Awesome

NEFI2 is a Python tool created to extract networks from images.

Given a suitable 2D image of a network as input, NEFI2 outputs a mathematical representation of the structure of the depicted network as a weighted undirected planar graph. Representing the structure of the network as a graph enables subsequent studies of its properties using tools and concepts from graph theory.

NEFI2 builds on top of well-documented open source libraries in order to provide a reliable, transparent and extendable collection of interchangeable solutions. NEFI2 facilitates single image analysis as well as batch processing and aims to enable scientists and practitioners of various domains to freely explore, analyze and process their data in an intuitive, hands-on fashion.

Our major motivation in developing NEFI2 is to enable virtually everyone to automatically extract networks from images. NEFI2 was designed to be an extensible image processing pipeline which can be augmented with custom algorithms and algorithm configurations. For example, you can add your own faster implementation of "Adaptive Threshold" or "Guided Watershed", you can easily set default settings and even construct a complete pipeline of your custom algorithms that solve a particular image processing task. You don't need to write tons of boilerplate code, reimplement existing UI widgets and then connect them.

Installation

Linux

Make sure you have your Python 3.8 installed before performing the steps below.
Install PyQt5 using your default package manager.
Install opencv-python via pip:

pip install opencv-python

Depending on your distrbution, you may need to replace the pip command by pip3.

Next, clone the github repository and run the installation script.

git clone https://github.com/05dirnbe/nefi.git
cd nefi
./linux_install.sh

If everything goes well, you can run NEFI2 by typing nefi2 in the console.

Compiling OpenCV (deprecated)

If you decide not to install OpenCV via pip, you can try to compile OpenCV 3.1.0 for your Python 3. Note that these instructions are most likely outdated and will no longer work.

    git clone https://github.com/Itseez/opencv.git
    git checkout 3.1.0a
    mkdir release
    cd release
    cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=$(python3 -c "import sys; print(sys.prefix)") -D PYTHON_EXECUTABLE=$(which python3) ..
    make -j4
    sudo make install

Note: If your Linux installation uses python instead of python3 to call your python 3 interepreter, you have to replace python3 with just python for the OpenCV installation. It should look like this:

    git clone https://github.com/Itseez/opencv.git
    git checkout 3.1.0a
    mkdir release
    cd release
    cmake -D CMAKE_BUILD_TYPE=RELEASE -D CMAKE_INSTALL_PREFIX=$(python -c "import sys; print(sys.prefix)") -D PYTHON_EXECUTABLE=$(which python) ..
    make -j4
    sudo make install

Windows (64 Bit)

You can use our precompiled launcher to start NEFI. https://github.com/05dirnbe/nefi/archive/windows_64bit_build.zip

(Based on commit 1d774aad7478f69deeac5c4fdb5a4716a3894417)

OSX (64 Bit)

You can use our precompiled launcher to start NEFI. https://github.com/05dirnbe/nefi/archive/mac_64bit_build.zip

(Based on commit 1d774aad7478f69deeac5c4fdb5a4716a3894417)