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Dr. Martin Falk

Dr. rer. nat. Martin Falk

Büro: Informatikgebäude

Universität Stuttgart
Universitätsstraße 38
70569 Stuttgart

Telefonnummer: +49 (711) 685-88269

Telefaxnummer: +49 (711) 685-88340

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

Curriculum Vitae

seit Oktober 2013 Promovierter wissenschaftlicher Mitarbeiter (Postdoc) bei Anders Ynnerman in der Scientific Visualization Group an der Linköpings universitet, Schweden
seit Juni 2007 Wissenschaftlicher Mitarbeiter und Doktorand am Visualisierungsinstitut der Universität Stuttgart (VISUS)
Mitglied der Graduiertenschule des Exzellensclusters Simulation Technology
Titel der Dissertation: Visualisierung und Mesoskopische Simulation in der Systembiologie
Okt. 2001 - April 2007 Diplomstudium der Informatik an der Universität Stuttgart
Juni - Dez. 2006 Diplomarbeit, School of Computing Science, Simon Fraser University, Kanada
Titel: GPU-basierte Vektorfeldvisualisierung mittels 3D LIC
Okt. 2005 - April 2006 Studienarbeit, Institut für Visualisierung und Interaktive Systeme, Universität Stuttgart
Titel: Landkartengenerierung mittels GPU-basiertem, nichtlinearen Raytracing
2005 - 2007 Wissenschaftliche Hilfskraft am Institut für Visualisierung und Interaktive Systeme, Universität Stuttgart

Auszeichnungen

2012 Eurographics Workshop on Visual Computing for Biology and Medicine (VCBM) 2012 - NVIDIA Best Paper Award
2009 ASIM GMMS Workshop 2009 - Publikumspreis für Poster, zweiter Platz [PDF]
2007 infos award 2007 - Auszeichnung für eine hervorragende Diplomarbeit

Forschung

  • Visualisierung und Mesoskopische Simulation der zellulären Signaltransduktion

    In der Systembiologie spielen Zusammenhänge eine große Rolle und Visualisierungen sind sehr gut dafür geeignet diese sichtbar zu machen. Daher liegt der Schwerpunkt dieser Arbeit in der Visualisierung und interaktiven Exploration von Daten aus diesem Umfeld. Die zu visulisierenden Daten werden von in silico Simulationen erzeugt. Besonderer Wert wird auf die Entwicklung von Methoden gelegt, welche auf modernen Grafikprozessoren (GPUs) ausgeführt werden. Die parallele Architektur von GPUs ist von Interesse, da sie ein großes Potential für das Beschleunigen von Berechnungen besitzt.

    Das Ziel dieser Arbeit ist die Entwicklung einer mesoskopischen Simulation von ausgewählten intra- und extrazellulären Prozessen. Weiter sollen Visualisierungen entwickelt werden, welche in der Lage sind die Simulationsergebnisse sinnvoll darzustellen. Insbesondere werden zelluläre Signaltransduktionsprozesse, d.h. die Signalübertragung innerhalb der Zelle, untersucht.

    Forschungsfragen sind:

    • Wie beeinflussen die verschiedenen Transportarten die Signalausbreitung?
    • Welches Signalmolekül erreicht den Zellkern als Erstes?
    • Wie sieht die ausgeprägte Signalfront aus?
  • CellVis

    CellVis LogoDas Visualisierungswerkzeug CellVis erlaubt die Datenanalyse der in silico Simulationsergebnisse. CellVis nutzt überwiegend GPU-basierte Visualisierungstechniken wie beispielsweise glyphenbasiertes Rendering oder Volumenraycasting. Zwei grundlegende Visualisierungstechniken stehen für die Darstellung zellulärer Prozesse zur Verfügung. Die schematische Darstellung stellt die Simulationsdaten so dar wie sie auch in der Simulation verwendet werden, d.h. interne Strukturen wie Filamente des Zellskeletts und sich bewegende Teilchen werden berücksichtigt. Die zweite Visualisierung erzeugt Bilder die denen aus der konfokalen Lasermikroskopie ähneln.

