Welcome

I am a researcher and entrepreneur in the field of computer-aided analysis, planning and design of products and procedures around the human body, mainly with respect to medical therapies and devices. My research interests are 3D geometry reconstruction of anatomical structures from measurement data and population-based 3D shape analysis.

Interests

  • Medical image processing
  • Shape matching/registration
  • Statistical shape analysis
  • 3D geometry and visualization

Education

  • Doctoral degree (PhD) in Mathematics/Computer Science, 2008

    Freie Universität Berlin

  • Diploma Degree in Physics, 2000

    Universität Heidelberg

News

Research Campus MODAL enters second funding phase

The MODAL research campus received funding approval for its second funding period from 2020 to 2025 on April 3, 2020.
Last updated on May 18, 2020
Research Campus MODAL enters second funding phase

Aortic Shape Synthesizer

We presented our work on shape synthetization at the ESC 2019 Congress.
Last updated on Sep 29, 2019
Aortic Shape Synthesizer

Book Chapter in Biomedical Visualisation

We contributed a chapter to the new book on Biomedical Visualisation. This book is targeted to a wide range of users from faculty and students, developers and computing experts, the wider public audience. It is hoped this will aid understanding of the variety of technologies which can be used to enhance understanding of clinical conditions using modern day methodologies.
Last updated on May 18, 2020
Book Chapter in Biomedical Visualisation

Publications

Quickly discover relevant content by filtering publications.

Unsupervised Learning and Statistical Shape Modeling of the Morphometry and Hemodynamics of Coarctation of the Aorta

Image-based patient-specific modeling of blood flow is a current state of the art approach in cardiovascular research proposed to …
Bente Thamsen, Pavlo Yevtushenko, Lina Gundelwein, Hans Lamecker, Titus Kühne, Leonid Goubergrits
Project Conference
Unsupervised Learning and Statistical Shape Modeling of the Morphometry and Hemodynamics of Coarctation of the Aorta

Anatomical Landmark Detection From X-Ray Images Using Convolutional Neural Networks

In this thesis, we propose an approach that robustly detects three-dimensional (3D) anatomical landmarks in two-dimensional (2D) …
Nicolás Pérez de Olaguer Santamaría
Anatomical Landmark Detection From X-Ray Images Using Convolutional Neural Networks

Automatic Quantification of Hip Osteoarthritis From Low Quality X-Ray Images

Diagnosis of hip osteoarthritis is conventionally done through a manual measurement of the joint distance between the femoral head and …
Giancarlos Gutiérrez C., Eveling Castro G., Javier Delgado O., Paúl Pauca, Stefan Klein, Hans Lamecker
PDF DOI
Automatic Quantification of Hip Osteoarthritis From Low Quality X-Ray Images

Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity

This study’s objective was the generation of a standardized geometry of the healthy nasal cavity. An average geometry of the healthy …
Jan Joris Brüning, Thomas Hildebrandt, Werner Heppt, Nora Schmidt, Hans Lamecker, Angelika Szengel, Natalja Amiridze, Heiko Ramm, Matthias Bindernagel, Stefan Zachow, Leonid Goubergrits
PDF DOI
Characterization of the Airflow within an Average Geometry of the Healthy Human Nasal Cavity

Morphological Indicators for Limitations in Nasal Breathing

In order to better understand the relationship between shape of the nasal cavity and to find objective classification for breathing …
Natalja Amiridze
Morphological Indicators for Limitations in Nasal Breathing
See all publications

Talks

3D Modelle aus medizinischen Bilddaten für Populations-basiertes 3D Produktdesign

Der Vortrag behandelt die Möglichkeiten 3D-Modelle anatomischer Strukturen für das Design neuer Produkte und Therapieansätze in der …
Aug 31, 2020 Fraunhofer-Konferenzzentrum, Potsdam
3D Modelle aus medizinischen Bilddaten für Populations-basiertes 3D Produktdesign

