Information for

Logo VISUS

Dr. Martin Falk

Dr. rer. nat. Martin Falk

Office: Informatikgebäude

Universität Stuttgart
Universitätsstraße 38
70569 Stuttgart

Phone Number: +49 (711) 685-88269

Telefax Number: +49 (711) 685-88340

E-Mail Address: martin.falk@visus.uni-stuttgart.de

Curriculum Vitae

since Oct. 2013 Postdoc with Anders Ynnerman in the Scientific Visualization Group at Linköping University, Sweden
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
Title of the dissertation: Visualization and Mesoscopic Simulation in Systems Biology
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

Awards

2012 Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) 2012 - NVIDIA Best Paper Award
2009 ASIM GMMS Workshop 2009 - Audience poster award, second place [PDF]
2007 infos award 2007 - Awarded for an excellent diploma thesis

Research

  • Visualization and Mesoscopic Simulation of Cellular Signal Transduction

    In systems biology, correlations play an important role and visualizations are a great way to make these visible. Hence, the focus of this work lies in the visualization and the interactive exploration of data from this environment. The data to be visualized will be generated by in silico simulations. Special emphasis is placed on the development of methods, which are carried out on graphic processing units (GPUs). The parallel architecture of GPUs is of interest, because it has the potential to allow high speed-ups of computations.

    The aim of this work is to develop a mesoscopic simulation of selected intra-cellular and extra-cellular processes and visualizations which are able to represent the simulation results in meaningful ways. In particular, cellular signal transduction processes will be studied.

    Subjects to research are:

    • How do different transport modes affect the signaling process?
    • What signaling molecule arrives first at the nucleus?
    • How does the signaling front look like?
  • CellVis

    CellVis LogoThe visualization tool CellVis allows the data analysis of the in silico simulation results. CellVis relies heavily on GPU-based visualizations like glyph-based rendering and volume ray casting. Two major techniques are available for the visualization of the cellular processes. The schematic visualization renders the data set as it is used during the simulation, i.e. the internal structures like cytoskeletal filaments and the moving proteins are considered. The second visualization generates images similar to confocal laser scanning microscopy.

    Screenshot of CellVis (nuclear pores) Screenshot of CellVis (MAPK simulation)Microscopic visualization in CellVis
  • Cellular Stochastic Simulation

    The underlying simulation of MAPK (mitogen-activated protein kinases) is a agent-based simulation with protein-protein interactions. It supports diffusion and transport by motor proteins as transport mechanisms of the signal toward the nucleus. CUDA and OpenMP are used for a parallel implementation on recent GPUs.

    Result of MAPK simulation Intracellular visualization of the nuclear pore import
  • Modeling of a Biological Cell Model

    The cellular model of the previous project is refined concerning shape and interior of the cell to allow for comparisons with wet lab experiments. Key aspects are:

    • Modeling of the cell membrane with freeform surfaces allowing deformation
    • Structure and layout of the microtubuli of the cytoskeleton
    • Organelles like Golgi apparatus, endoplasmatic reticulum (ER), and mitochondria
    • Integration into existing simulation model

     

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).

    Cell consisting of filaments and molecules (4 billion atoms) Close-up of filaments and molecules (4 billion atoms, moving proteins enlarged 10 times)Close-up with toon shading (4 billion atoms) Microtubule with toon shading (1.6 million atoms) Viral envelope (PDB-ID: 1SVA, 958,981 atoms)
  • 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).

    Receptors (green) and ligands (blue) in the 2D simulation domain Cluster are clearly separated by color coding Cluster visualization embedded into CellVis
  • 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).

    The cavity is hardly visible without the visualized segmentation Segmentation of the cavity visualized
  • 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).

    Pathlines used for FTLE computation visualize a double-gyre Flow separation in a buoyant flow Flow behaviour leading to FTLE ridges
  • 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).
    Accompanying movie.

    Signal concentration of a virtual cell Signaling front evolving over time
  • 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.

    Microscopic-like image for comparison with wet lab experiment Trajetory of a protein Schematic cell with closeup

    Diffusion of drug molecules into a tumor Transection of drug molecule diffusion
  • 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.

    Skiing region of Kronplatz, Italy Panorama Map of Whistler, Canada Non-linear Effects in the Whistler Panorama
  • 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.
    Accompanying material.

