Bi-Annual Report 2009-2010
Advanced School for Computing and Imaging
 2012 Advanced School for Computing and Imaging
p/a DUT / EWI
P.O. Box 5031
2600 GA DELFT
The Netherlands
Phone: + 31 15 27 88032
Fax: +31 15 27 86632
asci@ewi.tudelft.nl
http://www.asci.tudelft.nl
ASCI is a Dutch graduate school established in 1993 and accredited by the Royal Netherlands Academy of Arts and
Sciences. Research groups of Delft University of Technology, Vrije Universiteit, University of Amsterdam, Leiden University,
University Utrecht, University of Twente, University of Groningen, Eindhoven University of Technology, Erasmus University
Rotterdam and Radboud University Nijmegen participate in ASCI.
Contents
Preface ...................................................................................................................................................................................... 5
1
ASCI and its Research .................................................................................................................................................... 7
1.1
About ASCI ........................................................................................................................................................... 7
1.2
Participating Groups ............................................................................................................................................. 7
1.3
ASCI Research Themes ..................................................................................................................................... 10
2
Cooperation within ASCI .............................................................................................................................................. 12
3
Scientific Output along Research Themes ................................................................................................................. 13
3.1
Contribution of VU-EW-CS ............................................................................................................................. ….13
3.2
Contribution of UvA-FNWI-SNE ......................................................................................................................... 15
3.3
Contribution of UvA-FNWI-IAS ......................................................................... Error! Bookmark not defined.18
3.4
Contribution of UvA FNWI-ISIS .......................................................................................................................... 20
3.5
Contribution of UvA-FNWI-CSA ......................................................................................................................... 21
3.6
Contribution of TUD-EWI-ST-PGS ..................................................................................................................... 23
3.7
Contribution of TUD-EWI-MM-CGCC ................................................................................................................. 24
3.8
Contribution of TUD-TNW-QI ............................................................................................................................. 25
3.9
Contribution of UL-LIACS ................................................................................................................................... 27
3.10 Contribution of UU-ICS-GMT.............................................................................................................................. 29
3.11 Contribution of TUD-L&R-FRS ........................................................................................................................... 30
3.12 Contribution of RUG-CS-SVCG........................................................................................................................ 311
3.13 Contribution of RUG-CS-IS .............................................................................................................................. 333
3.14 Contribution of TUE-ET ...................................................................................................................................... 35
3.15 Contribution of TUE-WI .................................................................................................................................... 366
3.16 Contribution of TUE-BMT ................................................................................................................................... 38
3.17 Contribution of UL-LUMC ................................................................................................................................... 39
3.18 Contribution of UT-EWI-DACS ........................................................................................................................... 41
3.19 Contribution of UT-EWI-CAES ........................................................................................................................... 43
3.20 Contribution of EUR-UMCR................................................................................................................................ 45
3.21 Contribution of RUN-UMCR ............................................................................................................................... 46
Preface
Computer and network technology have a still rapidly increasing impact on society, business, and science. Digital media are
quickly replacing classic media, and due to the availability of huge data collections Big Data has become the major challenge
of Computer Science. The research of ASCI matches very well with these developments, as for instance fast networks,
parallel processing, multi-media analysis and visualization are vital ingredients to deal with the data flood and to make
optimal use of all opportunities.
In this report an overview is provided of the research of ASCI in the period 2009-2010. We have continued to produce a biannual report instead of annual ones. There ceased to be a need for presenting all results of individual groups, as these are
readily available through the web. However, this presumes that it is known who is doing what, which requires an overview of
a wide variety of groups and researchers. With this report we aim to provide such an overview, both for participants of ASCI
and for others that are interested in our research. Instead of a focus on exhaustive enumeration of all results, we collected
for each research group in ASCI a view on current and past research, future plans and key publications, and we hope this
will lead to increasing awareness, new ideas and new collaborations.
The period 2009-2010 marked an important change in the way of organization of our major event. In 2009 the 15th ASCIconference was held in Zeewolde, as a three-day event at a Center Parcs location, following tradition. The audience
consisted of some 75 ASCI PhD’s and 25 staff members. Keynote speakers were Marc Dacier, Symantec Research Labs;
David Hogg, University of Leeds and David Stork, Ricoh Innovations
In 2010 the ASCI-conference took place in Veldhoven as part of SIREN. SIREN stands for the Scientific ICT Research Event
Netherlands, and was held in 2010 for the first time, organized by IPN, the ICT-research Platform Netherlands. SIREN is one
example of the increasing awareness in the Computer Science research community that joining forces and exchanging
information across borders of research schools is important. The program included events of all three research schools in
Computer Science: the ASCI-conference, the IPA Fall days, and the Annual SIKS-day. As a result, a broad overview of ICT
research in the Netherlands was provided and ample opportunities to network. Keynote speakers were Jasmin Fisher of
Microsoft Research Cambridge and Daniel Rueckert of Imperial College London.
In the years 2009 and 2010 two ASCI GNARP workshops have been held on Parallel Systems, and one ASCI Winterschool
on Embedded Systems.
We hope you enjoy reading this report.
Henri Bal
Scientific Director
ASCI bi-annual Report 2009-2010
5
ASCI bi-annual Report 2009-2010
6
1
ASCI and its Research
1.1 About ASCI
ASCI is a national research school on advanced computer and imaging systems. The school was founded in December
1993, and it was approved by the KNAW (Dutch Royal Academy of Sciences) in May 1995. In 2005 the school got its new
accreditation for the coming six years.
Participants in ASCI are groups from Delft University of Technology, the University of Amsterdam, the Vrije Universiteit,
Leiden University and the University of Utrecht; the University of Twente, the University of Groningen, Eindhoven University
of Technology and Radboud University Nijmegen have joined ASCI by association agreements.
ASCI performs research in two main fields: computing and imaging. In the course of time ‘imaging’ broadened to ‘multimedia
data processing’. The activities within these fields are further classified based on their main target, either Methods and
Algorithms (development of models and tools for scientific and industrial applications) or Systems and Architecture (largescale integration in areas like telematics, embedded systems, communication and networks). In both categories fundamental
and applied research is done within ASCI. Much of the ASCI research is interdisciplinary, involving multiple groups and areas
from computer science, electrical engineering, physics, and other departments.
The school organizes a graduate program and a research program covering all major subjects concerning parallel,
distributed, embedded, and real-time systems, performance analysis, image processing, image analysis, image synthesis,
sensor interpretation, pattern recognition and computer vision. Every year ASCI organises the Annual ASCI Conference, the
scientific meeting place for all participants in ASCI. Another annual activity is the GNARP workshop (GNARP Graduate
Network of Applied Research in Parallel systems) which is organized by PhD students and which is a platform for presenting
work in progress. Every two years ASCI organizes a winter/springschool, in 2008 on Embedded Systems.
1.2 Participating Groups
The following reseach groups participate in ASCI. They are represented together with their abbreviations. For each group the
members are listed (situation January 2009).
VU-EW-CS
Vrije Universiteit, Faculty of Sciences, Division of Mathematics and Computer Science, Dept. of
Computer Science
http://www.cs.vu.nl
Prof.dr. A.S. Tanenbaum, Prof.dr.ir. H.E. Bal, Prof.dr.ir. M.R. van Steen, Dr.ing. T. Kielmann,
Dr. G.E.O. Pierre, Dr. R. van Nieuwpoort, Dr.ir. H.J. Bos, Dr.B. Crispo, Dr.ir. C. van Reeuwijk,
Dr. F.J. Seinstra
UvA-FNWI-SNE
University of Amsterdam, Department of Computer Science,System and Network Engineering
http://www.science.uva.nl/research/sne
Prof.dr.ir. C.T.A.M. de Laat, Dr. P. Grosso
UvA-FNWI-IAS
University of Amsterdam, Faculty of Science, Informatics Institute, Intelligent Autonomous
Systems
http://isla.science.uva.nl
Prof.dr.ir. F.C.A. Groen, Prof.dr. D.M. Gavrila, Dr.ir. B.J.A. Kröse, Dr.ir. L. Dorst, Dr. G. Pavlin
UvA- FNWI-ISIS
University of Amsterdam, Faculty of Sciences, Informatics Institute, Intelligent Sensory
Information Systems Group
http://isla.science.uva.nl
Prof.dr.ir. A.W.M. Smeulders, Dr.ir. R. van den Boomgaard, Dr. M. Worring, Dr.Ing. J.M.
Geusebroek, Dr. Th. Gevers, Dr. C.J. Veenman, R.F. Aldershoff, Drs. C.G.M. Snoek,
Dr. N. Sebe
UvA-FNWI-CSA
University of Amsterdam, Faculty of Sicence, Informatics Institute, Computer Systems
Architecture Group
http://www.science.uva.nl/research/csa
Prof.dr. C. Jesshope, Dr. A.D. Pimentel
ASCI bi-annual Report 2009-2010
7
TUD-EWI-ST-PGS
Delft University of Technology, Faculty of Electrical Engineering, Mathematics & Computer
Science, Parallel and Distributed Systems Group
http://www.pds.ewi.tudelft.nl
Prof.dr.ir. H.J. Sips, Dr.ir. D.H.J. Epema, Prof.dr.ir. A.J.C. van Gemund, Prof.dr. C. Witteveen,
Dr. K.G. Langendoen
TUD-EWI-MM-CGCC
Delft University of Technology, Faculty of Electrical Engineering, Mathematics & Computer
Science, Computer Graphics and CAD/CAM Group
http://graphics.tudelft.nl
Prof.dr.ir. F.W. Jansen, Dr. W.F. Bronsvoort, Ir. F.H. Post, Dr. C.P. Botha
TUD-TNW-QI
Delft University of Technology, Faculty of Applied Physics, Imaging Science & Technology,
Quantitative Imaging Group
http://www.ist.tudelft.nl/qi
Prof.dr. L.J. van Vliet, Dr. B. Rieger
UL-LIACS
Leiden University, Faculty of Mathematics and Natural Sciences, Leiden Institute of Advanced
Computer Science (LIACS)
http://www.liacs.nl/research
Prof.dr. H.A.G. Wijshoff, Dr. M.S. Lew, Dr. A.A. Wolters, Dr. D.P. Huijsmans, Dr. E.M. Bakker,
Dr.ir. T.P. Stefanov, Dr.ir. B. Kienhuis, Prof.dr.ir. E.F. Deprettere
UU-ICS-GMT
Utrecht University, Faculty of Science, Department of Information and Computing Sciences,
Center for Geometry, Imaging and Virtual Environments
http://www.cs.uu.nl/centers/give/give-center.html and http://www.cs.uu.nl/groups/MG
Prof.dr. M.H. Overmars, Dr. M. van Kreveld, Dr.ir. F. van der Stappen, Dr. R. Veltkamp,
Prof.dr P.J. Werkhoven
TUD-L&R-FRS
Delft University of Technology, Faculty of Aerospace Engineering
Department of Earth Observation and Space systems (DEOS), Optical and Laser Remote
Sensing Group
http://www.lr.tudelft.nl/olrs
Dr.ir. B.G.H. Gorte
RUG-CS-SVCG
University of Groningen, Faculty of Mathematics and Natural Sciences, Johann Bernoulli
Institute of Mathematics and Computer Science, Scientific Visualization and Computer
Graphics http://www.cs.rug.nl/svcg
Prof.dr. J.B.T.M. Roerdink, Dr. H. Bekker
RUG-CS-IS
University of Groningen, Faculty of Mathematics and Natural Sciences, Johann Bernoulli
Institute of Mathematics and Computer Science, Intelligent Systems
http://www.cs.rug.nl/is
Prof.dr. N. Petkov, Dr. M.H.F. Wilkinson, Prof.dr. M. Biehl
TUE-ET
Technische Universiteit Eindhoven, Faculty of Electrical Engineering, Design Methodology for
Electronic Systems
http://www.es.ele.tue.nl
Prof.dr.ir. R.H.J.M.Otten, Dr.ir. T. Basten, Prof.dr. H. Corporaal, Dr.ir. M.C.W. Geilen,
Prof.dr.ir. G. de Haan, Dr.ir. J.P.M. Voeten
TUE-WI
Technische Universiteit Eindhoven, Department of Mathematics and Computer Science,
Visualization Group
http://www.win.tue.nl/vis
Prof.dr.ir. J.J. van Wijk, Prof.dr.ir. R. van Liere, Dr.ir. H.M.M. van de Wetering,
Dr. M.A. Westenberg, Dr. A.C. Jalba
TUE-BMT
Technische Universiteit Eindhoven, Department of Biomedical Engineering
Biomedical Image Analysis
http://bmia.bmt.tue.nl
Prof.dr.ir. B.M. ter Haar Romeny, Prof.dr. F.A. Gerritsen, Prof.dr. L.M.J. Florack,
Dr. A. Vilanova Bartroli, Dr.ir. H.C. van Assen, Dr.ir. R. Duits, Dr.ir. B. Platel
ASCI bi-annual Report 2009-2010
8
UL-LUMC
Leiden University Medical Center, division of Image Processing, laboratorium voor klinische en
Experimentele Beeldverwerking
http://www.lumc.nl/con/1010/83058/87360/87377
Prof.dr.ir. Johan H.C. Reiber, Dr.ir. B.P.F. Lelieveldt, Prof.dr. R. Nelissen
UT-EWI-DACS
University of Twente, Faculty of Electrical Engineering, Mathematics and Computer Science,
Design and Analysis of Communication Systems
http://utwente.nl/ewi/dacs/
Prof.dr. B. Haverkort, Dr.ir. G.J. Heijenk, Dr.ir. A. Pras, Dr.ir. P.T. de Boer, Dr.ir. G. Karagiannis
UT-EWI-CAES
University of Twente, Faculty of Electrical Engineering, Mathematics an Computer Science,
Computer Architecture, Design & Test for Embedded Systems
http://caes.ewi.utwente.nl
Prof.dr.ir. G.J.M. Smit, Dr.ir. A.B.J. Kokkeler, Ir. E. Molenkamp
EUR-UMCR
Erasmus MC, Departments of Radiology and Medical Informatics, Biomedical Imaging Group
Rotterdam
http://www.bigr.nl
Prof.dr. W.J. Niessen, Dr. J. Veenland, Dr.Ir. H. Vrooman
RUN-UMCR
Radboud University Nijmegen Medical Centre, Department of Radiology, Diagnostic Image
Analysis Group (DIAG) Nijmegen
http://www.diagnijmegen.nl
Dr.ir. N. Karssemeijer, Dr.ir. H.J. Huisman, Dr. M. Velikova
ASCI bi-annual Report 2009-2010
9
1.3 ASCI Research Themes
ASCI research comprises historically two main interlocked themes. The ‘C’ in ASCI stands for Computing and the ‘I’ for
Imaging. One half of ASCI is still best represented by the ‘C’ for Computation, but the ‘I’ is gradually developing into Sensory
Information, which still justifies the ‘I’ if the emphasis is shifted from the word Imaging to Information.
Within the two ASCI themes, the scientific activities can be divided in Methods & Algorithms on the one hand and Systems &
Architectures on the other. Methods & Algorithms deal with the development of models and tools as such. They are
eventually directed towards particular applications in science or industry and non-profit organizations. Systems &
Architectures deal with the large-scale design and integration of tools, and the evaluation thereof at the system level. They
are eventually directed to exemplary systems such as embedded systems, communication networks, information analysis
systems, search engines, and visualization systems. Both types of activity are targets for fundamental and applied research.
These themes and target areas are combined in the following matrix, in which the different computer science research
disciplines covered by ASCI can be placed.
