Martin Falk

Assistant Lecturer (Biträdande Lektor)

Contact Information

Phone: +46 (0)11-36 33 11
Office: K2 2069

Background

Martin Falk is an assistant lecturer in the Scientific Visualization Group at Linköping University. He received his Ph.D. degree (Dr.rer.nat.) from the University of Stuttgart in 2013. His research interests include large-scale volume rendering, visualizations in the context of pathology and systems biology, large spatio-temporal data, glyph-based rendering, and GPU-based simulations.

Curriculum Vitae

since April 2016 Assistant Lecturer in the Scientific Visualization Group at Linköping University, Sweden
Oct. 2013 - March 2016 Postdoc with Anders Ynnerman in the Scientific Visualization Group at Linköping University, Sweden
April 2013 Received PhD degree in computer science (Dr.rer.nat.), supervisor Prof. Dr. Thomas Ertl
Title of the dissertation: Visualization and Mesoscopic Simulation in Systems Biology
June 2007 - June 2013 Research Assistant and PhD student at the Visualization Research Center of the University of Stuttgart (VISUS)
Member of the graduate school Cluster of Excellence Simulation Technology
Oct. 2001 - April 2007 Diploma Study in Computer Science at the University of Stuttgart
June - Dec. 2006 Diploma Thesis, School of Computing Science, Simon Fraser University, Canada
Title: GPU-based Vector Field Visualization with 3D LIC
Oct. 2005 - April 2006 Student Research Project, Institute for Visualization and Interactive Systems, University of Stuttgart
Title: Map Generation with GPU-based Non-linear Raytracing
2005 - 2007 Student assistant at the Institute for Visualization and Interactive Systems, University of Stuttgart

Prizes and Awards

2012 Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) 2012 - NVIDIA Best Paper Award
2007 infos award 2007 - Awarded for an excellent diploma thesis

Previous and Ongoing Projects

Ongoing Projects

  • 3D Digital Pathology Visualization

    The aim of the project is to develop efficient multi-scale visualizations of 3D stacks of collections of large-scale slide images used in pathology. These slide image, obtained by scanning of such tissue samples, can exceed resolutions of 100,000 by 100,000 pixels at an optical magnification of 40x. A stack of images can thus easily result in more than 100 GiB per tissue sample.

    More information is available on the project website.

  • Visualization of charge transports in organic solar cells

    In this project, trajectory ensembles of excitons moving inside organic solar cells are investigated. We use the charge trajectories to extract the backbone of the morphology and to identify, e.g., bottlenecks of the charge transport.

Completed Projects

  • Atomistic Visualization of Mesoscopic Whole-Cell Simulations

    With modern GPU ray casting approaches it is only possible to render several millions of atoms at interactive frame rates unless advanced acceleration methods are employed. But even simplified cell models of whole-cell simulations consist of at least several billion atoms. However, many instances of only a few different proteins occur in the intracellular environment, which is beneficial in order to fit the data into the graphics memory. One model is stored for each protein species and rendered once per instance. The proposed method exploits recent algorithmic advances for particle rendering and the repetitive nature of intracellular proteins to visualize dynamic results from mesoscopic simulations of cellular transport processes at interactive frame rates.

    Published at the EG Workshop on Visual Computing for Biology and Medicine (VCBM, 2012).

  • Visualization of Receptor Clustering on the Cellular Membrane (2011)

    Apoptosis, the programmed cell death, is initiated by two pathways, the extra-cellular and the mitochondrial pathway. In the extra-cellular pathway, the binding of ligands to death receptors on the cellular membrane leads to the activation of the pathway. We developed a mathematical model to simulate the stochastic process of receptor-ligand clustering. The in-silico results are visualized in CellVis by highlighting certain cluster properties supporting the model development by visual data analysis.

    Published at IEEE Symposium on Biological Data Visualization (BioVis 2011).

  • Interactive Exploration of Protein Cavities (2011)

    Inside a protein, cavities can often be found close to the active center. Therefore, when analyzing a molecular
    dynamics simulation trajectory it is of great interest to find these cavities and determine if such a cavity opens
    up to the environment, making the binding site accessible to the surrounding substrate. Volume ray casting is used to compute the boundary of the protein in real-time. Then, a partial segmentation is applied to the volume to obtain the user-selected cavity.

    Published in Computer Graphics Forum (EuroVis 2011).

