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https://github.com/05dirnbe/nefi
Network Extraction From Images
https://github.com/05dirnbe/nefi
Last synced: 2 months ago
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Network Extraction From Images
- Host: GitHub
- URL: https://github.com/05dirnbe/nefi
- Owner: 05dirnbe
- License: bsd-2-clause
- Created: 2016-03-31T08:20:18.000Z (almost 9 years ago)
- Default Branch: master
- Last Pushed: 2021-05-13T16:17:30.000Z (over 3 years ago)
- Last Synced: 2024-08-04T00:13:12.345Z (6 months ago)
- Language: Python
- Size: 1.09 GB
- Stars: 33
- Watchers: 7
- Forks: 14
- Open Issues: 26
-
Metadata Files:
- Readme: README.md
- License: LICENSE
Awesome Lists containing this project
- awesome-biological-image-analysis - NEFI2 - Python tool created to extract networks from images. (Other)
README
**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)