Building on Linux
This building guide was tested for Ubuntu 18.04 and 19.10. To build *.deb packages, you can alternatively use our Docker-based Linux build scripts. We also provide generic Linux build scripts that should work for any Linux distribution, given that the dependencies are installed.
Due to the differences between different Linux distributions, we cannot guarantee that the generic build script runs without error.
Building the C++ framework
MISA++ Core
The core library requires at least GCC version 8 and the Boost libraries.
sudo apt install libboost-filesystem-dev libboost-regex-dev libboost-program-options-dev build-essential gcc-8 git
git clone https://github.com/applied-systems-biology/misaxx-core.git
pushd misaxx-core
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
MISA++ Analyzer
The analyzer application requires an installation of the core libraries.
sudo apt install libsqlite3-dev
git clone https://github.com/applied-systems-biology/misaxx-analyzer.git
pushd misaxx-analyzer
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
MISA++ Imaging (OpenCV integration)
The OpenCV integration requires OpenCV 3.x or 4.x.
We have experienced that multiple installations of OpenCV can lead to the build system making use of the wrong library files - even with CMake claiming to have found the correct version.
sudo apt install libopencv-dev libtiff5-dev
git clone https://github.com/applied-systems-biology/misaxx-imaging.git
pushd misaxx-imaging
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
MISA++ OME (OME TIFF integration)
The OME TIFF integration requires an installation of misaxx-imaging and the
OME Files library.
We have experienced issues with Boost 1.70 or higher in building the OME libraries. This is caused by a change in how Boost handles CMake targets.
During the build process of OME Model, a Python2 script is used to generate C++ code. Due to lack of Python version specification, the script will crash if Python3 is the default Python. In this case, create a Python2 virtualenv and restart the build process.
sudo apt install libxerces-c-dev libxalan-c-dev python wget libboost-all-dev
git clone https://github.com/applied-systems-biology/misaxx-ome.git
wget "https://downloads.openmicroscopy.org/ome-common-cpp/5.5.0/source/ome-common-cpp-5.5.0.zip"
unzip ome-common-cpp-5.5.0.zip
wget "https://downloads.openmicroscopy.org/ome-model/5.6.0/source/ome-model-5.6.0.zip"
unzip ome-model-5.6.0.zip
wget "https://downloads.openmicroscopy.org/ome-files-cpp/0.5.0/source/ome-files-cpp-0.5.0.zip"
unzip ome-files-cpp-0.5.0.zip
pushd ome-common-cpp-5.5.0
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
pushd ome-model-5.6.0
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
pushd ome-files-cpp-0.5.0
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
pushd misaxx-ome
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
MISA++ OME Visualizer (Example application)
This application allows visualization of int32 OME TIFF files and requires
that misaxx-ome is installed.
git clone https://github.com/applied-systems-biology/misaxx-ome-visualizer.git
pushd misaxx-ome-visualizer
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
MISA++ Tissue segmentation (Example application)
This application segments tissue from whole-organ light-sheet microscopy images and requires
that misaxx-ome is installed.
git clone https://github.com/applied-systems-biology/misaxx-tissue.git
pushd misaxx-tissue
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd
MISA++ Kidney glomeruli segmentation (Example application)
This application segments the glomeruli in whole organ light-sheet microscopy images and requires
that misaxx-tissue is installed.
git clone https://github.com/applied-systems-biology/misaxx-kidney-glomeruli.git
pushd misaxx-kidney-glomeruli
mkdir build
pushd build
cmake -DCMAKE_BUILD_TYPE=Release ..
make
sudo make install
popd
popd