  • Visualization of Lagrangian Coherent Structures in Unsteady Flow (2010)

    Lagrangian coherent structures (LCS) separate regions of qualitatively different flow behavior. The LCS can be identified, as shown by Haller in 2001, as ridges (local maximizing curves or surfaces) in the finite-time Lyapunov exponent (FTLE). We introduce a twofold approach to visualizing pathlines in the context of to LCS generation: the selection of significant trajectories and their individual visualization.

    Published at International Symposium on Flow Visualization (ISFV14).

  • Visualizing Signal Concentrations (2010)

    An agent-based Monte Carlo simulation of a simplified Mitogen-Activated Protein Kinase (MAPK) is used to compute the trajectories of discrete signaling proteins. In this project, we create a continuous visualization from discrete particles for better insight. The concentration as well as the signaling front become visible.

    Published at IEEE International Symposium on Biomedical Imaging (ISBI '10).

  • CSB-Project A4 (Center Systems Biology) - Signal Transduction (2010)

    We developed two visualization techniques: a schematic cartoon-like representation and microscope-like images to allow comparison with wet lab experiments. Glyphs are used for interactive rendering of over 100,000 proteins and other cell structures. The data to be visualized is generated by a particle-based Monte Carlo simulation.

    Published at IEEE Pacific Visualization Symposium 2009.

  • Panorama Maps with Non-linear Ray Tracing (2007)

    Non-linear Ray Tracing is used to generate panorama maps by minimizing occlusion. The viewing rays are deflected by the underlying terrain. Techniques of Berann, an Austrian cartograph, are employed in this work like progressive perspective, vertical exaggeration, and rotation and translation of features.

    Published at Graphite '07.

  • 3D Line Integral Convolution (2007)

    Our approach of view-dependent visualization tightly links the LIC generation with the volume rendering of the LIC result in order to avoid the computation of unnecessary LIC points. A range of illumination models is applied to the LIC streamlines: different codimension-2 lighting models as well as a novel gradient-based illumination model that relies on precomputed gradients and does not require any direct calculation of gradients after the LIC integral is evaluated. This 3D LIC method allows users to interactively explore 3D flow by means of high-quality, view-dependent, and adaptive LIC volume visualization.

    Published in IEEE Transactions on Visualization and Computer Graphics 2008.

  • Real-Time Rendering of Planets with Atmospheres (2007)

    Published in the Journal of WSCG 2007.

Current Teaching

Teaching activities include:
  • TNG033 - Advanced C++ programming, part of MT study program
  • TND012 - Introduction to Programming, part of the MT, ED, and KTS study program
  • Supervision of Master's Thesis projects

PhD Thesis


Thesis cover Falk, Martin: Visualization and mesoscopic simulation in systems biology. Dissertation, Visualization Research Center, Universität Stuttgart, Germany (2013).

Link to PDF


Publications

Publications in 2019
Martin Falk, Anders Ynnerman, Darren Treanor, Claes Lundström
IEEE TVCG (SciVis Proceedings), Volume 29, Number 1 - 2019
 
Publications in 2017
Martin Falk, Ingrid Hotz, Patric Ljung, Darren Treanor, Anders Ynnerman, Claes Lundström
IEEE Pacific Visualization Symposium (PacificVis 2017), page 171--179 - 2017
 
Publications in 2016
Martin Falk, Sebastian Grottel, Michael Krone, Guido Reina
Morgan & Claypool Publishers, Volume 4(3) - 2016

Daniel Jönsson, Martin Falk, Anders Ynnerman
IEEE Transactions on Visualization and Computer Graphics (TVCG), Volume 22, Number 1, page 896 - 905 - jan 2016

Barbora Kozlíková, Michael Krone, Martin Falk, Norbert Lindow, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege
Computer Graphics Forum - 2016

Daniel Kauker, Martin Falk, Guido Reina, Anders Ynnerman, Thomas Ertl
Computational Visual Media, page 1--12 - jan 2016
 
Publications in 2015
Sathish Kottravel, Martin Falk, Erik Sundén, Timo Ropinski
IEEE Pacific Visualization Symposium (PacificVis 2015), page 255--262 - 2015

Erik Sundén, Peter Steneteg, Sathish Kottravel, Daniel Jönsson, Rickard Englund, Martin Falk, Timo Ropinski
Poster at IEEE Vis - 2015

Barbora Kozlíková, Michael Krone, Norbert Lindow, Martin Falk, Marc Baaden, Daniel Baum, Ivan Viola, Julius Parulek, Hans-Christian Hege
Eurographics Conference on Visualization (EuroVis) - STARs - 2015
 