Computing
(Sensory)
Information
Methods & Algorithms
Systems & Architectures
A
1. High Performance Computing
2. Computational Science
B
1. Large-Scale Information Systems
2. Distributed Systems
3. Embedded Systems
4. Sensor networks
C
1. Image and Multimedia Sensing
2. Processing
3. Interpretation and Visualization
D
1. MM Analysis & Search Systems
2. Sensing and Learning Systems
3. Acting and Visualization Systems
Within the area of Computing we have seen several important developments. The field of high performance computing
(HPC) and computational science (theme A) has shifted focus from exclusively computation-intensive computing to also
include data-intensive computing, which is required by many e-Science applications. Apart from traditional HPC, ASCI now
also studies data-centric aspects, including networking, high-performance communication, I/O, and security. The result is a
more balanced treatment of computation-intensive and data-intensive applications.
The field large-scale distributed information systems and embedded systems (theme B) has been extended considerably.
The work on operating systems is now focusing on the highly successful Minix-3. The distributed systems subtheme has
grown with many new activities on grids, peer-to-peer systems, and sensor networks, especially resource management,
network management, programming, and workflow systems. Much of this work is related to the national BSIK projects VL-e
and Freeband, and to the NWO program I-Science. ASCI´s research on embedded systems has expanded significantly.
Many ASCI groups are studying Systems-on-a-chip (SoC) designs, for example multiprocessor SoCs. They collaborate
extensively in ASCI and in large STW Progress projects. The field of sensor networks is gaining a lot of momentum within
the ASCI community. Many groups deal with aspects of sensor networks, including distributed communication protocol such
as gossiping, low-power sensor nodes, distributed information processing, and security aspects.
In the field of Sensory Information and Systems (theme D), large developments have taken place. Where sensory
information has been an academic topic of study for twenty years, it recently became part of mainstream information and
communication technology for two reasons. Firstly, massive digitization of all sensory data is taking place, for robots, science
or popular use alike. Secondly, very large-scale archives are disclosed through digital media networks, again in science and
society. Multimedia systems are no longer academic playgrounds but real platforms with many applications in science and
the arts, cultural heritage, safety services, medical imaging, industry and the population at large.
In the field of Sensory Data Methods and Algorithms (theme C), steady developments take place to unravel the structure of
multimedia data of many different sources. Examples are the understanding of the (deep) structure of images in for instance
medicine, the structure of space observed through sensor networks or mobile robots, the learning of facts from multimedia
information, and the understanding and exploitation of multimedia exchange, consumption, alteration and annotations in online social communities.
ASCI bi-annual Report 2009-2010
10
At the onset, ASCI anticipated the massive computation needs generated by the digitization of massive sensory data. This
expectation has come true as can be seen from the processing of popular resources such as Hyves and Flickr, or
professional archives like broadcast archives, or scientific resources with large archives in ecology, astronomy or geosciences. The research program and the educated PhD students of ASCI have and will remain to contribute to this
confluence.
Furthermore, for large repositories of data and knowledge, also the structuring and computation of heterogeneous and
multimedia sources of knowledge in ontologies and databases is increasingly important. This has lead to more co-operation
with members of the Research School SIKS.
ASCI bi-annual Report 2009-2010
11
2
Cooperation within ASCI
ASCI researchers collaborate through the DAS infrastructure and throught numerous externally funded collaborative
projects. Below, we describe DAS and some of the largest collaborative projects.
The DAS projects
DAS, Distributed ASCI Supercomputer, is the experimental infrastructure shared among all ASCI researchers. The first DAS
system was set up in 1997, while DAS-3 was operational in 2006. The successive systems were funded largely by three
equipment grants from NWO. Each generation consists of four to five clusters at different locations, connected by a widearea network and integrated into a single, shared, distributed system. DAS-3 pioneers a novel flexible dedicated optical
interconnect Starplane provided by SURFnet.
DAS is unique in that it is designed specifically for experimental computer science and (unlike grids) it is designed and
managed by a single organization (ASCI). The DAS systems have been highly successful and clearly demonstrated that
computer scientists need such a dedicated distributed infrastructure. Over a 100 researchers currently use DAS, including
dozens of PhD students. In the period 2005-2008, 36 PhD-students used DAS for their research project. Only few other
countries have such a facility; the most prominent similar system is the French Grid’5000, with which we collaborate
intensively.
Large-scale collaborative projects
Ever since the start of ASCI, its researchers collaborated in numerous joint projects. ASCI researchers also participated in
(or initiated) several very large collaborative programs, each involving many dozens of scientists, often from different areas.
ASCI played a leading role in most of these programs, and we feel that the efforts we invested during the preceding decade
in building a coherent research community paid off in these programs. The programs are described below.
MultimediaN is a 30 MEuro BSIK program that runs from 2004 to 2009 exploring (large-scale) digital sensory data, their
storage and their interaction. Sensory mostly focused on image and video data, with small excursions to audio, speech and
text processing. The program is well connected to industry and non-profit organizations. The operational model is based on
the work-table model where intensive co-operation at the lowest level of the organization takes place and immediate transfer
of knowledge and know-how is achieved.
VL-e (Virtual Laboratory for e-Science) is a 40 MEuro BSIK program running from 2004 to 2009 that studies virtual
laboratories for e-Science. About one third of this program consists of Computer Scientists (mostly from ASCI) who design
generic methods and tools for scientific applications from high-energy physics, medicine, bioinformatics, biodiversity, and
other areas. This program boosts our research on grid programming environments, workflow systems, problem solving
environments, resource management, and networking.
ICIS (Interactive Collaborative Information Systems) is a 14 MEuro BSIK project running from 2004 to 2009, to develop
techniques that support humans in complex information environments and to facilitate distributed decision-making
capabilities. ICIS emphasizes the importance of building actor-agent communities: close collaborations between human and
artificial actors that highlight their complementary capabilities, and in which task distribution is flexible and adaptive. It
moreover studies the interaction of humans with their artificial counterparts in such settings and how to meet the mutual
information needs.
STW Progress program. ASCI has set up a research program together with Philips Corporation on future consumer
electronics (CE) devices, resulting in three related projects that were granted from STW (the Dutch national technology
foundation) in the Progress program on embedded systems. They study different aspects of System-on-a-Chip (SoC)
architectures, including software engineering methods (SCALP), mapping domain specific (video) applications onto a domain
specific Network-on-a-Chip platform (Artemisia) and the design of NoC-based real-time systems (PreMaDoNa). The projects
collaborate intensively in regular tri-partite meetings.
NWO i-Science program. NWO has set up a cluster of three programs (GLANCE, VIEW, STARE) to advance the research in
e-Science in the Netherlands. Numerous collaborations within ASCI and between ASCI and other partners were funded by
these programs, including large-scale distributed systems projects in GLANCE (GUARD-MM, StarPlane, GUARD-G,
MicroGrids), visualization projects in VIEW (EIO, IMOVIS, MFMV, Multi-Vis), and research on astronomy applications in
STARE (Astrostream, SCARI, ASTROVIS). Almost two third of the i-Science projects contain ASCI researchers.
ASCI bi-annual Report 2009-2010
12
3
Scientific Output along Research Themes
This chapter contains the contributions of the various research groups in ASCI. The following table lists the enrollment of the
groups with respect to the themes.
Methods & Algorithms
Computing
(Sensory)
Information
Systems & Architectures
A
1. High Performance Computing
&
2. Computational Science
Wijshoff (UL)
B
1. Large-Scale Information Systems
Tanenbaum (VU)
2. Distributed Systems
Bal (VU), De Laat (UvA), Sips (TUD),
Pras (UT)
3. Embedded Systems
Corporaal (TUE), Smit (UT), Jesshope
(UvA), Haverkort (UT), Deprettere (UL)
4. Sensor networks
Langendoen (TUD), Van Steen (VU)
C
1. Image and Multimedia Sensing
Van Vliet (TUD),
Ter Haar Romeny (TUE)
2. Processing
Petkov (RUG)
3. Interpretation and Visualization
Roerdink (RUG), Jansen (TUD),
Van Wijk (TUE), Overmars (UU)
D
1. MM Analysis & Search Systems
Veltkamp (UU), Smeulders (UvA),
Lagendijk (TUD), Lew (UL)
2. Sensing and Learning Systems
Niessen (EUR), Lelieveldt (LUMC),
Karssemeijer (RUN), Reinders (TUD),
Groen (UvA)
3. Acting and Visualization Systems
Gorte (TUD)
3.1 Contribution of VU-EW-CS
Vrije Universiteit, Faculty of Sciences, Faculty of Sciences, Dept. of Computer Science
Prof.dr. A.S. Tanenbaum, Prof.dr.ir. H.E. Bal, Prof.dr.ir. M.R. van Steen, Dr.ing. T. Kielmann, Dr. G.E.O. Pierre, Dr. R.van
Nieuwpoort, Dr.ir. H.J. Bos, Dr.B. Crispo, Dr. F.J. Seinstra
Research 2009-2010
The Section Computer Systems of the VU comprises three programs: Secure and Reliable Computer Systems
(Tanenbaum), High Performance Distributed Computing (Bal), and Large-Scale Distributed Computer Systems (Van Steen).
Secure and Reliable Computer Systems
Our focus has been on doing research which we hope will lead to more dependable and secure computer systems. While
there are many aspects to the problem, much of our focus has been on operating systems. In particular, current operating
systems typically consist of millions of lines of code running together in kernel mode. A consequence of this design is that a
single bug anywhere in this code can bring down the system. We are trying to design a system that does not have this
unfortunate characteristic.
In our design, only a very small amount of code runs in kernel mode. The rest of the operating system runs as a collection of
user-mode processes. These include the file system, memory manager, process manager, and al the device drivers. We
have been able to make a design in which failures of most components are no longer fatal. In many cases a failed
component can be restarted without affecting running user processes.
In addition, we are working on a way to replace most of the operating system on the fly, while the system is running, and also
without affecting running user processes. This means that when a new release of the operating system comes out, it is not
necessary to stop and reboot the computer with the new version. For servers and embedded systems that must run 24 hours
a day, 7 days a week, this feature is quite important.
ASCI bi-annual Report 2009-2010
13
While this modular design improves security, we are also addressing security directly. This research includes novel
techniques for malware detection with particular interest in breaching-privacy software (e.g. keyloggers and spyware).
Different than other classes of malware, privacy-breaching are difficult to detect and current approaches based on attack
signatures or fingerprinting system calls of the attach do not work. We propose a class of new techniques based on memory
writes profiling that is both effective and efficient against this class of malware.
Another thread of research is related to smartphone security and privacy. We are working on extending the security model
of existing smartphone operating systems, with particular focus on Android. We designed new solution capable of enforcing
dynamically and seamless context-based policies and to provide full software isolation to protect selected application and/or
related data.
We are also investigating in new authentication methods suitable for modern platforms based on touch screens and typically
without keyboard (e.g. smartphone, tablets, ipad, etc.). We aim at transparent authentication methods, where users are not
required to perform any specific action for the sole purpose of authentication. The new methods are based on new
behavioural biometrics.
High Performance Distributed Computing
Modern real-world distributed systems consist of clusters, grids, clouds, desktop grids, and mobile devices, often extended
with accelerators like GPUs. Together with other researchers in ASCI, we have set up the DAS-4 system as a new
distributed testbed on heterogeneous distributed computing and Green IT. Writing applications for such systems has become
increasingly difficult. We try to drastically simplify the programming of such systems by studying the underlying fundamental
problems of distributed computing hand-in-hand with major applications. These efforts are integrated into a single system
called Ibis, consisting of:
-
The Ibis High-Performance Application Programming System, containing a communication library designed for
dynamically changing distributed environments (IPL), higher-level programming models, and a library
(SmartSockets) that automatically solves connectivity problems.
The Ibis Distributed Deployment System, containing the JavaGAT programming interface, a high-level GUI
(IbisDeploy) for running and managing grid applications, and the Zorilla peer-to-peer layer.
Together with other research groups, we use Ibis for research on multimedia content analysis, medical image processing,
distributed reasoning, graph algorithms, model checking, bioinformatics, and astronomy. Our work has won several awards
at international venues (e.g., CCGrid SCALE 2010).
Many scientific problems are of such complexity that solutions are obtained only by using the wide variety of computing
hardware all at once. Driven by this need for the concurrent use of multiple types of resources, we have laid the foundations
of a new computing paradigm: Jungle Computing. We have extended Ibis to enable easy implementation and deployment of
large-scale Jungle Computing applications consisting of any variety of tasks implemented using any popular language or
model (e.g. C, Java, MPI, Python, CUDA). It also can select one of several alternative implementations that calculate the
same result using different hardware. In the near future, we plan to work on real-life e-Science applications for Jungle
computing, especially Computational Astrophysics, Climate Modeling, and Remote Sensing, and to work on energy-aware
programming systems and applications.
We also study the usage of GPUs to speed up applications, especially from astronomy (LOFAR) and multimedia. In addition,
we use Ibis for distributed applications that involve mobile devices, in particular smart phones. We have built a framework
that enables context-aware applications, provides distributed decision support and advanced data-management features
(including versioning). It also supports offloading of computation and communication tasks to Clouds, to save energy and
improve performance.
Clouds have become an interesting platform for both commercial, Web-centric systems, as well as scientific computing. We
are studying cloud infrastructures and platforms for use with scientific workloads, especially the trade-offs among execution
speed and monetary costs. We have built a framework that schedules large, parameter-sweep applications within userdefined budget limitations.
We continue our work in the area of system security. Specifically, we increased our efforts in information flow tracking,
initially to chart out its usefulness and limitations. Based on this work, we then initiated a major new project on reverse
engineering, now supported by an ERC Starting Grant and a Microsoft Academic Research grant. These projects,
collectively referred to as Rosetta, aim to reverse complex binaries by extracting the data structures first. Unlike most other
projects, we use dynamic analysis and extensive information flow tracking. Once we have the data structures, we expect the
reversing of the code to be much simpler, but more importantly, we expect to be able to protect the binaries against common
memory corruption attacks like buffer overflows. In addition to these projects, we keep working on detecting attacks in fast
networks using Streamline (in the European i-Code and SysSec projects) and in mobile phones (Paranoid Android).
Large-Scale Distributed Computer Systems
LARGE-SCALE CLOUD INFRASTRUCTURES
Globule is now a subprogram lead by Guillaume Pierre. The research is dedicated to designing techniques for scalable Web
hosting. Initially, it started with the development of the Globule open-source collaborative content distribution network. It now
expands to other related topics such as scalable Web application hosting, Cloud data stores, resource provisioning, etc.
ASCI bi-annual Report 2009-2010
14
During the report period, major effort has been put into dynamically reserving resources, along with the design and
evaluation of a collaborative Wikipedia system. Future research concentrates on enhancing primitive cloud services (such as
for storage and resource allocation) with better and easier support.
EXTREME DISTRIBUTED SYSTEMS
In a separate program, we have been concentrating on very large wireless ad hoc systems. Starting with sensor networks,
this work has been extended to scenarios encompassing large crowds of people equipped with electronic badges or similar
devices. Research has concentrated on epidemic-based information dissemination and developing ultra-low duty-cycled
networks. Future work involves automatically deriving and analyzing social graphs, so that feedback to users can be
provided.
Next to wireless systems, we have started collaborations with the University of Oslo to develop secure, decentralized online
social networks.
Key Publications 2009-2010
Appuswamy, R., Moolenbroek, D.C., and Tanenbaum, A.S.: Loris - A Dependable, Modular File-Based Storage Stack, Proc.
16th Pacific Rim Int'l Symp. on Dependable Computing, pp. 165-174, 2010.
