Extraction and tracking of dynamic biopolymer networks.
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README.md

TSOAX

TSOAX is an open source software to extract and track the growth and deformation of biopolymer networks from 2D and 3D time-lapse sequences. It tracks each filament or network branch from complex network dynamics and works well even if filaments disappear or reappear.

TSOAX is an extension of SOAX (for network extraction in static images) to network extraction and tracking in time lapse movies.

If you find this repository helpful, please cite:

@article{XuTSOAX2018,
    author  = {T. Xu, C. Langouras, M. Adeli Koudehi, B. Vos, N. Wang,
        G. H. Koenderink, D. Vavylonis, and X. Huang},
    title   = {Automated Tracking of Biopolymer Growth and Network Deformation with TSOAX},
    journal = {biorxiv},
    year    = {2018},
}

Installation

Binaries

You can download and install binaries from TSOAX website.

From source

Linux and macOS (>=10.8)

  1. Install Eigen 3 and Qt 5 using your package manager (Homebrew or dnf, apt):

    $ brew install eigen qt  # for macOS
    $ sudo dnf install eigen3-devel qt5-devel libXt-devel  # for Fedora

    (macOS only) Add environment variables in your .bash_profile:

    export Qt5_DIR=/usr/local/opt/qt
    export PATH=/usr/local/opt/qt/bin:$PATH

    and apply them:

    $ . ~/.bash_profile
  2. Install VTK. Download VTK 8.1.0 and do an out-of-source build

    $ mkdir your-vtk-build-dir
    $ cd your-vtk-build-dir
    $ cmake -DCMAKE_BUILD_TYPE=Release -DVTK_Group_Qt=ON /path/to/VTK-8.1.0/
    $ make -j 4

    Add environment variable VTK_DIR in your .bash_profile:

    export VTK_DIR=/path/to/your-vtk-build-dir
  3. Build TSOAX.

    $ git clone --recursive https://github.com/tix209/TSOAX.git
    $ cmake -DCMAKE_BUILD_TYPE=Release /path/to/tsoax/src/
    $ make -j 4

    In macOS, you can launch the program by searching for "TSOAX" in the spotlight (+Space).

Windows

  1. Download and install Microsoft Visual Studio 2015 or newer, CMake, and Qt 5.
  2. Configure VTK 8.1.0 with CMake (cmake-gui).
    • Enter the folder path of where you extracted VTK source code
    • Enter another folder path for vtk_binary_dir
    • Click Configure
    • Specify generator e.g., Visual Studio 14 2015 Win64
    • After the configuration is done, check VTK_Group_Qt and VTK_USE_CXX11_FEATURES
    • Click Configure, and change VTK_QT_VERSION to 5 and QT_QMAKE_EXECUTABLE to C:/Qt/5.10/msvc2015_64/bin
    • Click Configure. Change Qt5_DIR to C:/Qt/5.8/msvc2015_64/lib/cmake/Qt5
    • Click Configure
    • Click Generate and then Open Project
    • In Visual Studio, change Debug to Release mode and build solution.
  3. Download Eigen 3. Extract the zip file and rename it to eigen3.
  4. Open Git Bash then $ git clone --recursive https://github.com/tix209/TSOAX.git.
  5. Configure TSOAX in CMake
    • Enter folder path of TSOAX source code
    • Enter folder path for tsoax_binary_dir
    • Click Configure
    • Specify generator e.g., Visual Studio 14 2015 Win64
    • Set Qt5_DIR to C:/Qt/5.8/msvc2015_64/lib/cmake/Qt5Widgets
    • Click Configure. Set VTK_DIR to vtk_binary_dir
    • Click Configure
    • Click Generate and then Open Project
    • In Visual Studio, change Debug to Release mode. Click TSOAX project and press ALT+ENTER. In VC++ Directories, add the path containing eigen3 in Include Directories
    • Build the release version of TSOAX
    • Copy Qt5Core.dll, Qt5Gui.dll, Qt5Widgets.dll from C:/Qt/5.8/msvc2015_64/bin/ to tsoax_binary_dir/src/Release.