    Screenshot of CellVis (nuclear pores) Screenshot of CellVis (MAPK simulation)Microscopic visualization in CellVis
  • Stochastische zelluläre Simulation

    Die zugrunde liegende Simulation für unser MAPK-Modell (mitogenaktivierte Proteinkinase) ist eine agentenbasierte Simulation mit Protein-Protein Interaktionen. Sie unterstützt sowohl die Diffusion als auch den Transport mittels Motorproteinen als Transportmechanismen für das Signal in Richtung des Zellkerns. CUDA und OpenMP werden für eine parallele Implementierung auf modernen Grafikkarten und CPUs eingesetzt.

    Result of MAPK simulation Intracellular visualization of the nuclear pore import
  • Modellierung eines biologischen Zellmodells

    Das zelluläre Modell der vorherigen Projekte soll hinsichtlich Form und Innenleben verfeinert werden, um beispielsweise Vergleiche mit Laborexperimenten zu ermöglichen. Schwerpunkte sind dabei:

    • Modellierung der Plasmamembran mit Freiformflächen, um Deformationen zu erlauben
    • Struktur und Layout der Mikrotubuli des Zellskeletts
    • Weitere Organellen, z.B. der Golgiapparat, das endoplasmatische Retikulum (ER) und die Mitochondrien
    • Integration in das bestehende Simulationsframework

Abgeschlossene Projekte

  • 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 2010).
    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 2007.

    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

Lehre

Wintersemester 2010/11

Sommersemester 2010

Wintersemester 2009/10

Wintersemester 2008/09

Sommersemester 2008

Wintersemester 2007/08

Betreute Studentische Arbeiten

Masterarbeiten

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

Diplomarbeiten

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

Studienarbeiten

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

Software Praktika

  • Louis Bergmann, Sanda Leko, Ernst Stamp:
    Animierte Fische welche auf Benutzerinteraktionen mittels Kamera reagieren
    (SOPRA - Software for Oceanic Pattern Recognition and Animation)
  • Kai Jauch, Helena Löwenstein, Sebastian Konle, Bettina Ohlhausen:
    Hubschraubersimulation gesteuert mit einem Hometrainer

Publikationen

2016

Kauker, Daniel; Falk, Martin; Reina, Guido; Ynnerman, Anders; Ertl, Thomas: VoxLink - Combining sparse volumetric data and geometry for efficient rendering. In: Computational Visual Media (2016) (Noch nicht erschienen).
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]
Visualization of Molecular Structure: State of the Art Revisited
Kozlíková, Barbora; Krone, Michael; Falk, Martin; Lindow, Norbert; Baaden, Marc; Baum, Daniel; Viola, Ivan; Parulek, Julius; Hege, Hans-Christian: Visualization of Molecular Structure: State of the Art Revisited. In: Computer Graphics Forum (2016).
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]
Interactive GPU-based Visualization of Large Dynamic Particle Data
Falk, Martin; Grottel, Sebastian; Krone, Michael; Reina, Guido: Interactive GPU-based Visualization of Large Dynamic Particle Data. San Rafael, CA: Morgan & Claypool Publishers, 2016.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

2015

Visualization of Molecular Structure: State of the Art
Kozlíková, Barbora; Krone, Michael; Lindow, Norbert; Falk, Martin; Baaden, Marc; Baum, Daniel; Viola, Ivan; Parulek, Julius; Hege, Hans-Christian: Visualization of Molecular Structure: State of the Art. In: Eurographics Conference on Visualization (EuroVis) - STARs, S. 61-81, 2015.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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: Ausgabe 32, Nr. 8 (2013), S. 195-206.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [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] [Vortragsfolien] [Details]

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), S. 123-130, 2012.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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: Ausgabe 30, Nr. 3 (2011), S. 673-682.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [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), S. 9-15, 2011.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [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), S. 73-82, 2011.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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, S. 35-43, 2010.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [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), S. 1301-1304, 2010.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [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] [Vortragsfolien] [Details]

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), S. 169-176, 2009.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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: Ausgabe 14, Nr. 4 (2008), S. 820-834.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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: Ausgabe 15, Nr. 1 (2007), S. 91-98.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [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), S. 9-16, 2007.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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: Ausgabe 12, Nr. 4 (2006), S. 522-534.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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, S. 583-590, 2005.
[XPS] [PDF] [DOI] [OpenXML] [BibTeX] [Vortragsfolien] [Details]

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.