Ruprecht-Karls-Universität Heidelberg

Open Positions


[ Scientific Software Designer | PostDocs | PhD Positions | Master Theses | Student Opportunities | Industry ]

Scientific Software Designer

The HCI at University of Heidelberg is inviting applications for a full position as Scientific Software Designer (m/f).

The main objective of the new position is the transformation of cutting-edge research code into consistent and (re)usable software, mainly in open source. In particular, job duties may include to

  • extend existing HCI open source software packages (see,, and for examples of our work)
  • create re-usable C++ libraries from cutting-edge research prototypes
  • ensure interoperability and platform independence of the resulting software
  • support and advise researchers regarding software design decisions (e.g. choice of tools, portability, software architecture)
  • provide and/or create common software infrastructure (e.g. data import/export facilities, automated build system, parallelization support, documentation generation)
  • participate in the enhancement and maintenance of software test suites, manage automated test runs
  • help establishing a flexible, agile development process with minimal overhead
  • communicate well with researchers designing new algorithms and users.
Details will be defined in accordance to the evolving needs of all HCI partners and the specific skills of the successful candidate. Experience in several of the following areas is required:
  • very good programming and software design skills, especially in scientific software development (implementation of advanced algorithms, knowledge of existing libraries, parallelization) and system integration
  • advanced template programming and generic library design in C++ (required)
  • use of scripting languages (preferably Python and Matlab) and interoperation between scripting and C++
  • good knowledge of software development infrastructure (e.g. github, cmake, doxygen, cppunit) and support libraries (e.g. boost, hdf5)
  • understanding of the mathematical background of scientific algorithms.

The HCI offers a friendly, cooperative working atmosphere with flexible working hours. The position shall be filled as soon as possible and will be paid according to prior experience up to TV-L level E13. The initial contract will be for a duration of two years, extension to October 2017 is intended (funding is secured). Please send applications by 15 March 2013 electronically (preferably as a single PDF file containing the usual documents) to and include (a link to) a representative code sample you have written.


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Six Postdoctoral or Senior Researcher Positions in:

Optical Imaging, Image Processing, Computer Vision, Mathematical Imaging, and Machine Learning



The University of Heidelberg invites applications for six senior research positions in the above areas for an initial duration of two years, with possible extension (funding already secured until October 2017).

Prospective candidates have a PhD in Computer Science, Electrical Engineering, Mathematics or Physics and must have published in first-rate venues. Besides a strong mathematical background, we require fluency in advanced C++, matlab or python programming as well as in English.

The positions will be affiliated with the Heidelberg Collaboratory for Image Processing (HCI).

The HCI is part of the Interdisciplinary Center for Scientific Computing (IWR) and comprises five research groups (Garbe, Hamprecht, Jähne, Ommer, Schnörr). It is funded within the German Excellence Initiative by the German Research Foundation (DFG), the University, and the industrial HCI partners Robert Bosch GmbH, Carl Zeiss AG, Sony Deutschland GmbH, Heidelberg Engineering GmbH, Silicon Software GmbH and PCO AG. The HCI is directed by a steering committee including the corresponding heads and representatives of the industrial partners. The mission of the HCI is to conduct basic research with the aim of providing cutting-edge solutions to basic image analysis problems for applications in industry, environmental, and life sciences.

The gross salary ranges from 39.8 to 54.2 kEUR (TVL/13 step 1 up to TVL/14 step 4) plus social benefits, depending on qualification and experience. The envisioned starting date is November 2012 but is negotiable (earlier or later).

Applications should include a motivation letter, complete CV, the PhD thesis (or a link to it), a list of publications, two references (name, homepage), and be sent by email in PDF format to

The search process starts now and will remain open until all positions are filled.


PhD Positions

Doktorand/in Merkmale für visuelle Lokalisierung und Navigation[Pdf]

The following PhD position is offered at Bosch Hildesheim in close cooperation with the HCI in Heidelberg. It is expected that a successful candidate spends part of this time at the HCI. Academic supervision by the group of Bernd Jähne.
Please address your application directly to Bosch (see below).