Herder, J.N., Moolenbroek, D.C. van, Appuswamy, R., Wu, B., Gras, B, and Tanenbaum, A.S.: Dealing with Driver Failures
in the Storage Stack, Proc. Fourth Latin American Symposium on Dependable Computing, pp. 119-126, 2009 (Best Paper
award).
Mazzoleni, P., Crispo. B., Sivasubramanian, S., Bertino, E. "Efficient integration of fine-grained access control and resource
brokering in grid", J. Supercomputing, Elsevier, vol.49 (1): pp. 108-126, 2009.
Henri E. Bal, Jason Maassen, Rob van Nieuwpoort, Niels Drost, Roelof Kemp, Timo van Kessel, Nick Palmer, Gosia
Wrzesinska, Thilo Kielmann, Kees van Reeuwijk, Frank J. Seinstra, Ceriel Jacobs, and Kees Verstoep Real-World
Distributed Computing with Ibis, IEEE Computer magazine, Aug. 2010
Rob V. van Nieuwpoort, Gosia Wrzesinska, Ceriel J.H. Jacobs and Henri E.Bal: Satin: a High-Level and Efficient Grid
Programming Model, ACM Transactions on Programming Languages and Systems (TOPLAS), Volume 32, Issue 3, ACM
Press New York, NY, USA, 2010
F.J. Seinstra, J. Maassen, R.V. van Nieuwpoort, N. Drost, T. van Kessel, B. van Werkhoven, J. Urbani, C. Jacobs, T.
Kielmann, and H.E. Bal. Jungle Computing: Distributed Supercomputing beyond Clusters, Grids, and Clouds In: M. Cafaro
and G. Aloisio, editors, Grids, Clouds and Virtualization, pp. 167-197, Springer-Verlag, September 2010.
Ana-Maria Oprescu, Thilo Kielmann, Bag-of-Tasks Scheduling under Budget Constraints, Proc. 2nd IEEE International
Conference on cloud Computing Technology and Science (CloudCom 2010), Indianapolis, USA, Nov/Dec 2010.
Asia Slowinska and Herbert Bos, Pointless tainting? Evaluating the practicality of pointer tainting, Proceedings of ACM
SIGOPS EUROSYS, 2009, Nuremberg, Germany.
P. Costa, J. Napper, G. Pierre and M. van Steen. Autonomous Resource Selection for Decentralized Utility Computing.
Proc. 29th Int'l Conference on Distributed Computing Systems (ICDCS), Montreal, Canada, June 2009.
K. Iwanicki, M. van Steen. On Hierarchical Routing in Wireless Sensor Networks Proc. 8th ACM/IEEE Int'l Conf. on
Information Processing in Sensor Networks (IPSN), San Francisco, California, April 2009
G. Urdaneta, G. Pierre, M. van Steen. Wikipedia Workload Analysis for Decentralized Hosting. Computer Networks, vol.
53(11), July 2009.
P. Garbacki, D. Epema, M. van Steen. The Design and Evaluation of a Self-Organizing Super-Peer Network. IEEE
Transactions on Computers, vol. 59(3):317-331, March 2010
Jiang Dejun, Guillaume Pierre and Chi-Hung Chi. Autonomous Resource Provisioning for Multi-Service Web Applications.
Proc. 19th Int'l World-Wide Web conference (WWW), April 2010.
3.2 Contribution of UvA-FNWI-SNE
System and Network Engineering research group, University of Amsterdam.
prof.dr.ir. C.T.A.M. de Laat, prof.dr. R. Meijer, dr. P.Grosso, dr. Y. Demchencko, drs. G. van 't Noordende.
The System and Network Engineering research group (SNE) focuses its research on the complexity of emerging hybrid
System and Network architectures and the associated models, protocols and system approaches for data processing in
science. The group is building tools and proof of concept applications that promote optimal use of high- speed networks. The
group develops middleware to empower applications to optimally allocate and use complex infrastructures. Security of the
required mechanisms, infrastructure, middleware, applications and the privacy of data in distributed processing environments
is an essential aspect of the research. The SNE research group is closely working together with the SNE Master
(www.os3.nl), Software Engineering Master (SE) and the Computer (Grid) Science Master programs to disseminate
knowledge through education. For more information see: System and Network Engineering (SNE)
ASCI bi-annual Report 2009-2010
15
Network Modeling
In 2009 and 2010 we have further developed the Network Description Language with support from the EU in the projects
GEYSERS, GEANT3 and NOVI, within our participation in the GigaPort3 project, and in the CineGrid project . We extended
our models to describe connected end system resources and the data they contain.
NDL is now a multi-schema language that can be used by network control planes to provision (i.e. configure) dedicated
optical connections in a hybrid network. To facilitate path finding in such environments we have developed technologyindependent schemas that wrap the multi-layer components of the network in standard interfaces. We have also further
developed NDL to make it suitable for network emulations and simulations, so that new protocols can be tested in realistic
network topologies. The group has also successfully enlarged the community of NDL users and to cooperate internationally
with other researchers toward a standardized language for network descriptions. This effort has been carried out within the
Open Grid Forum NML-WG (Network Markup Language Working Group). There have been demonstrations of the multi-layer
path finding algorithms based on NDL at several international venues as Terena, GLIF, GENI and SuperComputing
conferences. Two Ph.D thesis on the topic were awarded in 2009 and 2010.
In 2009 and 2010 we worked at the integration of two NOW-funded projects: SCARIe and StarPlane. The SCARIe project
was a collaboration between the JIVE, the UvA and SARA. StarPlane was a collaboration between UvA and VU.
SCARIe is focused on providing a software correlator for Very Long Base Interferometry, VLBI. In our implementation the
correlation task follows a hierarchical master-worker model. In StarPlane we implemented this model on top of MPI and of
the SATIN programming model, and we tested the high performances aspects of StarPlane. In our experiments Starplane is
delivering 400MB/s of throughput between the cluster sites and thus permits us to distribute medium correlation jobs to the
DAS-3 grid. This was demonstrated at the Terena and SC conferences in 2009.
CineGrid
The SNE group is a founding member of CineGrid, a collaboration in the field of high-quality media content delivery.
CineGrid recognizes the need of new collaborative tools to enable the transport of this content. Data need to move
seamlessly from the location where it is stored to the end user requesting it in a fast and automatic way. For this we need IT
infrastructures that offer enhanced Quality-of-Service suitable for real-time data distribution. In 2007 we built the first
European CineGrid distribution center. We now focus on the creation of a portal to the distributed resources that help the
Cinema community to accomplish its creative work using elastic virtualized cloud resources. This work was demonstrated in
the 2009 and in 2010 at the SuperComputing conferences.
Complex Resource Provisioning and Cloud Architecture Research
Complex Resource Provisioning (CRP) research focuses on models and architectures for on-demand CRP systems that may
include both computing resources and dedicated network. The proposed Composable Services Architecture (CSA) is used
as an architectural basis for developing GEANT Multidomain Service Bus (GEMBus). Currently this area of research is
evolving into using Clouds as a universal platform for CRP systems and general infrastructure services. Cloud architecture
research include definition and development of architectures and supporting services and mechanisms for on-demand
provisioning of Cloud based infrastructure services, including security infrastructure, considering multi-domain and multistakeholder environment.
Generic AAA architecture and policy based access control
The Generic AAA Authorization Framework architecture and its toolkit functionality was enhanced in order to support
Complex Resource Provisioning (CRP) in Cloud environment, including both network and ICT resources provisioned ondemand.
The management of the security context and authorization sessions in multi-domain dynamically provisioned services had
specific attention. The proposed solution uses the access and pilot tokens for authorization and provisioning sessions
management that allows communicating security context between domains and binding application related security context
to the provisioning session and trusted platform. Proposed solutions are being implemented in the framework of the
GEYSERS project, by extending the AAA Toolkit to work in the Enterprise Service Bus (ESB) and OSGi environments.
ASCI bi-annual Report 2009-2010
16
Actively contributed to OGF standardisation activity in the framework of the Infrastructure Services On-Demand provisioning
Research Group (ISOD-RG) and NIST collaboration on Clouds.
This work has been resulted in several publications and contribution to the OGF ISOD-RG. This work was done in the
context of the GigaPort research on networks, GEYSERS and the GEANT3 projects.
Programmable Networks and Clouds
We developed a framework that enables application developers to create complex and application specific network services.
The essence of our approach is to utilize programmable network elements to create a software representation of network
elements in the application. We show that the typical pattern of an application specific network service is a control loop in
which topology, paths, and services are continuously monitored and adjusted to match application specific qualities. We
present a platform in which network control applications can be developed and illustrate possible use cases. Based on these
use cases, new research questions are identified.
2. Korte beschrijving van verwachtingen voor de komende verslagperiode
The System and Network Engineering group is looking beyond the horizon to bring together applications and new
communication and computing technologies. We have introduced hybrid networking as a novel paradigm that provides
additional scaling capabilities to Internet communications for large sciences when using 10’s of gigabits of network links. The
technology has now further improved and it is now capable of delivering Terabit/s capacities. The coupling of this kind of
networks with computational, data and visualisation resources will require innovation in the ways applications can express
their needs to the infrastructure. Upcoming trends in e-Infrastructures for science include new capabilities in virtualisation,
Cloud based infrastructure services provisioning, programmable infrastructures, and sustainability. Planning in these kinds of
e-Infrastructures with constraints on all these capabilities gives an increase in flexibility, but also complexity. Harnessing the
complexity in planning and executing these workflows will require innovation on a fundamental level. Security, privacy, policy
and trust in data processing infrastructures are also major challenge that is under research in the group. [PG1] The handling
of medical data in distributed environments requires mechanisms that ensure privacy as required by law.
The research work is developed in the context of a number of national and international collaborations such as the EU NOVI,
GEYSERS, GEANT3 and ENVRI projects, the nationals COMMIT, Lifewatch, GigaPort3 and CineGrid-Amsterdam projects
and in communities as GLIF and CineGrid.org. We are addressing in the GEYSERS and NOVI projects, some of the key
technical challenges that enable on-demand service composition across multiple domains. We demonstrate solutions and
functionalities across test-beds involving European NRENs, GÈANT3, Cross Border Dark Fibre Initiatives, Internet2, ESNET
and GLIF connectivity infrastructure.
3. De 5-10 belangrijkste publicaties over de verslagperiode 2009-20010
Derek Groen, Steven Rieder, Paola Grosso, Cees de Laat, Simon Portegies Zwart, "A light-weight communication library for
distributed computing", IOP journal Computational Science & Discovery 3 (2010) 015002 (14pp) doi:10.1088/17494699/3/1/015002.
Simon Portegies Zwart, Tomoaki Ishiyama, Derek Groen, Keigo Nitadori, Junichiro Makino, Cees de Laat, Stephen McMillan,
Kei Hiraki, Stefan Harfst, Paola Grosso, "Simulating the Universe on an Intercontinental Grid", IEEE Computer, Volume 43,
Issue 8, Aug. 2010, page 63-70.
Guido J. van 't Noordende, Silvia D. Olabarriaga, Matthijs R. Koot, Cees Th.A.M. de Laat, "A Trusted Data Storage
Infrastructure for Grid-Based Medical Applications", International Journal of Grid and High Performance Computing, Vol. 1,
Issue 2, April-June 2009, pages 1-14.
Leon Gommans, Li Xu, Fred Wan, Yuri Demchenko, Mihai Cristea, Robert Meijer, Cees de Laat , “Multi-Domain Lightpath
Authorization using Tokens”, FGCS, Vol 25, issue 2, feb 2009, pages 153-160.
Freek Dijkstra, Jeroen J van der Ham, Paola Grosso, Cees de Laat, "A Path Finding Implementation for Multi-Layer
Networks", Future Generation Computer Systems, Volume 25, Issue 2, February 2009, Pages 142-146.
Paola Grosso, Damien Marchal, Jason Maassen, Eric Bernier, Li Xu, Cees de Laat, "Dynamic Photonic Lightpaths in the
StarPlane Network", FGCS, Vol 25, issue 2, feb 2009, pages 132-136.
ASCI bi-annual Report 2009-2010
17
Yuri Demchenko, Cees de Laat, Thierry Denys, Christian Toinard, "Authorisation session management in on-demand
resource provisioning in collaborative applications", Proceedings of the 2009 International Symposium on Collaborative
Technologies and Systems, ISBN:978-1-4244-4584-4, 2009, pages 201-208
Matthijs R. Koot, Guido van 't Noordende, Cees de Laat, "A Study on the Re-Identifiability of Dutch Citizens", 3rd Hot Topics
in Privacy Enhancing Technologies (HotPETs 2010), PETS workshop, Berlin, Germany, July 21 - 23, 2010,
http://petsymposium.org/2010/.
Rudolf Strijkers, Mihai Cristea, Cees de Laat, Robert Meijer, "Application Framework for Programmable Network Control," in
1st International Workshop on Network Embedded Management & Applications Niagara Falls, Canada: Springer, 2010.
Zhiming Zhao, Paola Grosso, Ralph Koning, Jeroen van der Ham, Cees de Laat, "Network resource selection for data
transfer processes in scientific workflow", in: Workflows in Support of Large-Scale Science (WORKS10), New Orleans in
conjunction with Supercomputing 10, 14th November.
Non-scientific book chapter publication:
Gordon Cook, "Building a National Knowledge Infrastructure; How Dutch Pragmatism nurtures a 21st Century Economy",
ISBN 978-90-814102-2-9, February 2010.
3.3 Contribution of UvA-FNWI-IAS
University of Amsterdam, Faculty of Science, Informatics Institute, Intelligent Autonomous Systems
Prof.dr.ir. F.C.A. Groen, Prof.dr. D.M. Gavrila, Dr.ir. B.J.A. Kröse, Dr.ir. L. Dorst, Dr. G. Pavlin
Research 2009-2010
We focus on intelligent autonomous systems operating in a world inhabited by humans, explored within two themes:
‘Perception and Modeling’ of the world, and `Decision Making’ to use these models for goal-directed behavior.
Perception and Modeling
This theme develops cognitive sensors that enable machines to interact intelligently and naturally with a human-inhabited
environment. We want to localize humans in their environment, track them over time, and recognize their activities. Also, we
are interested in modeling the environment the humans are living in, typically from distributed or moving sensor systems. We
have a number of projects addressing these issues.
In the project ‘Zorgen voor Morgen’ we equipped 6 assisted living apartments with sensor systems in order to monitor
Activities of Daily Living (ADL) of elderly. This project is a collaboration with the Hogeschool van Amsterdam and nursing
home Naarderheem, part of Vivium and is funded in the Pieken in de Delta program.
Another collaboration with the Hogeschool van Amsterdam is the ‘Mens voor de Lens’ project, aimed at the valorization of
knowledge in the field of computer vision. In collaboration with a company ‘Eagle Vision’ we develop an study algorithms for
people counting and pose estimation.
In the project AnaSiD we Analyse Social Interactions from a Distance using cameras and microphones. Social signal
processing is becoming extremely important and we use advanced datafusion methods for detecting dominance in a group.
The project is funded by EU Intra-European Fellowships (IEF) Marie Curie
In the NW0 CASSANDRA project we enriched the visual features used in our system for automatic aggression estimation by
tracking multiple persons with overlapping cameras as “3D blobs”: the visual features now relate to 3D human body motion
rather than to 2D scene motion. We furthermore developed a method for the adaptation of a generic 3D human model to a
particular individual in a multi-view image sequence; we showed that the use of the resulting personalized model improves
3D articulated pose recovery.
In the DIADEM project, we investigated the use of image associations in mobile phone apps to report suspicious smells more
accurately, and did large scale experiments with suitable feedback on text messages to increase the effectiveness of this
application by increasing willingness to participate. We also studied the social acceptance of robots in situations of care and
crisis management.