Shape Synthesiser Understanding and Mastering Anatomical Variations

Population-based models of morphological variability are useful for automating medical image processing tasks, diagnosis device and …
Oct 17, 2019 Kongress Palais, Kassel, Germany
Shape Synthesiser Understanding and Mastering Anatomical Variations

Lecture Series on Geometry and Image Processing for Medical Applications

Oct 31, 2016 — Nov 4, 2016 Universidad San Augustin, Arequipa, Peru
Lecture Series on Geometry and Image Processing for Medical Applications

Reconstruction of Partial Liver Shapes Based on a Statistical 3D Shape Model

Sep 30, 2015 MedTech Lab, Delémont, Switzerland
Reconstruction of Partial Liver Shapes Based on a Statistical 3D Shape Model

Image and Geometry Processing for Anatomy Reconstruction

Oct 10, 2014 Würzburg, Germany
See all talks

Curriculum Vitae

 
 
 
 
 

Guest research associate

Zuse Institute Berlin

Jan 2015 – Present Berlin / Germany
Working within the BMBF Forschungscampus MODAL and the DFG Math+ Research Center in the Visualization department.
 
 
 
 
 

Co-founder and CEO

1000shapes GmbH

Feb 2010 – Present Berlin / Germany
Co-founded the ZIB and Matheon spin-off company 1000shapes GmbH together with Stefan Zachow.
 
 
 
 
 

Postdoctoral research

INRIA

Jan 2009 – Dec 2009 Sophia-Antipolis / France
Member of the Asclepios group, working on brain image segmentation within the Health-e-Child project and cardiac simulation within the euHeart project. Working under Nicolas Ayache, Xavier Pennec and Hervé Delingette.
 
 
 
 
 

PhD studies in mathematics and computer science

Freie Universität Berlin

Apr 2001 – Sep 2008 Berlin / Germany
The topic of my research was variational and statistical shape modeling for 3D geometry reconstruction. As an alumni, I am a member of the Ernst-Reuter-Gesellschaft der Freunde, Förderer und Ehemaligen der Freien Universität Berlin e.V..
 
 
 
 
 

Research associate

Zuse Institute Berlin

Sep 2000 – Dec 2014 Berlin / Germany

I was part of the Visual Data Analysis department, member of the Therapy Planning Group, and involved in the Amira development. Working under Prof. Deuflhard, Hans-Christian Hege and Stefan Zachow. I became a member of the SIG Visual Computing in Biology and Medicine.

My research was funded by

  • DFG research center Matheon (FZT86)
  • European Commission project MXL (FP7-2009-ICT-248693)
  • DFG collaborative research center Hyperthermia: Clinical Aspects and Methodology (SFB273)
 
 
 
 
 

Research internship

Massachusetts Institute of Technology

May 2000 – Jun 2000 Cambridge/MA, USA
As part of my diploma thesis, I worked on numerical solutions to chiral dynamics in strong interaction physics.
 
 
 
 
 

Research internship

Zuse Institute Berlin

Feb 1998 – Apr 1998 Berlin / Germany
Development of an active-contour-based interactive image segmentation algorithm
 
 
 
 
 

Studies of physics

University of Heidelberg

Apr 1995 – Jul 2000 Heidelberg / Germany
Specialization in theoretical elementary particle physics; graduation as Diplomphysiker with a thesis on the chiral dynamics in strong interaction physics.
 
 
 
 
 

Studies of mathematics, physics and computer science

University of Auckland

Jan 1994 – Dec 1994 Auckland / New Zealand
 
 
 
 
 

Highschool

Max-Born-Gymnasium

Sep 1984 – Jun 1993 Germering near Munich, Germany
As an alumni, I am a member of the Max-Born-Netzwerk.

