Labels on Levels

Textual annotation for large biological models with multi-scale hierarchical organization

Roles: primary programmer, first author

Technologies: C++, Qt, OpenGL

Labels on Levels was the first major project of my PhD at TU Wien. The goal was to come up with a solution to annotate with textual labels big molecular models that Ivan Viola's group was rendering in their cellVIEW tool. The core of the problem was to transfer existing label layout techniques onto a model with very specific characteristics that made it impossible to directly use them. These scenes were multi-scale (having structures on different levels), multi-instance (very many instances of several structure types), dense (molecules are tightly packed together), and 3D (as opposed to maps, for example). The technique I ended up implementing builds up on the previous work of Ladislav Čmolík, who’s also been a co-author of the paper.

As a part of the project, I reimplemented the rendering pipeline of cellVIEW using C++ and OpenGL into Marion, a new visualization framework developed at the VisGroup. The FreeType library has been used for the text rendering.

Paper

This project has culminated into a scientific paper accepted at IEEE Vis 2018 conference and afterwards published in IEEE Transactions on Visualization and Computer Graphics (TVCG) journal:

D. Kouřil, L. Čmolík, B. Kozlíková, H-Y. Wu, G. Johnson, D. Goodsell, A. Olson, M. E. Gröller, I. Viola, “Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments”, IEEE Transactions on Visualization and Computer Graphics, 25(1):977-986, January 2019. Doi: 10.1109/TVCG.2018.2864491

The paper has received the SciVis Best Paper Honorable Mention.

Process - Video

Throughout the design and development of the labeling technique, I recorded many videos which I afterwards compiled into a short behind-the-scenes video:

Process - Sketches

Very early on during my PhD I realized that making sketches is an important part of my process. I took a lot of notes and produced many design artifacts as I developed the design and implementation of the labeling technique.