This project takes a .swc
file downloaded from NeuroMorpho.org
and generates:
- 1D geometry refinements in
.swc
format - 3D surface mesh geometries in .ugx format, I used the strategy described here:
Framing Parametric Curves
The code allows the user to use spline interpolation for regularizing/refining the geometry or the user can produce refinements on the original .swc
file. Below is a figure showing refinments generated using spline interpolation from Python's module scipy
, details on the specific function are found here: scipy.interpolate
.
The project uses Parallel Transport Frames
to generate the contours used in the mesh generation. Below is a figure showing some meshes with increasing refinements. Wikipedia on parallel tranpsport
.
The project uses Python in particular I provide some version information that is currently used.
I recommend using Jupyter-Notebooks and downloading Promesh4
for view the geometries.
Other than that there is nothing else to install.
Python version: 3.8.10 (default, Mar 13 2023, 10:26:41)
[GCC 9.4.0]
Version info: sys.version_info(major=3, minor=8, micro=10, releaselevel='final', serial=0)
Argparse: 1.1
networkx: 3.1
scipy: 1.10.1
numpy: 1.24.3
maplotlib: 3.7.1
JSON: 2.0.9
This code was developed on a Windows Machine using Windows Subsystem for Linux (WSL) below are the computer specs:
Host Name: DESKTOP-R1UGLGT
OS Name: Microsoft Windows 11 Home
OS Version: 10.0.22621 N/A Build 22621
OS Manufacturer: Microsoft Corporation
OS Configuration: Standalone Workstation
OS Build Type: Multiprocessor Free
System Manufacturer: Alienware
System Model: Alienware m15 R4
System Type: x64-based PC
Processor(s): 1 Processor(s) Installed.
[01]: Intel64 Family 6 Model 165 Stepping 2 GenuineIntel ~2208 Mhz
BIOS Version: Alienware 1.17.0, 3/14/2023
Windows Directory: C:\WINDOWS
System Directory: C:\WINDOWS\system32
Boot Device: \Device\HarddiskVolume1
System Locale: en-us;English (United States)
Input Locale: en-us;English (United States)
Here is WSL information
NAME STATE VERSION
* Ubuntu Running 2
Welcome to Ubuntu 20.04.2 LTS (GNU/Linux 5.4.72-microsoft-standard-WSL2 x86_64)
If you are using Windows, then look here for a training module on WSL: Module-WSL
I also use Jupyter Notebooks
when developing the code, I found it easy to work with and maneuver through the codes. In wsl
I called
jupyter-notebook --allow-root --no-browser
and then select one of the links to copy and paste into a browser (Chrome worked for me).
You can also try using VSCODE
I haven't use this, but it should work just as well
When you git clone or download this project you should have the following items:
- Folder
cells
contains someNeuroMorpho.org
cells in.swc
format - Folder
papers
contains some papers in.pdf
format that are good references for proceeding in the project - Folder
src
is the course code, it only contains two.py
files which are the main codes for the mesh and geometry generation - (OLD) File
generate_meshes.py
is the main driver code which is described in the Usage section. - File
NEW_generate_meshes.py
is the main driver code which is described in the Usage section.
This usage example was done on wsl
, it 'should' work on Linux terminal as well (pending you have all the correct version of python and modules). I will try to include directions for PowerShell and GitBash.
There is a file called NEW_generate_meshes.py
if you execute in the commandline python3 NEW_generate_mesh.py
you will receive the following output
usage: NEW_generate_meshes.py [-h] [-n NUMREFINE] [-d STARTDX] [-c NUMCONTPTS] [-p SPHERECONTOURS] [-q SPHEREPOINTS] -i INPUT
NEW_generate_meshes.py: error: the following arguments are required: -i/--input
If you execute python3 NEW_generate_meshes.py -h
you will get some more help information:
usage: NEW_generate_meshes.py [-h] [-n NUMREFINE] [-d STARTDX] [-c NUMCONTPTS] [-p SPHERECONTOURS] [-q SPHEREPOINTS] -i INPUT
This program will generate .swc refinements, .ugx 1d refinements, and .ugx surface meshes and zip all files into a .vrn file,
usage: python3 NEW_generate_meshes.py -n 6 -c 6 -d 32.0 -p 10 -q 16 -i cells/<cellname>
optional arguments:
-h, --help show this help message and exit
-n NUMREFINE, --numrefine NUMREFINE
Number of Refinements
-d STARTDX, --startdx STARTDX
Largest DeltaX
-c NUMCONTPTS, --numcontpts NUMCONTPTS
Number of Contour points
-p SPHERECONTOURS, --spherecontours SPHERECONTOURS
Number of sphere contours
-q SPHEREPOINTS, --spherepoints SPHEREPOINTS
Number of points per sphere contour
-i INPUT, --input INPUT
The input .swc file
The folder cells
contains cells which were downloaded from NeuroMorpho.org
Example usage shown below
python3 NEW_generate_meshes.py -n 10 -c 10 -d 64.0 -p 16 -q 16 -i cells/Purkinje-slice-ageP43-6.CNG.swc
This will produce an output folder called <cell_name>.mesh
and it will contain .swc
files and .ugx
files which are numbered accordingly.
It will also produce a .vrn
file to be used in NeuroVisor
The parameter c
affects the type of regular polygon used for the contours, in the figure below the far left mesh uses 32-ngons for contours and the far right uses equilateral triangles (3-gons) for contours.
- Here is a link to using parallel frame transport (PFT) with Unity:
PFT
- Here is another website that discussed parallel frames:
Mathematical Visualization SS 2013
- Another interesting link:
Tutorial 3: Framed Closed Curves
- Video on PFT:
TD Essentials: Parallel Transport
- PFT on a torus:
PFT Torus
- Here is alink on spline interpolation for C#:
C# Spline
- Here is a video I made using Yale Neuron, there is a notebook in the
notebooks
folder where I do this:
Here is a lists of tasks that need to be completed and questions that need to be answered
- Can now generate meshes for
NeuroVisor
inUnity
β , but the mapping is not right --> TO DO!β οΈ π§ Generate surface triangulations that are saveed toβ.ugx
format. DONE!Check orientation of surface triangulations i.e. check normals. DONE!βFixed the "bad element" message in Promesh4, issue was too many indexes for edges/faces. DONE!β- I have executed the code on the commandline through WSL --> can this be done using Powershell or Gitbash? this would be nice to write up directions β
ADD MAPPING TO .UGX FILE --> TODO!:collision:Have to checkβ οΈ π§TURN 1D .SWC TO .UGX (MAKE SURE INDEXING MATCHED .UGX SURFACE MAPPING) --> TODO!:collision:Have to checkβ οΈ π§IMPORTANT: RESOLVE SOMA!! -->I am using a soma sphere seepaper
β- IMPORTANT: RESOLVE BRANCH POINTS!! β(see fig below)
CLOSE THE END OF THE DENDRITES!! β (see fig below)βFix subset assignment inβ.ugx
right now when you open the.ugx
nothing appears because you have to manually select all and assign the subset DONE!Add jupyter-notebooks for more exploration of code.DONE!β
Currently theβ.ugx
geometries only distinguish between two subsets, the neurites and the soma, below is a figure fromPromesh4
. I would like to improve the writing to.ugx
to be more elegant and handle a variety of subsets (for the 1d and surface meshes). DONE!
- Now can handle subsets