Awards

Shape Challenge Best Prize

Shape Symposium Jun 2015
Partial shape reconstruction of resected livers

VCBM 2012 Best Poster Award

VCBM Sep 2012
Efficient projection and deformation of volumetric shape and intensity models for accurate simulation of X-ray images

Ausgründungspreis / Spin-off Award

Matheon Jun 2012

Second-Best Auto-Segmentation Method

MICCAI 2010 Grand Challenge Jun 2010
Knee/Cartilage from MR images

Best Auto-Segmentation Method

MICCAI 2009 Grand Challenge Oct 2009
Manibular bone and nerve from DVT images

Karl-Heinz Höhne Preis

GI Special Interest Group MedVis Oct 2008
Atlas-based 3D-Shape Reconstruction from X-Ray Images

Best Auto-Segmentation Method

MICCAI 2007 Grand Challenge Oct 2007
Liver from contrast-enhanced CT images

Best Podium Presentation

CAS-Head International Conference Jun 2005

Scholarship

German National Academic Foundation / Studienstiftung des deutschen Volkes Jan 1997 – Jun 2000

Mentoring

I gladly serve as a supervisor or mentor for academic works, such as bachelor, master or PhD theses. Here are the students, whom I mentored or (co-)supervised:

Anatomical Landmark Detection From X-Ray Images Using Convolutional Neural Networks

In this thesis, we propose an approach that robustly detects three-dimensional (3D) anatomical landmarks in two-dimensional (2D) …
Nicolás Pérez de Olaguer Santamaría
Anatomical Landmark Detection From X-Ray Images Using Convolutional Neural Networks

Morphological Indicators for Limitations in Nasal Breathing

In order to better understand the relationship between shape of the nasal cavity and to find objective classification for breathing …
Natalja Amiridze
Morphological Indicators for Limitations in Nasal Breathing

Deep Learning for Boundary Detection in Model-Based Segmentation

We propose an algorithm to segment 3D medical images that combines deformable anatomical models and deep learning. The aim is to …
Marilia de Almeida Lirio Dourado
Deep Learning for Boundary Detection in Model-Based Segmentation
See all publications

Teaching

I like to teach courses on my research topics. Here are some examples:

Malen nach Zahlen - Wissenschaftliche Visualisierung

Deutsche Schülerakademie July 8, 2004 – July 24, 2004
Creation of course material, coordination and instruction

Scientific Visualization with Amira

Summer school on Geometry and Visualization June 21, 2004 – June 25, 2004
Course instructor in Maubeuge / France

Introduction to Quantum Mechanics

Deutsche Schülerakademie July 19, 2001 – August 4, 2001
Creation of course material, coordination and instruction

Introduction to the Theory of Relativity

Deutsche Schülerakademie August 2, 2000 – August 19, 2000
Creation of course material, coordination and instruction

Lecture accompanying Tutorials

University of Heidelberg March 1, 1996 – June 20, 1999

Course instruction and correction of exercises for the following lectures:

  • Theoretical mechanics (Prof. Dr. F. Wegner)
  • Analysis II (Prof. Dr. H. Rost)
  • Analysis I (Prof. Dr. H. Rost)
  • Algorithms and data structures (Prof. Dr. G. Reinelt)

Conferences

I have helped to organize, consult and support scientific events:

Workshop on Clinical Image-based Procedures: From Planning to Intervention

MICCAI 2012 Jun 2012
Program Commitee Member

Session XVI - Registration, Segmentation and Modeling

CAOS International Jun 2012
Session Chair

Workshop on Computational and Clinical Applications in Abdominal Imaging

MICCAI 2011 Jun 2011
Program Commitee Member

Focus Session on Evaluation

Medical Physics and Biomedical Engineering World Congress Jun 2009
Session Chair

Tandem Workshop on Geometry, Numerics and Visualization

DFG Research Center Matheon Jun 2003
Co-organization with M. Wardetzky and J. Bloch

International Workshop on Visualization and Mathematics

Zuse Institute Berlin Jun 2002
Staff member

First SIAM-EMS Conference: Applied Mathematics in our Changing World

Zuse Institute Berlin Jun 2001
Staff member

Reviewing

I serve as an expert reviewer for contributions in scientific journals and conferences. Here are some examples: