and no refinements) which should be free from defects (These cells are replicated in the main VR project repository here

The same as Cells above but with blowups and refinements found in Full Cells.

Cylinders with a length of 100 units, with varying degree of grid resolution, radius of cylinder is 1.

Two way branches generated from SWC files.

A collection of previously used cells, which suffer from grid artifacts and other defects. 1d grid hierarchies contained (Regularly refined 1d grids) and the corresponding 2d surface meshes. Test folder includes grids used to debug mesh artifacts (Thin dendrites, Twists and False Face Orientation)

• pipeline_vr.sh: The main grid generation pipeline. Generates a hierarchy of 1D and 2D surface meshes and inflated 2D surface meshes. HINES ordering of the graph is ensured. Refinements are generated by sub-sampling the splines defined on the points of the original 1D SWC geometry in prescribed arclength by the user or as the minimum distance between branching points leading to regularized or quasi uniform edge length distribution.
• coarsen.sh: Grid coarsening based on the 1D SWC mesh without using splines
• sparse.py: Matplotlib script to visualize sparsity pattern of 1D graphs
• edges.py: Creates plots of edge length statistics (boxplots and histograms) of the original and regularized 1D meshes.
• remove_attachments.sh: Removes attachments if they might not be readable by ProMesh