HDILib: High Dimensional Inspector Library

Slimmed-down fork of HDILib: mainly no external dependencies like FLANN, that have to be compiled. To be compatible with the HDILib, you may want to include nanoflann, which is already present in hdi/data/nano_flann.h.

HDILib is a library for the scalable analysis of large and high-dimensional data. It contains scalable manifold-learning algorithms, visualizations and visual-analytics frameworks. HDILib is implemented in C++, OpenGL and JavaScript. It is developed within a joint collaboration between the Computer Graphics & Visualization group at the Delft University of Technology and the Division of Image Processing (LKEB) at the Leiden Medical Center.

Authors

• Nicola Pezzotti initiated the HDI project, developed the A-tSNE and HSNE algorithms and implemented most of the visualizations and frameworks.
• Thomas Höllt ported the library to MacOS.

Used

HDI is used in the following projects:

• Cytosplore: interactive system for understanding how the immune system works
• Brainscope: web portal for fast, interactive visual exploration of the Allen Atlases of the adult and developing human brain transcriptome
• DeepEyes: progressive analytics system for designing deep neural networks

Reference

Reference to cite when you use HDI in a research paper:

@inproceedings{Pezzotti2016HSNE,
  title={Hierarchical stochastic neighbor embedding},
  author={Pezzotti, Nicola and H{\"o}llt, Thomas and Lelieveldt, Boudewijn PF and Eisemann, Elmar and Vilanova, Anna},
  journal={Computer Graphics Forum},
  volume={35},
  number={3},
  pages={21--30},
  year={2016}
}
@article{Pezzotti2017AtSNE,
  title={Approximated and user steerable tsne for progressive visual analytics},
  author={Pezzotti, Nicola and Lelieveldt, Boudewijn PF and van der Maaten, Laurens and H{\"o}llt, Thomas and Eisemann, Elmar and Vilanova, Anna},
  journal={IEEE transactions on visualization and computer graphics},
  volume={23},
  number={7},
  pages={1739--1752},
  year={2017}
}

Building

GIT Cloning

When cloning the repo be aware that it includes submodules. With the latest git versions you should use the following command:

git clone --recurse-submodules https://github.com/alxvth/HDILibSlim.git

Dependencies

• Eigen 3.4

Ubuntu

On Ubuntu 16.04 you can build and install HDI by running the following commands

./scripts/install-dependencies.sh
mkdir build
cd build
cmake  -DCMAKE_BUILD_TYPE=Release ..
make -j 8
sudo make install

Windows

On Windows use CMake and set a custom_install_path

cmake .. -DCMAKE_BUILD_TYPE=Release -DCMAKE_INSTALL_PREFIX="custom_install_path"

Applications

A suite of command line and visualization applications is available in the original High Dimensional Inspector repository.