Installation

ilastik binaries are provided for Windows, Linux, and Mac at our download page.

Note: ilastik requires a 64-bit machine. We do not provide 32-bit binaries.

Most workflows are available with the basic ilastik installation.

Some workflows, however, require the manual installation of a commercial solver. On Windows, the following workflows will only be available after installing the IBM CPLEX solver:

  • Boundary Segmentation with Multicut
  • Tracking (all flavours)
  • Counting (better results with CPLEX)

In order to enable these workflows, please follow the instructions in the section about commercial solver installation.

On Mac and Linux only Learning the weights in the Tracking with Learning Workflow requires a commercial solver (CPLEX or Gurobi). Furthermore, the results of the Boundary Segmentation with Multicut Workflow and the Tracking Workflow tend to be more accurate using one of the two commercial solvers.

Basic Installation

Installation on Windows

Download the Windows self-extracting installer and run it. The installer will guide you through the installation process. You can find an entry for ilastik in the start menu and click it to launch the program.

Installation on Mac

Download the .tar.bz2 file for your version of OSX and extract its contents with a simple double-click. Copy ilastik.app to the folder of your choice (usually your Applications folder), and double-click to begin.

Installation on Linux

Download the Linux .tar.bz2 bundle and extract its contents from the terminal:

tar xjf ilastik-1.*-Linux.tar.bz2

To run ilastik, use the included run_ilastik.sh script:

cd ilastik-1.*-Linux
./run_ilastik.sh


Commercial Solver Installation

For some workflows in ilastik, installation of a commercial solver is required. IBM CPLEX is supported by ilastik on all platforms. Alternatively, GUROBI can be used on Linux and Mac.

CPLEX Installation and Setup

Application for Academic License at IBM

IBM CPLEX is a commercial solver which is free for academic use. Details on the application for an academic license, may be found on the IBM Academic Initiative website. Please note that it might take some days until the application gets approved by IBM.

Download IBM CPLEX

Once the license has been approved by IBM, instructions for download will be provided.

The current version of ilastik works with IBM ILOG CPLEX Optimization Studio V12.6. After choosing the appropriate platform, you have to agree with the IBM license. Finally, CPLEX may be downloaded and is ready to install.

Important note: It is not sufficient to download the Trial version of CPLEX since its solver can only handle very small problem sizes. Please make sure, the correct version is downloaded as described here.

The following sections contain platform-specific instructions for CPLEX installation on Windows as well as on Linux and Mac.

Setup on Windows

Run the installer by double clicking the executable that you’ve downloaded.

On Windows, there are typically no further modifications needed after installing CPLEX. After successful installation the Automatic Tracking Workflow is displayed on the Start-Screen of ilastik.

If this workflow is not present, something went wrong with the CPLEX installation. To track down the problem, proceed like this:

  • Make sure that the environment variable CPLEX_STUDIO_DIR1263 is set and points to the proper location. You can check this by typing echo %CPLEX_STUDIO_DIR1263% at the DOS command prompt. The output should be something like C:\Program Files\IBM\ILOG\CPLEX_Studio1263.
  • Make sure that cplex is in the PATH. Type where cplex at a DOS prompt. It should produce something like C:\Program Files\ibm\ILOG\CPLEX_Studio1263\cplex\bin\x64_win64\cplex.exe (the path prefix should match the contents of the CPLEX_STUDIO_DIR1263 variable).
  • Make sure that the directory containing cplex.exe also contains cplex1263.dll, ILOG.CPLEX.dll, and ILOG.Concert.dll.

The Automatic Tracking Workflow should now be displayed on the start screen. If it doesn’t, you may copy the files cplex1263.dll, ILOG.CPLEX.dll, and ILOG.Concert.dll (if you can locate them somewhere) to the binary folder of the ilastik installation, usually located at C:\Program Files\ilastik\bin. If it still doesn’t work, please contact us.

Setup on Linux and Mac

On Linux and Mac, the CPLEX installer comes as a commandline executable (cplex-someversion.sh on Linux and cplex-someversion.bin on Mac). To install it, open a terminal and run bash /path/to/your/cplex-someversion.sh (or bash /path/to/your/cplex-someversion.bin on Mac).

Hint: on Mac and most Linux distributions you can drag and drop the installer file into the terminal to get the full path appended to your command line.