Im Zentralbereich Research and Advance Engineering fördern wir die Entwicklung und Fertigung innovativer Produkte und stärken damit langfristig die Kernkompetenzen der einzelnen Geschäftsbereiche. In Hildesheim entwickeln wir hoch- innovative Funktionen, Komponenten, Systeme und Systemarchitekturen bis hin zum Prototyp auf den Gebieten Telematik, Funk-und Bildverarbeitung sowie digitale Kommunikation/Multimedia für den Einsatz im Kraftfahrzeug und der Sicherheitstechnik.



Ihre Aufgaben:
Zukünftig werden die Anforderungen an Sensoren, speziell an Kameras, zur Erfassung des
Umfeldes um ein Vielfaches steigen. Mit Ihrer Arbeit können Sie dazu beitragen, dieser
Herausforderung ein Stück näher zu kommen. Die Schwerpunkte dabei sind:


  • Entwicklung und Untersuchung von Merkmalen für visuelle Lokalisierungs- und
    Navigationsverfahren auf der Basis von Kartenrepräsentationen für Anwendungen
    im Bereich der videobasierten Umfelderfassung, z.B. autonomer mobiler
  • Abschätzung der Möglichkeiten und Grenzen visueller Lokalisation und Navigation
    hinsichtlich Positioniergenauigkeit, Wiederholbarkeit und ihrer hardwarenahen

Ihr Profil:

  • sehr guter Hochschulabschluss in der Fachrichtung Informatik, Geodäsie oder
  • nachweisbare Vertiefung der Kenntnisse in einschlägiger Richtung (visuelle
    Lokalisation, fundierte Kenntnisse auf dem Gebiet der Bildverarbeitung)
  • gute Kenntnisse in der objektorientierten Software-Entwicklung in C++
  • schnelle Auffassungsgabe, analytische und systematische Arbeitsweise,
  • Freude am wissenschaftlichen Arbeiten und an der Lösung von wissenschaftlichen
  • interdisziplinäre Teamfähigkeit, Bereitschaft zur Entwicklung kreativer


Wir freuen uns auf Ihre Bewerbung unter!






PhD in data analysis


Two scholarships are available for excellent students from Nankai and Tsinghua University to study towards their PhD at the University of Heidelberg.
The students will work in the group for Multidimensional Image Processing. You can choose from a range of topics in


  • Data mining of mass spectrometric data in proteomics
  • State-space modeling of single molecule spectroscopic data
  • Image processing for microscopy in systems biology
  • Novel algorithms for inference on spectral images



Master Theses

Not all projects are outlined below. Please contact the respective group leaders to find out about the latest offers.

Master Thesis Projects at the Multi-Dimensional Image Processing Group

If you are interested, send an email to Fred Hamprecht or Ullrich Köthe. Our topics are particularly suitable for students of physics, mathematics, and computer science, but motivated people from other fields are also welcome!

Neuro Segmentation

A major goal of neuro-science is the understanding of basic neural circuits. To this end, novel electron microscopic methods acquire 3-dimensional images of the brain at a resolution of 10-20 nm and a field of view of up to 0.1 mm. These huge datasets can only be analyzed automatically, and our group is a major algorithm provider for this application. We continuously offer interesting master projects dealing with specific subproblems, for example:
  • Design and implementation of new features that capture important image properties such as the shape and layout of candidate regions.
  • Detection methods for organelles such as mitochondria and vesicles.
  • Novel optimization algorithms that efficiently find the best among many candidate segmentations.
  • Development of semi-automatic tools that optimally combine automatic methods with interactive user guidance to arrive at high quality results as quickly as possible.

The Digital Embryo

Biologist are making rapid progress towards the understanding of embryonic development. Thanks to novel light-sheet microscopes that can capture fully 3-dimensional volume data at a temporal resolution of under one minute over several days, they can now study how initially independent cells manage to group themselves into all the different organs of an organism. Our group addresses the algorithmic challenge to track all visible cells in such a dataset over time. We continuously offer interesting master projects dealing with specific subproblems, for example:
  • Design of a reliable detector for cell division events, where the track of a single cell splits up into two child tracks.
  • Hierarchical segmentation algorithms that reliably find all visible cells even under high noise levels.
  • Efficient methods to estimate the uncertainty of the results of our analysis.
  • Algorithms for the intuitive visualization of 3D+time data on 2-dimensional displays.

