https://github.com/arosh/vaa3d-sigen
SImulation system for Geometrical and Electrical properties of Neuron
https://github.com/arosh/vaa3d-sigen
Last synced: 8 months ago
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SImulation system for Geometrical and Electrical properties of Neuron
- Host: GitHub
- URL: https://github.com/arosh/vaa3d-sigen
- Owner: arosh
- Created: 2016-01-11T06:06:15.000Z (over 10 years ago)
- Default Branch: master
- Last Pushed: 2016-03-29T14:27:22.000Z (about 10 years ago)
- Last Synced: 2025-10-28T22:48:44.961Z (8 months ago)
- Language: C++
- Homepage: https://github.com/Vaa3D/vaa3d_tools/tree/master/released_plugins/v3d_plugins/bigneuron_hide_ikeno_SIGEN
- Size: 11.4 MB
- Stars: 1
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
Awesome Lists containing this project
README
# Vaa3D-SIGEN
## Requirements for Vaa3D Plugin
* [CMake](https://cmake.org/) >= 2.8
* [Boost](http://www.boost.org/)
* [Vaa3D/v3d_external](https://github.com/Vaa3D/v3d_external)
## Requirements for Runner
* [CMake](https://cmake.org/) >= 2.8
* [google-glog](https://github.com/google/glog)
* [OpenCV](http://opencv.org/)
* [Boost](http://www.boost.org/)
## How to Build Plugin
```
$ cd vaa3d
$ nano SIGEN.pro # edit `VAA3DPATH` variable
$ qmake
$ make
```
`libSIGEN.*` will be located in `SIGEN_ROOT/vaa3d/build`. Please put `libSIGEN.*` in `vaa3d/plugins/neuron_tracing/SIGEN` directory.
## How to Build Standalone Runner
```
$ mkdir build
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=Release -DBUILD_MAIN=ON ..
$ make
```
If you run `cmake .` in project top directory, `CMakeFiles`, `CMakeCache.txt`, `cmake_install.cmake`, `Makefile` will be located in undesirable directories.
## How to Test
```
$ mkdir build
$ cd build
$ cmake -DCMAKE_BUILD_TYPE=Debug -DBUILD_MAIN=ON ..
$ make
$ make test
```
If you run `cmake .` in project top directory, `CMakeFiles`, `CMakeCache.txt`, `cmake_install.cmake`, `Makefile` will be located in undesirable directories.
## Setting
* Interpolation (VT, DT)
* Clipping (level)
* Smoothing (level)
## License
This software is released under the MIT License.
Copyright (c) 2016 Sho Iizuka
## References
* Yamasaki, T., Isokawa, T., Matsui, N., Ikeno, H. and Kanzaki, R.: Reconstruction and simulation for three-dimensional morphological structure of insect neurons, Neurocomputing, Vol.69, pp.1043-1047 (2006). \[[link](http://dx.doi.org/10.1016/j.neucom.2005.12.042)\]