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This framework allows the segmentation, classification and tracking of immune cells such as PMNs or macrophages and fungal cells in migration and confrontation assays.

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Dependencies

AMIT depends on following libraries:

Library	Version	Author	URL
JSON for modern C++	2.1.1- or higher	Niels Lohmann	https://github.com/nlohmann/json/
Boost	1.65 or higher	Boost Community	https://www.boost.org/
OpenMP	5.0.1	OpenMP ARB	https://www.openmp.org/
OpenCV	3.2 or higher	OpenCV	https://opencv.org/releases/
LEMON Graph library	0.7 or higher	Egerváry Research Group on Combinatorial Optimization	https://lemon.cs.elte.hu/trac/lemon

You need a compiler capable of C++ version 2017 or higher to compile AMIT.

Installation

Install it by building it yourself

If all dependencies are installed on the system, just run:

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make

Building missing dependencies

OpenCV

For servers:

wget https://github.com/opencv/opencv/archive/3.2.0.zip -O opencv-3.2.0.zip
unzip opencv-3.2.0.zip
cd opencv-3.2.0
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX=$HOME/opencv-3.2.0 -DCMAKE_BUILD_TYPE=Release -DWITH_IPP=OFF -DBUILD_TIFF=ON -DWITH_GTK=OFF ..
make
make install

-DWITH_IPP=OFF and -DBUILD_TIFF=ON can be left out, but are usually required for our servers. -DWITH_GTK=OFF is necessary.

LEMON

wget http://lemon.cs.elte.hu/pub/sources/lemon-1.3.1.tar.gz
tar -xvf lemon-1.3.1.tar.gz
cd lemon-1.3.1
mkdir build
cd build
cmake -DCMAKE_INSTALL_PREFIX="$HOME/lemon-1.3.1" -DCMAKE_BUILD_TYPE=Release ..
make
make install

nlohmann_json

sudo apt-get update
sudo apt-get install nlohmann-json-dev

Building with custom dependencies

Add the install directories to the CMake prefix path:

mkdir build
cd build
cmake -DCMAKE_BUILD_TYPE=Release -DCMAKE_PREFIX_PATH="$HOME/opencv-3.2.13.6;$HOME/lemon-1.3.1" ..
make

Usage

Take a closer look at the corresponding README - files in the respective subfolders for each application (AMITSegmentation, AMITStateClassification, AMITTracking).

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Citation

Please cite AMIT if you are using this work in your publication. Here is an example BibTeX entry:

@article{Belyaev2021,
  doi = {10.1002/cyto.a.24466},
  url = {https://doi.org/10.1002/cyto.a.24466},
  year = {2021},
  month = jun,
  publisher = {Wiley},
  author = {Ivan Belyaev and Jan-Philipp Praetorius and Anna Medyukhina and Marc Thilo Figge},
  title = {Enhanced segmentation of label-free cells for automated migration and interaction tracking},
  journal = {Cytometry Part A}
}