Development of Novel Machine Learning Methods

Machine learning has become the method of choice to solve complex image analysis problems. It allows non-expert users to train a generic analysis algorithm by showing examples of desired outcomes. To extend the scope of this approach to more complex problems, we investigate new learning methods and novel ways to train them. Interesting master projects in this context include:
  • Development of active learning methods that minimize training time by guiding the user towards particularly valuable examples.
  • New image features that capture important aspects of the data for subsequent use by learning methods.
  • Intuitive training strategies for non-standard types of training data such as object shape and layout.
  • Design of novel ensemble methods that combine analysis results from several sources into an integrated result of much higher quality than any of the inputs.

Scientific Software Design

Our image analysis solutions apply complex algorithms to huge amounts of data and yet must be intuitively operable by non-experts. This poses great challenges on careful software design, and our group maintains a number of major open-source projects to address these challenges. Fast and flexible modules for fundamental image analysis and optimization algorithms are mainly implemented in the VIGRA and OpenGM C++ libraries, whereas the Python-based ilastik project takes care of the high-level organization, parallelization, and graphical user interface. Students who want to master advanced software development techniques can contribute to these projects in many ways, for example:
  • Design of easy-to-use workflows for recurring tasks in the application fields we address.
  • Reusable integration of novel algorithms developed by our group or elsewhere into these projects.
  • Implementation of advanced parallelization strategies to fully utilize the power of modern multi-core CPUs and clusters.
  • Powerful 3-dimensional visualization of analysis results for rapid user feedback and presentation.


Master Thesis Project at BOSCH:
Geometrie-Rekonstruktion mit Multi-View Video

Innovationsfähigkeit und Know-how-Vorsprung bestimmen den Bosch Unternehmenserfolg. Meistern Sie zusammen mit uns neue Aufgaben durch Ihre Bereitschaft, ständig Neues zu lernen.


Im Zentralbereich Forschung und Vorausentwicklung entwerfen, prüfen und erforschen wir Systeme, Komponenten und Technologien. Unsere Innovationen zielen dabei stets auf eine Verbesserung der Lebensqualität. In Schwieberdingen bei Stuttgart - dem größten Entwicklungszentrum unseres Unternehmensbereichs Kraftfahrzeugtechnik - arbeiten wir an Zukunftsthemen für Kfz-Systeme, Gebrauchsgüter und Industrietechnik sowie Produktionstechnik.


Ihre Aufgaben:


  • Aufbau eines Demonstrationssystems für Multi-View Video Aufnahmen
  • Implementierung von 3D-Rekonstruktionsverfahren in CUDA C
  • Untersuchung der Qualität der Rekonstruktion bei schwierigen Objekteigenschaften, wie z.B. Reflexionen auf Metallen und Lacken
  • Die Arbeit wird in enger Zusammenarbeit mit dem HCI in Heidelberg durchgeführt.

Ihr Profil:

  • Studium der Mathematik, der Natur- oder Computerwissenschaften
  • Sehr gute Programmierkenntnisse in C oder C++
  • Interesse an Programmierung in CUDA


Beginn: nach Absprache Dauer: 4 - 6 Monate Für weitere Informationen steht Ihnen Herr Dr. Ralf Zink gerne zur Verfügung
Tel.: +49(0)711/811-34571. Voraussetzung für die Abschlussarbeit ist die Immatrikulation an einer Hochschule.
Bitte fügen Sie Ihrer Bewerbung eine aktuelle Immatrikulationsbescheinigung sowie ggf. eine gültige Arbeits-
und Aufenthaltserlaubnis bei. Haben wir Ihr Interesse geweckt? Dann freuen wir uns auf Ihre Online-Bewerbung!