CPLEX packages for Linux and Mac do not provide shared versions of all required libraries, but only static variants. In order to enable CPLEX with ilastik, the static libraries have to be converted. Before you can convert your static CPLEX libraries into shared library versions, you need to have a compiler installed on your machine. You can check whether you already have a compiler installed by running the following command in a terminal (open the Terminal app!).

gcc --version

If no compiler is installed, choose what to do depending on your OS version:

  • For Linux, use your OS package manager (e.g. apt-get) to install the gcc package.
  • For all OSX < 10.9, so up to Mountain Lion, you need to install XCode from the AppStore. Then you need to go to XCode’s Preferences, to the Downloads tab, and install the command line tools.
  • For OSX 10.9 Mavericks it suffices to install the command line tools using the following command without installing XCode.

    xcode-select --install
    

    Then you need to accept the XCode licence by running “sudo gcc” once.

Now you can run a script, that will convert your CPLEX static libraries into shared libraries, and install them into the appropriate directory of your ilastik directory. Starting with ilastik-1.1.7, this script can be found in ilastik-1.*/ilastik-meta/ilastik/scripts. Prior to that version the script needs to be downloaded manually in the terminal:

wget https://raw.githubusercontent.com/ilastik/ilastik/master/scripts/install-cplex-shared-libs.sh

Navigate to the directory containing the script and execute it:

# navigate to the script location, e.g. /path/to/ilastik-1.*-Linux/ilastik-meta/ilastik/scripts
cd /path/to/script
# Linux:
bash install-cplex-shared-libs.sh /path/to/your/cplex-root-dir /path/to/ilastik-1.*-Linux
# Mac:
bash install-cplex-shared-libs.sh /path/to/your/cplex-root-dir /path/to/ilastik-1.*-OSX.app

In the command above, /path/to/your/cplex-root-dir is the location of your cplex studio installation. It should contain directories named concert and cplex, among others.

Note: The above script installs CPLEX directly into your ilastik installation. Once you’ve done that, you should not distribute your copy of ilastik to others, unless you have a license to distribute CPLEX.

After a successful installation, the Tracking with Learning Workflow will appear on the Start-Screen of ilastik.


GUROBI Installation and Setup

On Linux and Mac, a second commercial solver, GUROBI, is supported. As with CPLEX, a free academic license can be obtained for GUROBI.

Application for Academic License at GUROBI

Application for an academic license is available after registration with your institution email address at the GUROBI website. Details can be found here. The easiest way is to obtain a free named-user academic license. Instructions are provided on this page. At the end of the process, you will be provided with your license key. You will need the license key to activate your GUROBI installation.

Installation

Download the appropriate package from the GUROBI download page. Unpack the downloaded archive:

tar -xvf gurobi7.0.2_linux64.tar.gz -C /your/target/directory

And activate your installation by invoking grbgetkey with your license:

cd /your/target/directory/gurobi702/linux64/bin
# use the obtained license key here
./grbgetkey your-license-key-here
# Follow the instructions and take note of the license path.

In the next step you have to execute a script that will link your GUROBI libraries to your ilastik installation. The script can be found in your-ilastik-installation-folder/ilastik-meta/ilastik/scripts. With versions prior to ilastik-1.1.7, this script is not included and has to be downloaded manually:

wget https://raw.githubusercontent.com/ilastik/ilastik/master/scripts/install-gurobi-symlinks.sh

Navigate to the script directory and run it:

# the following line is only necessary if you have used a custom location for the
# license file when invoking `grbgetkey`
export GRB_LICENSE_FILE=/path/to/license/gurobi.lic

# navigate to the script location, e.g. /path/to/ilastik-1.*-Linux/ilastik-meta/ilastik/scripts
cd /path/to/script
# Linux:
bash install-gurobi-symlinks.sh /your/target/directoy/gurobi702/linux64 /path/to/ilastik-1.*-Linux
# Mac:
bash install-gurobi-symlinks.sh /your/target/directoy/gurobi702/linux64/ /path/to/ilastik-1.*-OSX.app

In order to run ilastik with GUROBI support, make sure to always set the path to the license file (in case of a non-standard location):

# set-up environment
export GRB_LICENSE_FILE=/path/to/license/gurobi.lic

# run ilastik
cd /path/to/ilastik-1.*-Linux
./run_ilastik.sh

After a successful installation, learning the weights in the Tracking with Learning Workflow will be enabled.

Should you run into any problems, please contact us.