Publications in 2014
Stefan Lindholm, Martin Falk, Erik Sundén, Alexander Bock, Anders Ynnerman, Timo Ropinski
Computer Graphics Forum, Volume 34, Number 1, page 74--85 - 2014


Previous Publications

  • Lindholm, Stefan; Falk, Martin; Sundén, Erik; Bock, Alexander; Ynnerman, Anders; Ropinski, Timo: Hybrid Data Visualization Based on Depth Complexity Histogram Analysis. Computer Graphics Forum, online (2014). DOI: 10.1111/cgf.12460
  • Falk, Martin; Krone, Michael; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations using Ray-Casted Instancing. Computer Graphics Forum 32(8), pp. 195-206 (2013).
  • Falk, Martin; Krone, Michael; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations. In: EG Workshop on Visual Computing for Biology and Medicine (VCBM), pp. 123-130 (2012).
  • Falk, Martin; Daub, Markus; Schneider, Guido; Ertl, Thomas: Modeling and Visualization of Receptor Clustering on the Cellular Membrane. In: IEEE Symposium on Biological Data Visualization (BioVis 2011), pp. 9-15 (2011).
  • Falk, Martin; Klann, Michael; Ott, Michael; Koeppl, Heinz; Ertl, Thomas: Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology. In: International Conference on Computational Methods in Systems Biology (CMSB 2011), pp. 73-82 (2011).
  • Krone, Michael; Falk, Martin; Rehm, Sascha; Pleiss, Jürgen; Ertl, Thomas: Interactive Exploration of Protein Cavities. Computer Graphics Forum 30 (3), pp. 673-682 (2011).
  • Falk, Martin; Grottel, Sebastian; Ertl, Thomas: Interactive Image-Space Volume Visualization for Dynamic Particle Simulations. In: Proceedings of The Annual SIGRAD Conference, pp. 35-43 (2010).
  • Falk, Martin; Klann, Michael; Reuss, Matthias; Ertl, Thomas: 3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations. In: IEEE International Symposium on Biomedical Imaging: From Nano to Macro (ISBI ’10), pp. 1301-1304 (2010).
  • Falk, Martin; Seizinger, Alexander; Sadlo, Filip; Üffinger, Markus; Weiskopf, Daniel: Trajectory-Augmented Visualization of Lagrangian Coherent Structures in Unsteady Flow. In: International Symposium on Flow Visualization (ISFV14) (2010).
  • Falk, Martin; Klann, Michael; Reuss, Matthias; Ertl, Thomas: Visualization of Signal Transduction Processes in the Crowded Environment of the Cell. In: IEEE Pacific Visualization Symposium (PacificVis 2009), pp. 169-176 (2009).
  • Falk, Martin; Weiskopf, Daniel: Output-Sensitive 3D Line Integral Convolution. IEEE Transactions on Visualization and Computer Graphics 14 (4), pp. 820-834 (2008).
  • Falk, Martin; Schafhitzel, Tobias; Weiskopf, Daniel; Ertl, Thomas: Panorama Maps with Non-linear Ray Tracing. In: International Conference on Computer Graphics and Interactive Techniques (GRAPHITE 2007), pp. 9-16 (2007).
  • Schafhitzel, Tobias; Falk, Martin; Ertl, Thomas: Real-Time Rendering of Planets with Atmospheres. Journal of WSCG 2007 15 (1), pp. 91-98 (2007).
  • Weiskopf, Daniel; Borchers, Marc; Ertl, Thomas; Falk, Martin; Fechtig, Oliver; Frank, Regine; Grave, Frank; King, Andreas; Kraus, Ute; Müller, Thomas; Nollert, Hans-Peter; Rica Mendez, Isabel; Ruder, Hanns; Schafhitzel, Tobias; Schär, Sonja; Zahn, C.; Zatloukal, Michael: Explanatory and Illustrative Visualization of Special and General Relativity. IEEE Transactions on Visualization and Computer Graphics 12 (4), pp. 522-534 (2006).
  • Weiskopf, Daniel; Borchers, Marc; Ertl, Thomas; Falk, Martin; Fechtig, Oliver; Frank, Regine; Grave, Frank; King, Andreas; Kraus, Ute; Müller, Thomas; Nollert, Hans-Peter; Rica Mendez, Isabel; Ruder, Hanns; Schafhitzel, Tobias; Schär, Sonja; Zahn, Corvin; Zatloukal, Michael: Visualization in the Einstein Year 2005: A Case Study on Explanatory and Illustrative Visualization of Relativity and Astrophysics. In: Proceedings of IEEE Visualization ’05, pp. 583-590 (2005).