Master Thesis Projects in the Digital Image Processing Group

Charakterisierung von Oberflächenfilmen im Hinblick auf den Gasaustausch mit Hilfe der Blasenmethode

Es soll ein Messverfahren aufgebaut werden, mit dem sich direkt im Windkanal die Oberflächenspannung und damit die Bedeckung der Wasseroberfläche mit organischen monomolekularen Filmen bestimmt werden kann. Mit der Blasenmethode kann insbesondere der zeitliche Verlauf der Bildung von Oberflächenfilmen an einer neu gebildeten Oberfläche studiert werden...

Vergleich aktiver und passiver Thermographiemethoden zur Untersuchung des Wärmetransfers zwischen Atmosphäre und Meer

Die Aufnahme von Wärmbildsequenzen ist eines der wichtigsten Instrumente, zur Untersuchung der kleinskaligen, windinduzierten Turbulenz an der Meeresoberfläche. Sobald die Nettowärmeflussraten an der Wasseroberfläche ungleich null ist, gibt es einen Temperaturgradienten, durch den die Turbulenz sichtbar wird. Der Wärmefluss kann in Windkanälen durch Verdunstung von Wasser...

Labormessungen zum Gasaustausch zwischen Atmosphäre und Meer bei hohen Löslichkeiten mittels UV-Spektroskopie

Der Austausch von volatilen Substanzen ist bei hohen Löslichkeiten zum Teil durch die luftseitigen als auch die wasserseitigen Austauschprozesse an der Wasseroberfläche kontrolliert. Das Wechselspiel dieser beiden Prozesse ist bisher so gut wie nicht untersucht und erlaubt interessante Einblicke in die Intermittenz dieser Prozesse. In den letzten Jahren haben wir Messmethoden entwickelt, ...


Master Thesis Projects in the Image Processing and Modelling Group

Strukturanalyse von polaren und alpinen Eisbohrkernen mittels digitaler Bildverarbeitung

Eiskernstudien bieten eine der erfolgreichsten Methoden in der modernen Klimaforschung, wobei auch die mit der Tiefe sich ändernden physikalischen Eigenschaften des Gletschereises eine zentrale Rolle spielen. Zum Beispiel sind Größe, Wachstum und Orientierung der Eiskristalle zum Verständnis der Gletscherdynamik als auch des Einbaus atmosphärischer Spurenstoffe unerlässlich.

Development of a Motion Estimation and Segmentation Framework

Motion estimation from sequences of images is a hot topic in signal processing with challenges ranging from classical image processing to the fundamentals of machine learning. While research has recently focused on global optimization techniques, the full potential of approaches that estimate optical flow independently for pixel neighborhoods has not yet been fully exploited. ...

Motion and Brightness Variation Models in Optical Flow Estimation

Motion estimation is one of the most fundamental research topics in Computer Vision and is applied as first step in almost all applications that involve image sequences or other time series that produce vast amounts of data. In such algorithms, two types of models are used - one type defining how the brightness of objects vary through time, the other type describing how neighboring flow vectors realte to each other. ...

Pyramids and The State of the Art in Motion Estimation

Some extremely accurate optical flow algorithms have recently been proposed in literature. Unfortunately, it remains unclear which of the several introduced extensions to the previously known methods led to the dramatic increase of quality. Therefore, in this thesis the effects of different aspects of the new algorithms are to be studied. ...

New Ground Truth for Motion Estimation

Up to now, so-called optical flow algorithms have not been tested thoroughly enough on relevant real-world data. The reason lies in the fact that it can be extremely costly and time-consuming to create such data with real physical setups. To alleviate the problem several synthetic sequences have been proposed in literature. Unfortunately, there are still too few of such sequences and they do not cover all important situations in which motion estimation can become difficult...




Student Opportunities: Miniforschung


We offer the possibility to do small projects (Miniforschungsprojekte, Softwarepraktika, Projektpraktika, ...) in the fields of computer vision, image processing and the analysis of industrial or biomedical data. Please contact one of the group leaders to find out more.


Student Assistant


We are currently looking for an assistant researcher (HiWi) who likes to program in C++. Please contact Prof. Jaehne or Prof. Hamprecht for different projects.


Industry Partners

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Last update: 11.03.2013, 14:59
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