    Tornado Data Set: Oriented LIC Clipped Tornado Data Set Illumination based on Gradients Vortex Flow with highlighted
Lambda2-values
  • Real-Time Rendering of Planets with Atmospheres (2007)

    Blue Marble The Alps in the Morning
  • Flight over Marsian Surface (2005)

    Mars Valles Marineris, Mars

Student Supervision

Master Theses

  • Ana Cristina Pintilie (2012):
    Statistical Analysis and Comparative Visualization of Cellular Particle-based Simulations
    (Statistische Analyse und vergleichende Visualisierung zellulärer partikelbasierter Simulationen)

Diploma Theses (Diplomarbeiten)

  • Michael Ott (2009):
    Simulation and Visualization of Biological Processes Utilizing CUDA
    (Simulation und Visualisierung biologischer Prozesse mit CUDA)
  • Mikael Vaaraniemi (2008):
    Very Detailed Navigation Maps on 3D Terrain Models
    (Hochdetaillierte Navigationskarten auf 3D Geländemodellen)

Student Research Projects (Studienarbeiten)

  • Hendrik Hochstetter (2010):
    Modeling of a Biological Cell Model
    (Modellierung eines biologischen Zellmodells)

Software Laboratory (Software Praktikum)

  • Louis Bergmann, Sanda Leko, Ernst Stamp:
    Animated fishes reacting to user interaction via camera
    (SOPRA - Software for Oceanic Pattern Recognition and Animation)
  • Kai Jauch, Helena Löwenstein, Sebastian Konle, Bettina Ohlhausen:
    Helicopter simulation controlled by a home trainer

Publications

2013

Atomistic Visualization of Mesoscopic Whole-Cell Simulations using Ray-Casted Instancing
Falk, Martin; Krone, Michael; Ertl, Thomas: Atomistic Visualization of Mesoscopic Whole-Cell Simulations using Ray-Casted Instancing. In: Computer Graphics Forum: No. 8 (2013), pp. 195-206.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
Visualization and mesoscopic simulation in systems biology
Falk, Martin: Visualization and mesoscopic simulation in systems biology. Diss., Visualization Research Center, Universität Stuttgart, 2013.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 2

2012

Atomistic Visualization of Mesoscopic Whole-Cell Simulations
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 1

2011

Interactive Exploration of Protein Cavities
Krone, Michael; Falk, Martin; Rehm, Sascha; Pleiss, Jürgen; Ertl, Thomas: Interactive Exploration of Protein Cavities. In: Computer Graphics Forum: No. 3 (2011), pp. 673-682.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
Modeling and Visualization of Receptor Clustering on the Cellular Membrane
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
Parallelized Agent-based Simulation on CPU and Graphics Hardware for Spatial and Stochastic Models in Biology
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 3

2010

Interactive Image-Space Volume Visualization for Dynamic Particle Simulations
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
Trajectory-Augmented Visualization of Lagrangian Coherent Structures in Unsteady Flow
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 3

2009

Visualization of Signal Transduction Processes in the Crowded Environment of the Cell
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 1

2008

Output-Sensitive 3D Line Integral Convolution
Falk, Martin; Weiskopf, Daniel: Output-Sensitive 3D Line Integral Convolution. In: IEEE Transactions on Visualization and Computer Graphics: No. 4 (2008), pp. 820-834.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 1

2007

Real-Time Rendering of Planets with Atmospheres
Schafhitzel, Tobias; Falk, Martin; Ertl, Thomas: Real-Time Rendering of Planets with Atmospheres. In: Journal of WSCG 2007: No. 1 (2007), pp. 91-98.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
Panorama Maps with Non-linear Ray Tracing
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 2

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, C.; Zatloukal, Michael: Explanatory and Illustrative Visualization of Special and General Relativity. In: IEEE Transactions on Visualization and Computer Graphics: No. 4 (2006), pp. 522-534.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 1

2005

Visualization in the Einstein Year 2005: A Case Study on Explanatory and Illustrative Visualization of Relativity and Astrophysics
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.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Slides] [Details]
total number: 1

Poster

2012

CellVis – Modeling, Simulating, and Analyzing Cellular Processes
Falk, Martin; Ertl, Thomas: CellVis – Modeling, Simulating, and Analyzing Cellular Processes. Workshop on Statistical and Dynamical Models in Biology and Medicine, Stuttgart, Germany, 2012.
Stochastic Single-Cell Simulation: The External Signal
Falk, Martin; Ertl, Thomas: Stochastic Single-Cell Simulation: The External Signal. Visualizing Biological Data (VIZBI 2012), Heidelberg, Germany, 2012.

2011

Stochastic Simulation of Cellular Signal Transduction: Spatial Impact of the External Signal
Falk, Martin; Ertl, Thomas: Stochastic Simulation of Cellular Signal Transduction: Spatial Impact of the External Signal. International Conference on Simulation Technology, Stuttgart, Germany, 2011.
CellVis - Interactive Exploration and Simulation of Cellular Transport Processes
Falk, Martin; Ertl, Thomas: CellVis - Interactive Exploration and Simulation of Cellular Transport Processes. Visualizing Biological Data (VIZBI 2011), Cambridge, MA, USA, 2011.

2010

3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations
Falk, Martin; Klann, Michael; Reuss, Matthias; Ertl, Thomas: 3D Visualization of Concentrations from Stochastic Agent-based Signal Transduction Simulations. IEEE International Symposium on Biomedical Imaging (ISBI 2010), Rotterdam, The Netherlands, 2010.

2009

GPU-based Visualization of Simulation Results
Falk, Martin; Üffinger, Markus: GPU-based Visualization of Simulation Results. ASIM GMMS Workshop, Stuttgart, Germany, 2009.