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Software preparation

During this course you will develop code in Matlab using the DIPimage package. This manual helps with the installation and configuration of these packages and services.

All packages are available for Windows, macOS and Linux.

You will also need the default image set which can be retrieved via this link.

Matlab installation

Matlab is a programming platform designed specifically for engineers and scientists. The heart of Matlab is the Matlab language, a matrix-based language allowing the most natural expression of computational mathematics (from what is matlab). You need to have a recent version of Matlab installed on your computer (newer than 2018a). This can be done via the instructions for Matlab on this site:

Matlab Toolboxes

Make sure to install the Wavelet toolbox. We do not need additional toolboxes.

Alternatively you can contact the servicedesk at this e-mail servicepunttnw@tudelft.nl for more help.

Long installation time

The registration and installation process can take some time (> 1h)! Make sure you plan the installation of Matlab in advance of the course.

DIPimage installation

For the advanced image processing you will use the DIPimage package. DIPimage is a Matlab toolbox for quantitative image analysis, built on DIPlib. It is a mature toolbox, and offers much more than access to DIPlib from within Matlab. It includes a GUI and an interactive image display that can be used to explore 1D, 2D, 3D and 4D images. This package must be installed on your computer.

Windows

Follow the instructions and download the dipimage_3.2_windows_fftw.zip file from this location:

You can also compile the library yourself from the source. Follow the instructions for Windows on this location:

While you’re at it, have a look at the DIPimage Users Manual. This manual will give you a good understanding of the workings of this package needed for this course.

macOS

There is no installer package for macOS. You need to build (compile) your own version of DIPimage on your computer. Please read the instructions here and note these important remarks when following the instructions:

  • You will need to use Homebrew, follow the instructions
  • You don’t need DIPviewer, do not install glfw
  • You don’t need to compile the documentation
  • You don’t need to compile PyDIP, do not install python3
  • Skip the instructions in OpenMP

  • Use this command to compile:

    cmake .. -DCMAKE_INSTALL_PREFIX=$HOME/dip -DDIP_BUILD_DIPVIEWER=Off -DDIP_BUILD_JAVAIO=Off -DDIP_BUILD_PYDIP=Off

    After that skip until Using DIPimage and follow instructions from there

  • Skip the instructions in Enabling Bio-Formats

  • Skip the instructions in Using PyDIP

Linux

There is no installer package for Linux. You need to build (compile) your own version of DIPimage on your computer. Please read the instructions here. Follow the remarks above as written for macOS.