For ego-motion estimation of moving robots in collaboration with TNO, we developed a novel fast and robust outlier-filtering
method called EM-SE(3) that utilizes Expectation Maximization (EM) on a local linearization of the rigid body motions group
i.e. SE(3). With TNO, we study 3D reconstructioin based on handheld cameras. For the 3D reconstruction of environments
ASCI bi-annual Report 2009-2010
18
and (articulated) structures, we are extending the data processing aspects of the new field of geometric algebra, partly within
the NWO project ‘Discovery of Articulated Structures in Image Sequences’
Decision Making research theme
This theme focuses on the action side of the complete perception-action loop of an intelligent autonomous system, which
requires robust handling of uncertainty due to incomplete information. We are interested in real-world applications with direct
relevance to society. Examples include crisis management, wherein intelligent systems must analyze crises and help human
managers make decisions in real time; rescue robot teams, which help people in disaster areas; and traffic management,
which can be optimized via intelligent agents. Funding is obtained via an NWO Free Competition grant.
We developed methods using neuroevolution for the autonomous control of helicopters under unknown conditions. We also
developed new reinforcement learning algorithms that can trade off the sample efficiency of model-based methods with the
space efficiency of model-free methods without compromising convergence guarantees. Finally, we developed methods for
applying reinforcement learning to automatically optimize online learning-to-rank systems for information retrieval, such as
search engines.
Our intelligent Decision Making methods are also being applied in the RoboCup international robot competitions, notably the
Virtual Rescue competition aims to develop robot control systems in crisis environments. In this competition Amsterdam has
a shared team with Oxford University. The heterogeneous team of robots (both ground and air robots) has to coordinate
their actions with limited communication. Our effective methods have earned us several prices in the past few years.
In the problem of decentralized planning under uncertainty for teams of collaborating agents, we have focused on the case
where the agents are fully cooperative. Finding a solution for the corresponding stochastic game model (known as
DECPOMDP model) is NEXP-complete. We have provided theory concerning the existence of an optimal value function for
DECPOMDPs, as well as tighter upper bounds to this optimal value function. We also proposed algorithms that use these
tighter bounds to either obtain more accurate approximate results or to find exact solutions faster. We collaborated with
international partners to develop a multi-agent decision library, which provides functionality for planning in multi-agent
domains, as well as a set of benchmark problems.
Future research plans
Perception and modeling
In the “Looking at People” area, we will develop 3D human pose estimation algorithms that are robust to occlusion and work
with several people in the scene. We aim to integrate the richer 3D pose human pose features (MultimediaN – Professional
Dashboard) into our aggression detection system (CASSANDRA).
We will further focus on health monitoring systems. A proposal was granted to start a ‘living lab’ on health, in which we
monitor a number of elderly with simple sensor systems. This is a collaboration with VU, HvA and SIGRA (Amsterdam Care
organizations). The work on distributed cameras that was carried out two years ago will continue in the project ‘SCAN’, a
PointOne project with Philips and Eagle Vision, on the calibration of cameras in intelligent street lighting posts.
Decision Making
We will continue our work developing efficient, scalable methods for decision-theoretic planning and learning. In particular,
we will undertake new directions concerning the use of reinforcement learning to improve human-computer interaction and
the development of multi-objective methods for multi-agent planning and learning, with applications in traffic control.
Key Publications 2009-2010
Babuška, R. & Groen, F.C.A. (Eds.). (2010). Interactive collaborative information systems. (Studies in computational
intelligence, 281). Berlin: Springer.
Balaguer, B., Carpin, S., Balakirsky, S. & Visser, A. (2009). Evaluation of RoboCup maps. In Proceedings of the 9th
Performance Metrics for Intelligent Systems workshop (PerMIS'09). Association for Computing Machinery (ACM).
Tutorial: Structure-preserving representation of Euclidean motions through conformal geometric algebra.
In E. Bayro-Corrochano & G. Scheuermann (Eds.), Geometric algebra computing in engineering and computer science (pp.
35-52). London: Springer.
Relating conversational expressiveness to social presence and
acceptance of an assistive social robot. Virtual Reality, 14(1), 77-84
· Hofmann, M. & Gavrila, D.M. (2009). Multi-view 3D human pose estimation combining single-frame recovery, temporal
integration and model adaptation. In 2009 IEEE Conference on Computer Vision and Pattern Recognition: CVPR 2009 ;
Miami, Florida, USA, 20 - 25 June 2009 (pp. 2214-2221). Piscataway, NJ: IEEE.
ASCI bi-annual Report 2009-2010
19
3.4 Contribution of UvA FNWI-ISIS
University of Amsterdam, Faculty of Sciences, Informatics Institute, Intelligent Sensory Information Systems Group
Prof.dr.ir. A.W.M. Smeulders, Dr.ir. R. van den Boomgaard, Dr. M. Worring, Dr.Ing. J.M. Geusebroek, Dr. Th. Gevers,
Dr. C.J. Veenman, R.F. Aldershoff, Drs. C.G.M. Snoek, Dr. N. Sebe
Research 2007-2008
We consider the research areas of content-based access of visual data, computer vision, and systems for retrieval of video,
more specifically:
Visual search engines
For the retrieval of videos the aim is to make multimedia archives as accessible as their textual counterpart. To that end, our
research efforts concentrate on automatic semantic indexing and interactive retrieval of multimedia sources. We have
developed the MediaMill semantic video search engine, which uses a lexicon of detectable concepts in combination with
several advanced user interfaces. To value the merit of our efforts on the highest international standards, all research is
evaluated within the international TRECVID benchmark for multimedia retrieval, organized by NIST. In 2008, we obtained top
rank performance in both the concept detection task and the supervised search task, and we secured the second rank in the
automatic search task. Furthermore, we participated in the international PASCAL-VOC Visual Object Categorization
challenge for image categorization, organized by the EU funded PASCAL network. We obtained top rank performance in the
VOC challenge. These results, in such strong international benchmarks, confirm our research efforts over the past few years
have given us a leading position in the field of image and video retrieval.
Computer vision and visual cognition
An import asset in our endeavor for semantic access is indexing of semantic concepts. One approach is scene
categorization by modeling ambiguity in the popular codebook approach. There are two drawbacks to the traditional
codebook mode, which stem from the hard assignment of visual features to a single codeword. We have studied the learning
of soft relations between visual words, and the effect on categorization of many popular datasets.
Another line of research is on emotion recognition and categorization. We considered the question: can a machine learn to
perceive emotions as evoked by an artwork? Therefore, we proposed an emotion categorization system, trained by ground
truth from psychology studies. The training data contains emotional valences scored by human subjects on the International
Affective Picture System (IAPS), a standard emotion evoking image set in psychology. Our approach is based on the
assessment of local image statistics which are learned per emotional category using support vector machines.
Colour in computer vision
Our research on colour has led to an evaluation of edge-based colour constancy algorithms. The goal of color constancy is
to measure image colors despite differences in the color of the light source. Traditionally, the computational method of
obtaining this ability is by using pixel values only. Recently, methods using edges instead of pixel values have been
proposed. However, different edge types exist, such as material, shadow and specular edges. Therefore, we analyzed the
influence of different edge types on the performance of edge-based color constancy. We have shown that, on generated
data without color clipping, specular edges deliver near-perfect color constancy and that shadow edges are more valuable
than material edges. However, with color clipping, the performance using the specular edges decreases significantly, while
the performance using the material or shadow edges is less affected.
Computer vision for humans
The main direction of research here addresses the problem of sensing and understanding users’ interactive actions and
intentions for achieving multimodal human-computer interaction in natural settings. To that end, we developed and evaluated
and algorithm for accurate eye center location and tracking. The ubiquitous application of eye tracking is precluded by the
requirement of dedicated and expensive hardware, such as infrared high definition cameras. Our aim is to perform very
accurate eye center location and tracking using a simple web cam. The proposed method makes use of isophote properties
to gain invariance to linear lighting changes (contrast and brightness), to achieve rotational invariance and to keep low
computational costs. We have tested our approach for accuracy and robustness using the BioID and the Yale Face B
databases. Our system can achieve a considerable improvement in accuracy over state of the art techniques.
Spatial and extensible databases
The activities are realized in close co-operation with the CWI-database group. Amongst the results obtained the Monet
database kernel and its modules for image and geo-spatial reasoning stands out. In the area of database kernels, an
innovative experimental analysis uncovered the lack of performance improvement in database technology over the last
decade. The underlying reason is the relative progress in CPU- and RAM-technology, which shows an increasing
ASCI bi-annual Report 2009-2010
20
performance bottleneck. This observation has led to novel techniques to measure the resource waste and new database
algorithms to avoid resource stales. The open-source version of the MonetDB system has been downloaded more than
30.000 times.
Future Research Plans
Colour in computer vision will be structurally positioned within the Faculty by the recent VICI award for Dr. Gevers.
For video search engines, we are starting a close collaboration with the Faculty of Humanities, aiming at combined research
in a Centre for Content Culture and Technology. Furthermore, we intent to collaborate with the Cognition Centre of the
university on various aspects of vision. For computer vision and learning, we intent to concentrate on recognition and
similarity-learning of scenes, objects, and actions.
We will continue the line of research as initiated for computer vision for humans and for visual data mining for safety. Recent
EU funding has strengthened this line of research.
Key Publications 2007-2008
A. Diplaros, N. Vlassis and Th. Gevers. A Spatially Constrained GenerativeModel and an EM Algorithm for Image
Segmentation. IEEE Trans. on Neural Networks, 18(3), 798-808, 2007.
J.C. van Gemert, J.-M. Geusebroek, C.J. Veenman, A.W.M. Smeulders, Kernel Codebooks for Scene Categorization, ECCV,
Volume 3, page 696-709, 2008.
H.T. Nguyen, Q. Ji, and , A.W.M. Smeulders, Spatio-Temporal Context for Robust Multitarget Tracking. IEEE Transactions
on Pattern Analysis andMachine Intelligence, 29, 52-64, 2007.
K. van de Sande, Th. Gevers, C. G. M. Snoek, Evaluation of Color Descriptors for Object and Scene Recognition, IEEE
Conference on Computer Vision and Pattern Recognition, 2008.
Cees G. M. Snoek, M. Worring, O. de Rooij, K. E. A. van de Sande, R. Yan, A. G. Hauptmann, VideOlympics: Real-Time
Evaluation of Multimedia Retrieval Systems, IEEE Multimedia, Volume 15 (1), page 86-91, 2008.
H.M.G. Stokman and Th. Gevers, Selection and Fusion of Colour Models for Image Feature Detection. IEEE Trans. on
Pattern Analysis and Machine Intelligence, 29, 371-381, 2007.
R. Valenti and Th. Gevers, Accurate Eye Center Location and Tracking Using Isophote Curvature, IEEE Conference on
Computer Vision and Pattern Recognition, 2008.
A. Gijsenij, Th. Gevers, M. Lucassen, A Perceptual Comparison of Distance Measures for Color Constancy Algorithms,
European Conference on Computer Vision, Volume 1, page 208-221, 2008.
J. van de Weijer, Th. Gevers and A. Gijsenij, Edge-Based Colour Constancy. IEEE Trans. on Image Processing, 16, 22072214, 2007.
M. Worring and G. Schreiber, Semantic, image and video indexing in broad domains, IEEE Transactions on Multimedia, 9,
909-911, 2007.
3.5 Contribution of UvA-FNWI-CSA
UvA-FNWI-csa
Computer Systems Architecture Group
Informatics Institute, Faculty of Sciences, University of Amsterdam
Dr. Clemens Grelck, Prof. Dr. Chris Jesshope, Dr. Andy Pimentel
Research 2009-2010
The predictable but quite unprepared for shift from frequency scaling to concurrency in computer systems architecture has
played into the strengths in the computer systems architecture group. We have extensive expertise both in concurrency
ASCI bi-annual Report 2009-2010
21
management for systems-on-chip (SoC) design and in the design and use of high-performance computing (HPC) systems.
This shift now puts concurrency firmly into mainstream computing. The major motivation for this seismic shift in computer
architecture is power dissipation and we see power management as a key motivator for our research over the coming fiveyear period. It will span a broad range of computing platforms, from SoC to HPC, although we anticipate a convergence of
techniques and methodology used to optimise design across this range. In all areas we see a shift in the provisioning of
computing away from a focus on achieving theoretical peak performance and more towards achieving optimal efficiency
while a resource is being used. This in turn leads to a requirement for dynamic provisioning. Our strategy will be to match the
specific requirements of the heterogeneous components of a computation to processing resources in order to minimize
energy consumption. This in turn requires the characterisation of both computations and targets for non-functional
capabilities and requirements. A major emphasis here will be on maintaining spatial locality. We will therefore adopt
appropriate concurrency models (with formal contacts) that expose these requirements and our approach will embrace both
static and dynamic optimizations.
In the embedded system domain, one of the most important challenges is the development of design tools that allow for fully
automated system-level synthesis and programming of multi-processor SoC architectures. Our joint work with Leiden
University in developing the Daedalus system-level MP-SoC synthesis framework offers a fully integrated tool-flow in which
the various steps of system-level MP-SoC synthesis, such as parallelisation, design space exploration, hardware-software
partitioning, application mapping and system prototyping, are highly automated.
Our work on fine-grain threaded architectures with data-driven scheduling using the SVP concurrency model will continue but
we are also exploring software implementations of SVP on other emerging multi-core architectures such as Niagara and
Intel's SCC. This allows us to explore multi-grain architecture and develop an infrastructure to support such an approach.
One of the major directions in this work is the development of a coherent set of operating system services that support space
sharing in these heterogeneous environments and yet provide a secure operating environment that can be scaled from chiplevel micro-grids to globally distributed Grids.
Future research plans
One of the major challenges, especially in mainstream computing, will be in making these systems programmable without
specialised concurrency knowledge and we have designed programming language support to express parallel computations
and systems at a very high level of abstraction and developed compilation technologies that effectively map the abstract
descriptions to concurrent computing environments. Our long-term vision is in the direction of a compilation infrastructure
that automatically adapts running programs derived from high-level specifications to a heterogeneous and dynamically
varying execution environment based on continuous reflection of execution parameters. For our work in the embedded
systems domain, future research extends in two main directions: 1) introducing technology awareness at the system level to
e.g. improve the performance and energy-efficiency of the resulting designs, and 2) introducing adaptivity to handle changing
workloads by dynamically (re-)mapping applications or even reconfiguring system components.
Key publications 2009 – 2010

M. W. van Tol, C. R. Jesshope, M. Lankamp and S. Polstra, “An implementation of the SANE Virtual Processor
using POSIX threads”, Journal of Systems Architecture, Volume 55, Issue 3, March 2009, pp 162-169.

K. Bousias, L. Guang, C.R. Jesshope, M. Lankamp, “Implementation and Evaluation of a Microthread Architecture”,
Journal of Systems Architecture, Vol. 55, Issue 3, March 2009, pp 149-161.

Thomas A. M. Bernard, Clemens Grelck, Chris R. Jesshope, “On the Compilation of a Language for General
Concurrent Target Architectures”, Parallel Processing Letters 20(1): 51-69, 2010.

Chris R. Jesshope, Mike Lankamp, , “The implementation of an SVP many-core processor and the evaluation of its
memory architecture”, SIGARCH Computer Architecture News 37(2): 38-45, 2009.

Clemens Grelck, Sven-Bodo Scholz, Alexander V. Shafarenko, “Asynchronous Stream Processing with S-Net”,
International Journal of Parallel Programming 38(1): 38-67, 2010.

P. van Stralen and A. D. Pimentel, "A High-level Microprocessor Power Modeling Technique based on Event
Signatures", in the Journal of Signal Processing Systems, pp. 239-250, Vol. 60 (No. 2), Aug. 2010, Springer.
ASCI bi-annual Report 2009-2010
22

S. Jaddoe, M. Thompson, and A. D. Pimentel, "Signature-based Calibration of Analytical Performance Models for
System-level Design Space Exploration", in Transactions on High-Performance Embedded Architectures and
Compilers (Trans. on HiPEAC), Vol. 4 (No. 4), 2009.

Gerstlauer, C. Haubelt, A.D. Pimentel, T. Stefanov, D.D. Gajski, and J. Teich, "Electronic System-Level Synthesis
Methodologies", in IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems, pp. 15171530, Vol. 28 (No. 10), Oct. 2009.

P. van Stralen and A.D. Pimentel, "Scenario-Based Design Space Exploration of MPSoCs", in the Proc. of the
IEEE Int. Conference on Computer Design (ICCD '10), Amsterdam, Netherlands, Oct. 2010.
3.6 Contribution of TUD-EWI-ST-PGS
Delft University of Technology, Faculty of Electrical Engineering, Mathematics & Computer Science, Parallel and Distributed
Systems Group
Prof.dr.ir. H.J. Sips, Dr.ir. D.H.J. Epema, Prof.dr.ir. A.J.C. van Gemund, Prof.dr. C. Witteveen, Dr. K.G. Langendoen
Research Report
The mission of the PDS group of TU Delft is to contribute to the scientific advancement in selected fields of parallel and
distributed systems both in fundamental as well as application driven aspects; fundamental in the sense that we aim at the
development and evaluation of generic methods and techniques, application-driven in the sense that also actual
implementations of the concepts are investigated. The PDS group performs research in the following three areas.
In the area of grid and cloud computing, we focus on many aspects of resource management and scheduling, with as our
research vehicle the KOALA multicluster scheduler, which has been deployed on different generations of the DAS. We have
added support to KOALA for Bags-of-Tasks (BoTs) and workflows, and scheduling policies for these application types. We
have also completed our research into processor co-allocation for parallel applications. In addition, we have done a thorough
investigation into failures and their correlations in large-scale distributed systems of many different types. Finally, we have
started working on the performance analysis of clouds.
In the area of multi-core programming, we have worked on case-studies, programming models, and application
characterization. We have started with hardware-centric programming of several case-studies: image content analysis, radioastronomy, medical imaging, basic and advanced signal processing. We have done several studies to compare the available
multi- and many-core platforms in terms of performance and we have thoroughly investigated the programming models used
for these architectures, with a special focus on portability and programmability. Finally, we have started to work on
application characterization, using quantitative metrics to determine good matches between applications and platforms.
In the area of peer-to-peer and online social networks, we focus on many aspects of video distribution, with as our
research vehicle the BitTorrent-based P2P system Tribler, of which we have made available multiple releases. In particular,
we have included support for video-on-demand and live streaming into Tribler, and we have improved and investigated the
BarterCast reputation mechanism. In addition, we have completed our research into super-peer networks, we have
performed a large-scale measurement of private and public BitTorrent communities, and we have performed multiple
performance analysis studies of swarm-based P2P systems.
Research Plans
In the area of grid and cloud computing, we will incorporate support and scheduling policies for MapReduce applications
into KOALA, we will investigate cloud performance, and we will perform a thorough application-oriented investigation of the
current KOALA mechanisms and policies. In the area of multicore programming, we will continue working on many-core
programming, tackling three issues: (1) novel optimizations and auto-tuning techniques for many-core architectures, (2)
application characterization and its applicability to application-centric programming of many-cores, and (3) we will start a new
direction of research towards large-scale graph-processing algorithms for heterogeneous systems built with many-core
architectures. In the area of peer-to-peer and online social networks, we will continue our investigations of reputation
mechanisms, our performance modeling studies of swarm-based P2P systems, and our design and implementation efforts in
video-on-demand. Furthermore, we will investigate wiki-style P2P systems, a new Internet transport protocol for P2P video
distribution, and online social networks for games.
ASCI bi-annual Report 2009-2010
23
Key publications
A.S. van Amesfoort, A.L. Varbanescu, H.J. Sips, and R.V. van Nieuwpoort, “Evaluating Multi-Core Platforms for HPC DataIntensive Kernels,” In Proceedings ACM Computing Frontiers, pp. 207-216, 2009.
O.O. Sonmez, B. Grundeken, H.H. Mohamed, A. Iosup, and D. Epema, “Scheduling Strategies for Cycle Scavenging in
Multicluster Grid Systems,” 9th IEEE/ACM Int'l Symp. on Cluster Computing and the Grid (CCGrid), pp. 12-19, 2009.
O.O. Sonmez, N. Yigitbasi, A. Iosup, and D.H.J. Epema, “Trace-based Evaluation of Job Runtime and Queue Wait Time
Predictions in Grids,” Proceedings of the 18th ACM International Symposium on High Performance Distributed Computing
(HPDC), pp. 111-120, 2009.
A.L. Varbanescu, H.J. Sips, K.A. Ross, Q. Liu, A. Natsev, J.R. Smith, and L.-K. Liu, “Evaluating Application Scenarios on the
Cell/B.E.,” Concurrency and Computation: Practice and Experience, Vol. 21, pp. 85-100, 2009.
P. Garbacki, D.H.J. Epema, and M. van Steen, “The Design and Evaluation of a Self-Organizing Super-Peer Network,” IEEE
Transactions on Computers Vol. 59, pp. 317-331, 2010.
D. Kondo, B. Javadi, A. Iosup, and D.H.J. Epema, “The Failure Trace Archive: Enabling Comparative Analysis of Failures in
Diverse Distributed Systems,” 10th IEEE/ACM Int'l Symp. on Cluster, Cloud, and Grid Computing (CCGrid), pp. 398-407,
2010 (Best Paper Award).
M. Meulpolder, L. D'Acunto, M. Capota, M. Wojciechowski, J.A. Pouwelse, D.H.J. Epema, H.J. Sips, “Public and private
BitTorrent communities: A measurement study,” In IPTPS 2010.
O.O. Sonmez, H.H. Mohamed, and D.H.J. Epema, “On the Benefit of Processor Co-Allocation in Multicluster Grid Systems,”
IEEE Trans. on Parallel and Distributed Systems, Vol. 21, pp. 778-789, 2010.
3.7 Contribution of TUD-EWI-MM-CGCC
Delft University of Technology, Faculty of Electrical Engineering, Mathematics & Computer Science, Computer Graphics and
CAD/CAM Group
Prof.dr.ir. F.W. Jansen, Dr. W.F. Bronsvoort, Ir. F.H. Post, Dr. C.P. Botha
ASCI report 2009 – 2010
Delft University of Technology
Faculty of Electrical Engineering, Mathematics and Computer Science
Computer Graphics
http://graphics.tudelft.nl
Dr. Ir. A.R. Bidarra, Dr. Ir. C.P. Botha, Dr. W.F. Bronsvoort, Prof. Dr. Ir. F.W. Jansen, Ir. F.H. Post
Computer graphics
Research in this programme is concerned with modelling of 3D objects for virtual worlds (gaming), and with visualisation for
scientific and medical applications.
Visualisation is concerned with analysis and display of large data sets. The purpose is to provide insight by extracting
important information from data sets, and supporting interactive exploration of the data. The
focus of our research is on improved 3D interaction tools, on data reduction and data
exploration techniques. The developed techniques are integrated within a virtual envrionment.
A typical application is the visualization of environmental data (point clouds) and climate data
(e.g. for extreme weather predictions). Real-time simulation and integrated visualisation and
computational steering is now feasible on desktop computers with GPU support.
Another important application area is the processing and visualization of various medical imaging modalities, such as CT and
MRI. Medical visualization in the group runs along two major lines: Visual Analysis for Medical
Applications and Surgical Planning. In the first line, we work on the visualisation of multi-field
data and higher order data such as diffusion tensor imaging. We have recently started projects
ASCI bi-annual Report 2009-2010
24
on molecular imaging in order to visualize biological processes at cellular and molecular level
over multiple time points and across multiple subjects, and also on the visual analysis of
medical retrospective cohort studies, containing multi-modal multi-timepoint datasets of multiple
patients. In the second line, we develop surgical simulation tools for the pre-operative planning
of shoulder replacement surgery and minimally-invasive hip refixation.
Game technology is concerned with advanced modelling for the next generation of entertainment and serious games, in
particular the dynamic generation and consistency maintenance of virtual worlds. Ultimate goal
is to effectively assist game level designers in expressing and consistently maintaining in a
model of the virtual world all intent specified throughout the various iterations of the design
process.
Research Plan
In the coming years, we will focus our research efforts on the following goals:
 Game adaptivity of content and gameplay: enable runtime content generation in order to materialize playermatching game worlds from personal gameplay requirements.
 Large-scale modeling of semantics for (serious) games: in this area, we are investigating better and easier ways of
integrating semantics into the game development process.
 Extension and evaluation of visual analytics in population imaging (PI) research. In PI research, mixed-modality
(multiple image volumes, blood measurements, genetics) are made of thousands of persons over multiple
irregularly spaced timepoints, the research goal being to find retrospectively data features that predict pathology.
 Hyper-realism in interactive visualization: We have recently started investigating the role of raytraced lighting in
interactive volume rendering, resulting in new levels of realism.
 Model-based anatomy and surgical planning: The development of detailed models of human anatomy, based on
multiple data sources such as high-resolution crysections, immunohistochemistry and traditional 3D imaging
modalities, could lead to significantly improved anatomical visualization and surgical planning.
 Integrated Simulation and Visualization of Flow Phenomena: we initiated work on hardware-accelerated
simulations with integrated 3D visualization to allow real-time interactive exploration of flow phenomena for the first
time (collaboration with researchers on atmospheric processes, flooding scenarios).
 Interactive exploration of (3D) sensor data: While 3D sensing techniques (e.g. LIDAR, depth ranging) become more
prevalent, we aim to address the real-time aspects of processing and and visualization of this data work flow,
enabling touch-based, 3D and augmented reality interaction.
 For video surveillance tasks, we are exploring the integration of video streams with synthetic and reconstructed 3D
models.
Five Key Publications
1.
2.
3.
4.
5.
Bronsvoort WF, Bidarra R, van der Meiden H and Tutenel T (2010) The Increasing Role of Semantics in Object
Modeling. Computer-Aided Design and Applications 7(3): 431-440.
de Carpentier GJP and Bidarra R (2009) Interactive GPU-based procedural heightfield brushes. In: Proceedings of
Fourth International Conference on the Foundations of Digital Games, 26-30 April, Port Canaveral, FL, pp. 55-62.
P. Kok, M. Baiker, E. A. Hendriks, F. H. Post, J. Dijkstra, C. W. G. M. Löwik, B. P. F. Lelieveldt, and C. P. Botha,
"Articulated Planar Reformation for Change Visualization in Small Animal Imaging," IEEE Transactions on
Visualization and Computer Graphics, vol. 16, no. 6, pp. 1396–1404, 2010.
P. R. Krekel, E. R. Valstar, F. H. Post, P. M. Rozing, and C. P. Botha, “Combined Surface and Volume Processing
for Fused Joint Segmentation,” The International Journal for Computer Assisted Radiology and Surgery, vol. 5, no.
3, pp. 263–273, 2010.
Gerwin de Haan, Huib Piguillet, Frits Post, "Spatial Navigation for Context-Aware Video Surveillance," IEEE
Computer Graphics and Applications, pp. 20-31, September/October, 2010.
3.8 Contribution of TUD-TNW-QI
Delft University of Technology, Faculty of Applied Physics, Imaging Science & Technology, Quantitative Imaging Group
Prof.dr. L.J. van Vliet, Dr. B. Rieger
Quantitative Imaging Group (TUD-TNW-IST-QI) 2009-2010
ASCI bi-annual Report 2009-2010
25
The Quantitative Imaging Group invents new image-based measurement principles through a combination of imaging
physics and digital imaging leading to novel algorithms for image processing, image analysis, image reconstruction, and
image recognition. We perform fundamental research with a focus on applications in Life Sciences and Health in a multidisciplinary environment of technical and (pre-)clinical scientists and in close collaboration with leading industrial parties. The
core competence of the group is on quantitative imaging, i.e. extracting quantitative information from multi-dimensional
image data sets. Important contributions herein have been made to the field of computational microscopy, super-resolution
reconstruction, an medical imaging.
Computational microscopy offers tools to break the diffraction barrier in single molecule fluorescence microscopy and to
achieve nanometer resolution in 3D electron-tomographic image volumes of frozen hydrated biological specimen. These
techniques open new avenues for studying the molecular machinery inside the cell. We have developed an iterative
algorithm that converges to the maximum likelihood estimate of the position and intensity of a single fluorophore. Our
technique efficiently computes and achieves the Cramér-Rao lower bound, an essential tool for parameter estimation. An
implementation of the algorithm on graphics processing unit hardware achieved more than 105 combined fits and CramérRao lower bound calculations per second, enabling real-time data analysis for super-resolution imaging and other
applications
Super-resolution reconstruction. Combining breakthroughs in filtering, estimation and inverse problems have led to methods
capable of achieving super-resolution reconstruction in undersampled image sequences. We have obtained super-resolution
for small moving targets against a highly cluttered background, i.e. objects containing entirely of boundary pixels that mix a
space varying fraction of the object with a varying structured background.
In medical image analysis we have worked on virtual colonoscopy, dual tensor atlas building in DTI, and multiobject registration of wrist bones subject to global constraints. We realized Computer Aided Detection of polyps in CT
colonography, a diagnostic tool for minimally invasive early detection of colon cancer, based on protrusion detection in
surface rendered and volumetric data. In the coming years we further improve our methodology by permitting limited patient
preparations and low-dose CT recordings. In neuro image analysis we try to differentiate in an early stage between
physiologically (aging) and pathologically (e.g. Alzheimer's disease) in the brain, we search for spatiotemporal biomarkers of
neurological disorders using sophisticated image processing and pattern recognition methods in Diffusion Weighted MRI
data.
Expectations for 2011-2012
In computational microscopy we are developing novel algorithms for super-resolution. In optical microscopy we work on
exploiting the blinking characteristics of fluorophors to disentangle overlapping point-spread-functions and in electron
tomography we are working on better algorithms for modelling the imaging process. For phase contrast tomography with
electrons and x-rays we are developing quantitative forward models for designing new acquisition and reconstruction
strategies, sparsity promoting image reconstruction techniques for solving underdetermined problems, and image processing
algorithms capable of handling very noise data. In medical image analysis for CT colonography we expect to reach several
milestones: to develop novel algorithms for computer cleansing of mild patient preparations and of very low dose. In
abdominal imaging we are developing tools for non-invasive assessment of bowel inflammation in Crohn’s disease. In
diffusion weighted MRI we aim to develop advanced algorithms permitting the quantification of diffusivity in both constituents
of crossing fibre bundles in the human brain.
Key-publications 2009
1. M. van de Giessen, G.J. Streekstra, S.D. Strackee, M. Maas, K.A. Grimbergen, L.J. van Vliet, F.M. Vos, Constrained
registration of the wrist joint, IEEE Transactions on Medical Imaging, 28(12), 2009, 1861-1869
2. F.G.A. Faas, B. Rieger, L.J. van Vliet, D.I. Cherny, DNA deformations near charged surfaces: electron and atomic force
microscopy views, Biophysical Journal, Vol 97, 2009, 1148-1157.
3. S. Brinkers, H.R.C. Dietrich, F.H. de Groote, I.T. Young, B. Rieger, The Persistence Length of Double Stranded DNA
Determined Using Dark Field Tethered Particle Motion, Journal of Chemical Physics, 130(21):215105, 2009.
4. E.J. Aukema, M.W.A. Caan, N. Oudhuis, C.B.L.M. Majoie, F.M. Vos, L. Reneman, B.F. Last, M.A. Grootenhuis, A.Y.N.
Schouten-van Meeteren, White matter fractional anisotropy correlates with speed of processing and motor speed in
young childhood cancer survivors, International Journal of Radiation Oncology Biology Physics, Vol. 74, Issue 3, 2009,
837-843.
5. M.W.A. Caan, C.A. Sage, M.M. van der Graaf, K.A. Grimbergen, S.G. Sunaert, L.J. van Vliet, and F.M. Vos, Dual tensor
atlas generation based on a cohort of coregistered non-HARDI datasets, in: G.-Z. Yang et al. (Eds.), Medical Image
Computing and Computer-Assisted Intervention - MICCAI 2009 (12th International Conference, London, UK, September
20-24, 2009, Proceedings, Part I), Lecture Notes in Computer Science, vol. 5761, Springer-Verlag Berlin Heidelberg,
2009, 869-876.
Key-publications 2010
1. V.F. van Ravesteijn, C. van Wijk, F.M. Vos, R. Truyen, J.F. Peters, J. Stoker, L.J. van Vliet, Computer aided detection of
polyps in CT colonography using logistic regression, IEEE Transactions on Medical Imaging, Vol. 29, No. 1, 2010, 12031, art. no. 5196824.
ASCI bi-annual Report 2009-2010
26
2.
3.
4.
5.
C. van Wijk, V.F. van Ravesteijn, F.M. Vos, L.J. van Vliet, Detection and segmentation of colonic polyps on implicit
isosurfaces by second principal curvature flow, IEEE Transactions on Medical Imaging, Vol 29, No. 3, 688-698, 2010,
art.no. 5423301.
M. Vulovic, B. Rieger, L.J. van Vliet, A.J. Koster, R.B.G. Ravelli, A toolkit for the characterization of CCD cameras for
transmission electron microscopy, Acta Crystallographica Section D- Biological Crystallography, D66, 2010, 97-109.
C.S. Smith, N. Joseph, B. Rieger, K.A. Lidke, Fast, single-molecule localization that achieves theoretically minimum
uncertainty, Nature Methods, 2010, 7(5):373-375.
A.W.M. van Eekeren, K. Schutte, L.J. van Vliet, Multi-frame super-resolution reconstruction of small moving objects,
IEEE Transactions on Image Processing, Vol. 19, No. 11, 2010, 2901-2912.
3.9 Contribution of UL-LIACS
Leiden University, Faculty of Mathematics and Natural Sciences, Leiden Institute of Advanced Computer Science (LIACS)
Prof.dr. H.A.G. Wijshoff, Dr. M.S. Lew, Dr. A.A. Wolters, Dr. D.P. Huijsmans, Dr. E.M. Bakker, Dr.ir. T.P. Stefanov,
Dr.ir. B. Kienhuis, Prof.dr.ir. E.F. Deprettere
Research 2009-2010
The mission of LIACS research program ‘Computer Systems and Imagery & Media’ is to improve the state of the art in
systems and media analysis, and to guide new research areas which are of clear importance to society. In our research, we
rigorously demonstrate the effectiveness of the resulting novel techniques and contribute to the leading evaluation and
benchmarking projects. This programme covers a wide variety of research topics, including embedded systems and
software, parallel and distributed computing, and media research and technology, including imaging and its applications to
bio informatics. The research effort is clustered around three themes.
Embedded Systems and Software
The research in embedded systems and software deals with modelling of applications and multi-processor architectures, and
mapping methods in these domains, at various levels of abstraction, for exploration and design, theoretically and practically,
down to real platforms. The working methodologies relies on advocating and applying modern state–of–the–art Software
Engineering Practice both in the way the group’s projects are integrated, documented, and assessed, and in the way
software that implements research results is written, tested and assessed. There are several themes that are researched in
several projects and are jointly contributing to the knowledge, expertise, and skills on local, national, and international
competitive settings. The research focuses on strategically well-chosen core activities that are briefly described below:
•
Research on novel methods and tools for automated parallelization and porting of dynamic/adaptive applications
on an MPSoC architecture. These tools will simplify the manual effort that is currently needed by the application developers
to transfer sequential software in a concurrent programming model.
•
Research on novel methods, techniques, and tools for designing Embedded Multi-processor Systems-on-Chip with
adaptivity and reliability support. The static approach to embedded MPSoC design will be extended to address adaptivity
requirements by setting up a methodology and the corresponding tool support for adaptive (i.e., run-time) mapping of
application tasks to the underlying architecture resources to cope with QoS and/or dependability demands.
Research on novel techniques and tools to tightly couple system-level power/ energy modeling with system-level synthesis
techniques in order to significantly improve the trustworthiness of system-level power/energy models and to quickly explore
and design energy-efficient MPSoCs. More specifically, MPSoC synthesis and measurement techniques are investigated
that are needed for dynamically validating and calibrating system-level power/energy and performance models.
Parallel and Distributed Computing Systems
Research in parallel and distributed computing concentrates on: (optimizing) compilers, grid computing, application drivers
for large-scale applications, and large-scale database systems. As within the embedded system research activities the
approach taken evolves around the mapping problem of (large scale) applications onto (existing) computing platforms. The
research focuses on strategically well–chosen core activities that are briefly described below:
•
Performance Predictions and Resource Management in a Grid
To design an efficient scheduler is one of the most challenging problem for the efficient utilization of parallel computers. This
leads to a need for representative workload models that allow the generation of specific workloads for the evaluation of
different scheduling techniques. During 2009 and 2010 we have developed a new workload model toolkit. In addition an
efficient runtime predictor has been developed for designing smart scheduling decisions.
ASCI bi-annual Report 2009-2010
27
•
HIRLAM on a Grid Environment
The performance of the operational numerical weather forecast system HIRLAM on the new DAS-3 grid environment was
evaluated. DAS-3 consists of five clusters located at five different locations. Furthermore, we investigated the possibilities in
overlapping computations and communications for HIRLAM to decrease the communication overhead.
•
Data Structure Independent Programming
Traditional analyses break down when they encounter pointer based codes. Therefore, as the potential performance of
processors increases, new means must be explored to extract parallelism. We have developed new pointer optimizations by
using split pool techniques combined with aggressive sublimation techniques to eliminate pointer occurrences in scientific
computing based codes
•
Reshaping Memory Access Patterns
Using a combination of compile-time and run-time techniques, the access patterns of pointer based codes are restructured
such that the resulting code is analyzable by existing techniques for regular codes. These steps result in an intermediate
code, which is amenable to data dependency analysis and as such can be compiled into a highly optimized executable.
Media Systems
Media systems evolves around two approaches. The first approach focuses on the scientific investigation of novel directions
and paradigms in the field of multimedia retrieval with emphasis on content-based methods in images, video, audio, and
scientific data. As a special application, the integration bio-imaging information and image information with other biomolecular information resources is studied. The second approach is the embedding of human beings in a computerized
world, which is studied by creating such embeddings.
Media systems evolve around the scientific investigation of novel directions and paradigms in the field of multimedia retrieval
with emphasis on content-based methods in images, video, audio, and scientific data. As a special application, the
integration bio-imaging information and image information with other bio-molecular information resources is studied.
In multimedia retrieval, we completed the second stage of research and experiments on the new paradigm of Artificial
Imagination in multimedia information retrieval. We also introduced the largest open-access and legally redistributable
community benchmark for image retrieval (over a million images). We also developed a new salient point paradigm which
outperforms the leading descriptors from the research community such as SIFT and SURF.
In the area of bioinformatics, we developed new algorithms for genotype/phenotype data mining. The development of an
Hidden Markov Model based classifier for biological imagery was completed and tested under a wide variety of different
tissue samples. A new method for viewing the development of micro-tubules was completed.
In the next phase, we will continue investigating a general artificial imagination model. The artificial imagination will be used
for improving both machine learning and information retrieval.
Future Research Plans
The research activities changed over the last couple of years from a strong focus on high performance computer systems
towards more and more data-oriented computations. Specific examples of these shifts can be found in the themes “Content
based image retrieval”, in which the main challenge lies in indexing and classifying tremendous amounts of visual images,
“HIRLAM on the Grid”, in which the main challenge will be to integrate and reformat tremendous amounts of meteorological
data distributed over a number of different networks (the Internet, the world-wide meteorological World Weather Watch
network, etc.), “Data compilation”, in which the direct target is the integration and coupling of large legacy database
applications and “Hardware dependant Software (HdS) solutions to improve IP integration in the SoC design process (quality
/ productivity)”, in which the operating system and the application software are separated from the underlying hardware.
As our programme has grown, our research activities have also evolved to address important new research areas and critical
challenges in transferring technology from research labs to society. In particular, it is well known that research systems,
which work well in a laboratory environment, may not work well in the real world. In some cases, this is because there was a
significant lack of communication between the researchers and the practitioners/users. In other cases the problem has to do
with developing high quality evaluation and benchmarking procedures, which reflect real world usage.
The changes as described above became firmly incorporated into the research activities in this programme. In fact our
research activities became more focused on data representation, processing data representation, and the reduction of data
representation by employing (semantic) transformation and interpretation of media data.
Key publications
A. Gerstlauer, C. Haubelt, A.D. Pimentel, Todor Stefanov, D.D. Gajski, and J. Teich, "Electronic System-Level Synthesis
Methodologies", IEEE Transactions on Computer-Aided Design of Integrated Circuits and Systems (TCAD), vol. 28, No. 10,
pp. 1517-1530, Oct 2009.
ASCI bi-annual Report 2009-2010
28
Ozana Silvia Dragomir, Todor Stefanov, and Koen Bertels, "Optimal Loop Unrolling and Shifting for Reconfigurable
Architectures", ACM Transactions on Reconfigurable Technology and Systems (TRETS), vol. 2, No. 4, pp. 1-24, Sept 2009.
Harmen L.A. van der Spek, C.W. Mattias Holm, Harry A.G. Wijshoff, “Automatic Restructuring of Linked Data Structures”,
LCPC 2009, pp. 263-277, 2009.
Harmen L.A. van der Spek, C.W. Mattias Holm, Harry A.G. Wijshoff, “How to unleash array optimizations on codes using
recursive data structures”, Proceedings of the ACM International Conference on Supercomputing (ICS), pp. 275-284, 2010.
Bart Thomee, Mark J. Huiskens, Erwin M. Bakker, Michael S. Lew: Deep exploration for experiential image retrieval. ACM
Multimedia 2009: 673-676
Mark J. Huiskess, Bart Thomee, Michael S. Lew: New trends and ideas in visual concept detection: the MIR flickr retrieval
evaluation initiative. Multimedia Information Retrieval 2010: 527-536
3.10 Contribution of UU-ICS-GMT
Contribution of UU-ICS-GMT
Utrecht University, Faculty of Science, Department of Information and Computing Sciences, Multimedia and Geometry;
Games and Virtual Worlds
Prof.dr. M.H. Overmars, Dr. M. van Kreveld, Dr.ir. F. van der Stappen, Prof.dr. R. C. Veltkamp, Prof.dr P.J. Werkhoven
Research 2009-2010
Research in Games and Virtual World has focused on path planning and crowd simulation, and on manipulation planning.
One of the fundamental tasks that virtual characters have to perform is to plan their paths between different locations in the
virtual world. Modern virtual environment applications require a path planner that is fast to ensure real-time planning of large
crowds of characters and flexible so that the characters can avoid local hazards, such as small and dynamic obstacles. In
addition, the computed paths need to be smooth to ensure natural looking motions. To address these issues, we recently
introduced the Indicative Route Method as new path planning approach in interactive worlds and games.
Besides exhibiting believable path planning behavior, the virtual characters should also be able to move towards their
desired locations in a life-like manner avoiding collisions with each other. Therefore, we proposed a physically-based model
for solving interactions between virtual pedestrians that have converging trajectories]. The method is fast, simple to
implement and exhibits important emergent phenomena that have been noted in the pedestrian literature. We also
addressed the issue of realistic collision avoidance among virtual humans by exploiting experimental interaction data
between real pedestrians. In the resulting method, the characters predict collisions and take early action to avoid them by
adapting their direction and/or speed. Recently, we extended this technique to simulate small groups of virtual humans.
Research in manipulation planning has considered different forms of grasping. The efforts have focused on caging grasps
and grasps of flexible structures. Caging grasps are loose grasps that do not exclude all motions of the grasped object but
only prevent it from escaping, which is sufficient in many applications. We have studied algorithms for computing caging
grasps of an object, and have established a remarkable upper bound on the complexity of the set of all three-finger caging
grasps of a convex object, which stays several orders of magnitude below the best known bound for arbitrary objects. In
addition we have continued our work on the immobilization of hinged chains of rigid objects and obtained various new
insights. Finally we have developed algorithms for grasping and retracting layers of human tissue, in order to minimize
stress, strain, and tissue damage during surgery.
In media technology, research was performed in the following areas: image retrieval, shape retrieval, 3D modeling, and
music retrieval. We have developed a number of different methods for shape recognition, shape indexing with vantage
objects, and layout indexing with Laplacian and Hermitian graph spectra. Apart from provable properties, the behavior in
practice has been rigorously evaluated on the basis of ground truth test sets, and compared with many other content-based
image retrieval methods.
In computational geometry our research in data imprecision has continued, but will receive less attention since the relevant
project has ended. We have finished and published the obtained results regarding convex hulls and triangulations of
imprecisie points. We have also shown how to compute the similarity of two polyhedral terrains under vertical scaling and
translation.
Of relevance to GIS is our research on trajectories. We have developed the concept of a median trajectory and algorithms
that show how to compute it. Furthermore, we have developed an algorithmic framework for segmenting trajectories of
ASCI bi-annual Report 2009-2010
29
moving objects such that the pieces have similar characteristics within each piece. Also, we have given a new, efficient
algorithm for detecting the most similar subtrajectories for two given trajectories. In graph drawing, we have performed
research on drawing graphs with thick vertices and edges, and on simultaneous embeddings of two graphs. In 3D
reconstruction, we have performed research on LiDAR point sets from areal and ground-based scans. The resulting point
clouds were analyzed algorithmically, and more meaningful shapes like rectangles and composite objects were computed.
We have organized the 3D Shape Retrieval Contest (SHREC), which has a large impact on the community. We have
performed research on the mapping of music notation and audio into a symbolic representation. Then the symbolic
representation is indexed and matched to a query. One specific application is to find folk songs that are similar to a query,
yet not exactly the same, due to oral transmission. Our retrieval methods are integrated with the Nederlandse Liederenbank,
the Dutch folk songs database at the Meertens Institute for ethnological research.
Future Research Plans
The focus of our path planning and crowd simulation for the forthcoming years will be on crowd management in evacuation
scenarios. The goal of the work is a serious game for managing panicking crowds. The work takes place at three interrelated
levels. Path planning will play a role at the top level where the purpose of the training is to intervene in order to distribute and
steer groups of people. At the intermediate level, the actions of individuals as a result of external triggers is modeled and
executed. At the lower level, realistic emotions and gestures of individuals need to be animated.
In our manipulation planning research, we will concentrate on dealing with uncertainty. We will study imprecision in the
shape of the manipulated objects as well as inaccuracy of the manipulator. The aim is to develop algorithms that determine
manipulation plans that work despite the presence of uncertainty. We will also study grasps that do not immobilize an object,
but rather provide support in a limited set of directions.
While we plan to extend results in the above areas, new research directions will be animation, multi-modal interaction,
computer vision, game content generation, and mobile interaction. The animation research will mainly focus on generating
realistic virtual character motion. In the animation community, character motion is generally divided into facial and body
animation, which require different approaches. In collaboration with TNO, we will start a new line of research in multi-modal
interaction. The goal of this research is to develop new concepts and techniques with which users can steer the behavior of
virtual characters. In particular we are interested in techniques with which users can control the navigation and manipulation
performed by such characters. We will start working on detecting, tracking, modeling, and recognition of persons, their pose,
and gestures, from multiple video cameras. Our approach is to exploit 3D information that we derive from coherence in
views. Research on mobile interaction will be directed towards new, better ways for accessing, handling, and manipulating
different kind of media on handheld devices. With respect to spatial data mining we will study concepts like flocking, meeting,
convergence, etc., for set of trajectories, and developed algorithms to detect these patterns.
Key Publications 2009-2010
Maike Buchin, Anne Driemel, Marc J. van Kreveld, Vera Sacristan: An algorithmic framework for segmenting trajectories
based on spatio-temporal criteria. Proceedings of ACM SIGSPATIAL 2010: 202-211.
Marc J. van Kreveld, Maarten Löffler, Joseph S. B. Mitchell: Preprocessing Imprecise Points and Splitting Triangulations.
SIAM J. Comput. 39(7): 2990-3000 (2010).
M. Vahedi, A.F. van der Stappen, On the complexity of the set of three-finger caging grasps of convex
polygons, Proceedings of Robotics: Science and Systems (2009), pp. 57-64.
I. Karamouzas, R. Geraerts, and M. Overmars. Indicative Routes for Path Planning and Crowd Simulation. In: FDG '09: Proc.
of the 4th International Conference on Foundations of Digital Games, 2009, pp. 113-120.
I. Karamouzas and M. Overmars. Simulating the Local Behaviour of Small Pedestrian Groups. In: VRST '10: Proc. of the
17th ACM Symposium on Virtual Reality Software and Technology, 2010, pp. 183-190.
Frank B. ter Haar, Remco C. Veltkamp. Expression modeling for expression-invariant face recognition. Computers &
Graphics, vol. 34, 2010, 231–241.
Sergio Cabello, Mark de Berg, Panos Giannopoulos, Christian Knauer, René van Oostrum, Remco C. Veltkamp. Maximizing
the Area of Overlap of two Unions of Disks under Rigid Motion. International Journal of Computational Geometry and
Applications, 19(6), 2009, 533-556.
Frank B. ter Haar, Remco C. Veltkamp. A 3D face matching framework for facial curves. Graphical Models 71(2), 2009, 7791, DOI 10.1016/j.gmod.2008.12.003.
3.11 Contribution of TUD-L&R-FRS
Staff: Dr.ir. BGH Gorte
PhD Students: Alexander Bucksch, Fatemeh Karimi Nejadasl
ASCI bi-annual Report 2009-2010
30
Just before the start of the reporting period (December 2008) the chair of OLRS was re-occupied and subsequently two new
assistant professors were hired. Also the section saw an increase in the number of PhD candidates, which however did not
yet materialize into new ASCI memberships, as a consequence of a shift of focus in the section's research portfolio.
One project executed within the ASCI context concerned analysis of helicopter-recorded image sequences to measure and
monitor driver behaviour in traffic congestion at motorways. This was a collaboration with the faculty of Civil Engineering and
Geosciences at TU Delft with NWO funding.
The resulting thesis was defended in February 2010.
A second PhD project of an ASCI PhD student member concerned using terrestrial LiDAR to measure the structure of trees,
as well other forestry-parameters like wood volume and biomass. The thesis was defended shortly after the reporting period
(21 April 2011). The project was executed in cooperation with the University of Goettingen and the German LiDAR
manufacturer Z&F.
Earth observation from satellites operating in the visible, near infra-red and thermal infra-red ranges of the electromagnetic
spectrum is gaining significance with the increasing needs for high-frequency uniform monitoring of processes related to
vegetation and the water and carbon cycles, against the background of increasing population pressure and climate change.
In addition to imagery originating from satellite sensors also airborne and 'close range' image data are analysed at OLRS.
Interesting technology is provided by laser range measurement devices that nowadays can be operated 'close range',
airborne and even from satellite (ICESat). These three forms are studied with similarly large interest for very diverse
applications in hydrology, forestry, flood modeling, (urban) climate modeling and land use/land cover mapping.
As mentioned above, the range of subjects studied at the chair is being extended. The computer vision/automatic
interpretation based analysis of image and range data, as described above, will remain one of the the fields of focus. A new
activity (within the chair) is physics based retrieval of parameters of geo- and biodynamical processes on the basis of multitemporal, multi-angular and multi-spectral EM-radiation measurements, from both active and passive sensors. Naturally
these two fields will not be seen in isolation. Their integration into a comprehensive modeling and monitoring strategy will be
the focus of the chair during the coming years.
Key publications by ASCI members of OLRS:
Bucksch, A.K., Lindenbergh, R.C. and Menenti, M. (2010), "SkelTre - Robust skeleton extraction from imperfect point
clouds", The Visual Computer: International journal of computer graphics, Vol. 26(10), pp. 1283-1284.
Bucksch, A.K., Lindenbergh, R.C., Menenti, M. and Abd Rahman, M.Z. (2009), "Skeleton-based botanic tree diameter
estimation from dense LiDAR data". In: Proceedings Optics and Photonics 2009; LiDAR Remote Sensing for environment X,
Washington, USA, Vol. 7460, pp. 1-11. SPIE.
Abd Rahman, M.Z., Gorte, B.G.H. and Bucksch, A.K. (2009), "A new method for individual tree delineation and undergrowth
removal from high resolution airborne LiDAR". In: Proceedings ISPRS workshop laserscanning 2009, Paris, Vol. XXXVIII, pp.
283-288. ISPRS.
Bucksch, A.K. and Fleck, S. (2011), "Automated detection of branch dimensions in woody skeletons of fruit tree canopies",
Photogrammetric Engineering & Remote Sensing, Vol. 77(3), pp. 229-240. [article]
Karimi Nejadasl, F. and Lindenbergh, R.C. (2011), "Vehicle detection from an image sequence collected by a hovering
helicopter". In: Photogrammetric Image Analysis, ISPRS Conference, PIA 2011, Munchen, Vol. 38, pp. 209-214. Institute of
Photogrammetry and Cartography.
3.12 Contribution of RUG-CS-SVCG
1. Global research description
The research group Scientific Visualization and Computer Graphics carries out research in the area of scientific visualization,
information and software visualization, computer graphics and innovative interfaces using large, touch-sensitive displays.
With respect to applications, the research concentrates on fundamental and applied problems from the life sciences, in
particular functional brain imaging and bioinformatics, and astronomy.
In interactive data visualization, we worked on surface reconstruction from noisy and sparse data sets. Special attention is
devoted to acceleration of algorithms through special (multiscale) data structures and/or by mapping the involved
ASCI bi-annual Report 2009-2010
31
computations to programmable Graphics Processing Units (GPUs). Examples are accelerated wavelet lifting or sparse levelset methods on graphics hardware using CUDA. Previous research in skeletonization was extended by saliency-dependent
simplification. We have developed image-based edge bundles, which depict a bundled graph layout at increasingly coarse
levels of detail. A neurophysiologically plausible population code model for feature integration was developed which explains
visual crowding. In software visualization, we studied techniques for visualizing combinations of software architecture
diagrams and quality metrics. Several new methods were developed for interactive static analysis and understanding of large
software systems. The approaches were validated in collaboration with industrial partners and the open-source community.
In non-photorealistic rendering (NPR) we worked on hand-posture based interaction that supports the exploration and
visualization of flow datasets, and on illustrative visualization of line data. In addition, we explored interaction concepts for
digital concept sketching and extended it to support the interaction with 3D visualization spaces on large touch surfaces.
Applications. We applied our methodological work in several application domains. Anatomical and functional brain
visualization techniques were developed, based on a variety of data: EEG, functional MRI, or diffusion tensor imaging (DTI).
As an example, we developed the depth-dependent halo technique for illustrative visualization of fiber tracts that were
extracted from DTI data of the human brain. A method was proposed for quantifying differences between multichannel EEG
coherence networks. In bioinformatics, we worked on the visualization of gene expression time series in both a gene
regulatory network and metabolic pathway context. In astronomy, we used visual analytics methods to study the relations
between the spatial arrangement of galaxies and the distribution of various attributes in very high-dimensional parameter
spaces based on ranking subspaces for clustering. With partners from astronomy we are investigating collaborative
interaction using large touch-sensitive displays.
2. Expectations for the coming period
There are two new international initiatives in which the group is extending its efforts, i.e., Visual Analytics and
Neuroinformatics. Visual Analytics concerns the integration of visualization with other analytical methodologies, such as
statistics, data-mining, and cognition. The group already collaborated within the European project Vismaster (2008-2010),
which developed a European roadmap for Visual Analytics. The group is active in establishing new research networks in this
area on the international level. Interesting connections are being explored with artificial intelligence and cognitive science.
The second area is Neuroinformatics, which supports discovery and innovation in neuroscience by information technology,
for example in the study of neurodegenerative diseases. The group is actively participating in local, national and international
initiatives in this area.
3. Selected publications from the period 2009-2010
R. van den Berg, J.B.T.M. Roerdink, and F.W. Cornelissen (2010) A Neurophysiologically Plausible Population Code Model
for Feature Integration Explains Visual Crowding. PLoS Comput Biol, 6(1):e1000646, January 2010.
W.J. van der Laan, A.C. Jalba, and J.B.T.M. Roerdink (2010) A Memory and Computation Efficient Sparse Level-Set
Method. Journal of Scientific Computing, 2010.
A. Telea and O. Ersoy (2010) Image-Based Edge Bundles: Simplified Visualization of LargeGraphs. Computer Graphics
Forum, 29(3):843–852, June 2010. Second Best Paper Award at EuroVis 2010.
M.A. Westenberg, J.B.T.M. Roerdink and O.P. Kuipers, and S.A.F.T. van Hijum (2010) SpotXplore: a Cytoscape plugin for
visual exploration of hotspot expression in gene regulatory networks. Bioinformatics, 26(22):2922–2923, 2010.
L. Yu, P. Svetachov, P. Isenberg, M.H. Everts, and T. Isenberg (2010) FI3D: Direct-Touch Interaction for the Exploration of
3D Scientific Visualization Spaces. IEEE Transactions on Visualization and Computer Graphics, 16(6):1613–1622,
November/December 2010
H. Bekker, A.A. Brink, and J.B.T.M. Roerdink (2009) Reducing the time complexity and identifying ill-posed problem
instances of Minkowski sum based similarity calculations. International Journal of Computational Geometry and Applications,
19(5):441–456, October 2009.
M.H. Everts, H. Bekker, J.B.T.M. Roerdink, and T. Isenberg (2009) Depth-Dependent Halos: Illustrative Rendering of Dense
Line Data. IEEE Transactions on Visualization and Computer Graphics, 15(6):1299–1306, November/December 2009. Best
Paper Award at IEEE Visualization 2009
A.C. Jalba and J.B.T.M. Roerdink (2009) Efficient Surface Reconstruction from Noisy Data using Regularized Membrane
Potentials. IEEE Trans. Image Processing, 18(5):1119–1134, May 2009
M.M. Lorist, Eniko Bezdan, Michael ten Caat , M.M. Span, J.B.T.M. Roerdink, and N.M. Maurits (2009) The influence of
mental fatigue and motivation on task switching; an EEG coherence study. Brain Research, 1270:95–106, 2009.
ASCI bi-annual Report 2009-2010
32
L. Voinea and A. Telea (2009) Visual Querying and Analysis of Large Software Repositories. Empirical Software
Engineering, 14(3):316–340, 2009
3.13 Contribution of RUG-CS-IS
University of Groningen, Faculty of Mathematics and Natural Sciences, Johann Bernoulli Institute of Mathematics and
Computer Science, Intelligent Systems
Prof.dr. N. Petkov, Dr. M.H.F. Wilkinson
QUESTION 1
What’s the name of your group?
University of Groningen
Faculty of Mathematics and Natural Sciences
Johann Bernoulli Institute of Mathematics and Computing Science
Intelligent Systems
http://www.cs.rug.nl
QUESTION 2
Image processing, computer vision, pattern recognition, brain-inspired computing,
Applications in life sciences and health care, Connected filters and morphological operators (C.2)
Machine learning and neural networks (C.3)
Question 3
Brain-inspired computer vision
Models of information processing in visual cortex are developed and used in com- puter algorithms. This research is relevant
for the areas of image processing, com- puter vision, pattern recognition, visual perception, and computational neuroscience.
Our goal is to understand how people see and to deploy principles of natural vision in computer algorithms for artificial vision.
Using facts from neuroscience and vi- sual perception, we build models of visual information processing in the brain and use
them in computer simulations to obtain insights and derive practical computer vision algorithms.
One example is a model of a grating cell that we developed [Petkov, Kruizinga: 1997 Biological Cybernetics 76: 83-96] and
used in a texture operator [Kruizinga, Petkov: 1999 IEEE Trans. on Image Processing 8: 1395-1407], [Grigorescu, Petkov,
Kruizinga: 2002 IEEE Trans. on Image Processing 11: 1160-1167]. By means of computer simulations we demonstrated that
grating cells may play an important role in the disambiguation of edge information in early vision (texture vs. contours).
Another example is our model of non-classical receptive filed inhibition, also called surround suppression, in orientation
selective neurons [Petkov, Westenberg: 2003 Bi- ological Cybernetics 88: 236-246]. We demonstrated that the biological role
of this inhibitory mechanism is quick pre-attentive detection of object contours and region boundaries in natural images that
are rich in texture. We proposed various contour detection algorithms that deploy this mechanism and showed that they are more effective in detecting object contours and
region boundaries than traditional computer vision al- gorithms for edge detection [Grigorescu, Petkov, Westenberg: 2003
IEEE Trans. on Image Processing 12: 729-739], [Grigorescu, Petkov, Westenberg: 2004 Image and Vision Computing 22:
609–622], [Papari, Campisi, Petkov, Neri: 2007 EURASIP J. on Advances in Signal Processing, Article ID 71828]. This work
has been extended by applying gestalt principles to edge grouping [Papari, Petkov: 2008 IEEE Trans. Im- age Processing
17: 1950-1962], [Papari, Petkov: Proc. SPIE 2008, vol. 6812, art. no. 68121B]. Meanwhile, the article ”Contour detection
based on nonclassical recep- tive field inhibition” [Grigorescu, Petkov, Westenberg: 2003 IEEE Trans. on Image Processing
12: 729-739] received a large number of citations.
We also studied the orientation and speed tuning properties of spatio-temporal 3D Gabor and motion energy filters with
surround suppression as models of time- dependent receptive fields of simple and complex cells in primary visual cortex (V1)
[Petkov, Subramanian: 2007 Biological Cybernetics, 97: 423-439]. We demonstrated how these filters are related to motion
detection, noise reduction, texture suppression and contour enhancement.
In the same line of research we model the detection of contour segments and shape representation in areas V4 and TEO of
visual cortex.
Another result of our research that is inspired by psychological research on the human visual system is a method for the
evaluation of the robustness of shape recog- nition algorithms to incompleteness of contours [Ghosh, Petkov: 2005 IEEE
Trans. on Pattern Analysis and Machine Intelligence 27: 1793-1804].
Image processing and computer vision
In shape analysis we study geometrical approaches in which a feature point is char- acterized by the spatial arrangement of
other feature points around it. The collection of local geometrical descriptors for the different feature points of an object is
used as a shape characteristics of that object [Grigorescu, Petkov: 2003 IEEE Trans. on Image Processing 12: 1274-1286].
ASCI bi-annual Report 2009-2010
33
Another direction in our work is the development of image processing operators that add artistic effects to photographic
images [Papari, Petkov, Campisi: 2007 IEEE Trans. on Image Processing, 16: 2449-2662], [Papari, Petkov: 2009 IEEE
Trans. on Image Processing 18: 652-664].
On the applications side, we collaborate with researchers from the University of Leon, Spain, in the area of automatic
classification of boar spermatozoa [Sanchez, Petkov, Alegre: 2006 Cellular and Molecular Biology, 52: 38-43], [Petkov,
Alegre, Biehl, Sanchez: 2008 Comp. in Biol. and Medicine 38: 461-468]. We also collabo- rate with the Department of
Dermatology of the University Medical Center Groningen [Bosman, Petkov, Jonkman: 2010 Skin Research and Technology
16: 109-113] on the application of content based image retrieval and expert systems to dermatological prob- lems and with
the Department of Ophtamology on the automatic detection of diabetic retinopathy.
Connected filters, Connectivity Theory and Segmentation
Connected filters are a comparatively new field of research within mathematical morphology. They are edge preserving
operators which have found use in noise re- moval, texture analysis, image compression and description, and feature
extraction. Research on connected operators in our group entails algorithm development (includ- ing parallelization),
development of new classes of filters, applications to 2-D and 3-D medical images, and the development of new connectivity
measures for these filters for increased robustness. Recently, content-based image retrieval (CBIR) has been added to the
list of application areas. One line of this research links to visual cortex modelling: developing morphological analogues of
texture operators based on mod- els of certain visual cortical cells. It is hoped these morphological counterparts will be an
order of magnitude faster, whilst retaining the useful properties of the cortical cell models. Finally, fast visualization based on
connected attribute filters is being ex- plored. Recently, work has begun expanding this line into hyperconnected filters and
attribute-space-connected filters, which increase the flexibility of perceptual groupings available, and allow dealing with
overlap explicitly.
Segmentation is a core problem in image analysis, and methods based on both simple thresholding methods and more
advanced methods such as watersheds and de- formable models are being explored. Application areas are many, but the
focus lies on biomedical imaging, both macroscopic (MRI, CT) and microscopic. New application domains in astronomy are
also being explored.
Machine learning and neural networks
The term machine learning refers to an area of computer science in which given example data is analysed. The aim could
be, for instance, the identification of a classi- fication scheme based on labeled examples or interpolation/extrapolation in
regression problems. Methods of unsupervised learning address problems like clustering, dimen- sion reduction, or
correlation analysis in, potentially, high-dimensional data.
In our research group, learning algorithms are developed and employed for data driven parameter adaptation in, for instance,
prototype-based classifiers or other adap- tive systems.
In the context of supervised learning, the so-called Learning Vector Quantization (LVQ) constitutes a family of algorithms
which identify typical representatives of the classes. Together with a measure of distance or similarity, these prototypes are
used to parameterize the classification scheme. Similarly, in unsupervised Vector Quantization (VQ), prototypes are used to
represent large amounts of data by means of clustering or dimension reduction.
Obviously, a key question in the above mentioned and many other similarity based methods is the choice of an appropriate
distance measure. In recent years we have put forward methods of Relevance Learning, in which a generalized Euclidean
distance measure is parameterized and adapted in the training phase. Hence, the classifier and a discriminative similarity
measure are identified in the same data driven process.
As a particular successful approach we have established Matrix Relevance Learning and applied it in various practical
contexts, including content based image retrieval and tumor classification. Most recently we have applied matrix relevance
learning in the low-dimensional representation and visualization of complex, labeled data sets.
In a complementary line of research we investigate the use of novel, alternative distance measures which are not related to
conventional Euclidean metrics. Statistical divergences, for instance, can be used as meaningful distance measures
whenever the data consists of non-negative, potentially normalized features. Divergences are partic- ularly promising if
feature vectors comprise statistical or functional information, e.g. in the form of histograms or spectra.
In our theoretical investigations we aim at a better understanding of algorithms, learning processes and their performance. In
the framework of model situations, we study the dynamics of on-line learning and systematically compare different algorithms. Similar investigations, which borrow basic concepts from statistical physics, concern the typical properties of large
learning systems in the context of batch- or of- fline training. The ultimate goal of these studies is to design and optimize
practical training algorithms.
Consequently, we aim at testing the developed methods in real world applications. Recently, we have addressed several
classification problems in the life sciences and image processing. Important examples are the classification of adrenal
tumors based on metabolomics data and content based image retrieval in dermatology. Another project deals with the
detection of Cassava Mosaic Disease based on color histograms obtained from leaf images.
QUESTION 4
Please indicate in which external projects (2nd and 3rd funding projects) your group participated in in 2009-2010 – new and
old projects.
ASCI bi-annual Report 2009-2010
34
The position of Kerstin Bunte is financed by a grant to Biehl and Petkov in the Open Competition 2006/07 of NWO. New
funding for the project Connected Mor- phological Operators for Tensor Images (COMOTI) was awared to Jos Roerdink and
Michael Wilkinson in the Open Competition 2010 of NWO. A PhD student has now been appointed. Wilkinson is also coapplicant in the ASTROVIS project, which funds two PhD students (Hugo Budelmeijer at the Kapteyn Astronomical Institute,
and Bilkis Ferdosi at the Johann Bernoulli Institute). The positions of Tushabe and Kiwanuka are funded through a grant by
NUFFIC. The position of Emerencia is financed by a grant to Aiello and Petkov from NWO Medical Sciences, 2009.
QUESTION 5
Doctoral Degrees: Which promotions took place in 2009-2010?
a) G.K. Ouzounis. Generalized Connected Morphologcial Operators for Robust Shape Extraction. Promotor: N. Petkov, copromotor: M.H.F. Wilkinson, Uni- versity of Groningen, 2009, ISBN 978-90-367-3698-5, 140 pages.
b) G. Papari. Texture vs. Cotours: Explorations in the fields of contour detection and artistic imaging. Promotor: N. Petkov,
University of Groningen, 2009, ISBN 978-90-367-3837-8, 186 pages.
c) P. Schneider, Advanced methods for prototype-based classification. Promotors: M. Biehl, N. Petkov, Faculty of
Mathematics and Natural Sciences, University of Groningen, 2010, ISBN 978-90-367-4405-8, 95 pages.
d) F. Tushabe, Extending Attribut Filters to Color Processing and Multi-Media Ap- plications. Promotor: N. Petkov, copromotor: M.H.F. Wilkinson, Faculty of Mathematics and Natural Sciences, University of Groningen, 2010, ISBN 978- 90367-4630-4, 126 pages.
e) A. Witoelar, Statistical Physics of Learning Vector Quantization. Promotor: M. Biehl, N. Petkov, Faculty of Mathematics
and Natural Sciences, University of Groningen, 2010, ISBN 978-90-367-4409-6, 114 pages.
3.14 Contribution of TUE-ET
Technische Universiteit Eindhoven, Faculty of Electrical Engineering, Design Methodology for Electronic Systems
Prof.dr.ir. R.H.J.M.Otten, Dr.ir. T. Basten, Prof.dr. H. Corporaal, Dr.ir. M.C.W. Geilen, Prof.dr.ir. G. de Haan,
Dr.ir. J.P.M. Voeten
Research 2009-2010
Over decades the chair electronic systems has focused on iteration free design. This utopian goal has always provided upto-date challenges and resulted in a wealth of contributions to the field of design automation: "how to specify a function to be
implemented on a chip, feed it to an eda tool, and get, without further interaction, a design that meets all requirements
concerning functionality, speed, size, power, yield and other costs". The chair decided to embark on a more general
approach where the set of all possible performance characteristics and, in principle, all combinations of realization values
that can be optimal under the usual cost functions, are considered. Apart from the generalization from pairwise to multiple
trade-offs, the approach lends itself well to dynamic reconfiguration of modern systems, and multimedia systems in
particular, and offers a flexible transition between pre-silicon and post-silicon decision-making, without imposing any
compromise with respect to optimality. Such an approach reveals fundamental problems that are turned into the following
focus areas and results.
Composability. A composable real-time operating systems (RTOS) using a two-level arbitration scheme. Composable (and
predictable) Aethereal Network on Chip using pipelined virtual circuits based on TDM arbitration. Composable (and
predictable) memory controller supporting both SRAM and SDRAM and a wide range of arbiters. Composable power
management that enables independent dynamic voltage and frequency scaling per application.
Predictability. Cyclo-Static Dataflow (CSDF) based throughput and latency analysis techniques. CSDF buffer sizing
techniques to explore trade-offs between buffer size and throughput. SDF-based resource allocation and scheduling for
shared resources. Predictable RTOS for CSDF applications. Modeling and analysis techniques to predict performance tradeoffs in highly dynamic and distributed sensor networks. Predictable automatic synthesis for real-time control-dominated
systems from formal real-time concurrent specifications such that qualitative properties are preserved and all real-time
properties are preserved up to a small timing deviation.
Compositionality. Theoretic model of timed interfaces to support compositional step-wise refinement and abstraction of
worst-case performance models. Compositional (per-connection) communication models in RTOS and Network on Chip.
Scenario-aware design. New model-of-computation (MoC): Scenario-Aware Dataflow (SADF), combining the strengths of
determinate dataflow analysis and limited scenario indeterminacy. Analysis techniques leveraging the theory of Max-Plus
algebra. Automated design flow to map applications modeled with a SADF graph onto a multi-processor platform. Structured,
automated approach to identify and detect scenarios in application source code.
Low-power architectures and power-aware design. Technology-enabled design methodologies towards minimum-area
maximum-performance designs in sub-/near-threshold operation. Concurrent adaptive control of voltage scaling and forward
body biasing to minimize power consumption under fixed performance. Sub-threshold JPEG encoder (down-to 0.75
pJ/operation; in 65 nm CMOS) has been successfully realized and tested. Proposal for a scalable SIMD processor,
consuming down-to 1 pJ/operation (the first fully programmable processor beating the 1 pJ/op boundary),partly prototyped in
VHDL and CMOS 65 nm.
ASCI bi-annual Report 2009-2010
35
Complete mapping flow. The open-source software tool SDF3 implementing all developed dataflow analysis and mapping
techniques. A light-weight, open-source multi-processor platform, using SDF3, that can be used for educational purposes. An
industrial relevant multi-processor platform, using SDF3, offering composability, predictability and low power.
Video processing for multimedia systems. A versatile platform for high quality image enhancement, suitable for real-time
implementation of noise reduction, coding artifact reduction, sharpness enhancement, contrast enhancement, and resolution
up-conversion with very limited time for parameter optimization. A theoretical framework for describing the influence of
picture registration, picture reconstruction and perception on picture quality, extensively applied for industrial lcd displays. A
HW-platform for real-time 2Dto3D-conversion with low power dissipation (<20 Watt), small form factor (1 card in a 19 inch
rack), excellent video quality (1080 lines progressive with 60 frames per second), reliable and robust (24/7).
Smart camera. We have built an experimental set-up for heartbeat detection from camera signals in a gym-setting. Advanced
face detection where we can discriminate between actual people and pictures or other artifacts. Experimental set-up with
infrared cameras to monitor a sleeping person to replace accelerometers physically attached to the wrists and ankles of the
sleeper with motion analysis of video. Machine learning for detection of malaria infection in blood smears, the detection of
TB, and the detection of breast cancer.
Future Research Plans
There will be in the coming years, focus on the following fundamental topics. Composability refers to the methodology of
separating applications on a shared platform, in such a way that independent development, verification, and execution is
possible. Verifying (real-time) requirements becomes much easier, and a mix of real-time and non-real-time applications can
run on the same shared hardware. Predictability in real-time computing is a necessity for guaranteeing performance
properties and constraints. Timing is a performance characteristic that has been studied extensively in order to analyze
resource requirements for providing guarantees, but others deserve attention. Compositionality is a scalable approach to
predictability. It allows for the decomposition in smaller parts or views that can be re-assembled without re-analysis.
Scenario-aware design makes use of the fact that, when run-time conditions are known or can be predicted, applications can
often be mapped and executed more efficiently than when simply designed for the statically 'worst case'. Low-power
architectures and power-aware design are both essential in staying within realistic power budgets in the future. This requires
extremely computationally-efficient processing and the incorporation of adaptive techniques at all levels. A complete
mapping flow will be, faithful to the mission stated above, maintained and tools will be incorporated, whether in-house
developed or shared with partners. Our contributions will be in the design trajectory from data-flow specifications to multiprocessor systems realized/prototyped for field programmable gate arrays.
Key Publications 2009-2010
•
Marc Geilen, Stavros Tripakis, Maarten Wiggers: The earlier the better: a theory of timed actor interfaces. HSCC
2011: 23-32
•
Sander Stuijk, Marc Geilen, Twan Basten: A Predictable Multiprocessor Design Flow for Streaming Applications
with Dynamic Behaviour. DSD 2010: 548-555
•
Akash Kumar, Bart Mesman, Henk Corporaal, Yajun Ha: Iterative Probabilistic Performance Prediction for MultiApplication Multiprocessor Systems. IEEE Trans. on CAD of Integrated Circuits and Systems 29(4): 538-551 (2010)
•
Yu Pu, J. Pineda de Gyvez, H. Corporaal, Yahun Ya: “An ultra-low-energy multi-standard JPEG Coprocessor in 65
nm CMOS with sub/near threshold supply voltage”, IEEE Journal of Solid State Circuits, 2010, vol 45, n. 3, pp 668-680a.
•
Jeroen Voeten, Oana Florescu, Jinfeng Huang, Henk Corporaal: Error computation for predictable real-time
software synthesis. Simulation 87(4): 334-350 (2011).
3.15 Contribution of TUE-WI
Eindhoven University of Technology, Department of Mathematics and Computer Science, Visualization Group
Prof.dr.ir. J.J. van Wijk, Prof.dr.ir. R. van Liere, Dr.ir. H.M.M. van de Wetering, Dr. M.A. Westenberg, Dr. A.C. Jalba
Research 2009-2010
The aim of visualization is to develop methods and techniques using interactive computer graphics such that most insight in
large data sets can be obtained. The TU/e Visualization group is active in the following areas:
Information Visualization. We study how large amounts of abstract data, such as tables, trees, networks and combinations of
these, can be visualized. Our research has led a number of PhD theses, focusing on compound graphs (PhD Holten, 2009,
awarded as best PhD thesis TU/e 2009), support for navigation (PhD Shrinivasan, 2010), perceptual issues (PhD Li, 2011),
and vessel traffic (PhD Willems, 2011). Research included the development of new methods and techniques for
ASCI bi-annual Report 2009-2010
36
presentation and interaction, and evaluation based on user experiments; with application domains such as software analysis,
bio-informatics, and spatial movement analysis.
Scientific Visualization. Scientific visualization concerns data from simulations and measurements, defined over geometric
spaces. Within this area we study tensor field analysis and visualization, mathematical visualization, and, in cooperation with
the TU/e Department of Biomedical Engineering, medical visualization.
3D interaction. In cooperation with CWI we study how affordable desktop Virtual Reality systems (hard- and software) can be
designed to simplify interaction with 3D data and objects for interrogation and navigation. This has led to new methods and
techniques for interactive measurements of 3D objects (PhD Kruszynski, 2010), and on new insights on interactive 3D
manipulation (PhD Liu, 2011).
Future research plans
In the next period we aim to continue and expand our research. Visualization is almost by definition an applied discipline,
close cooperation with end-users is stimulating and rewarding. We currently work on visualization of bio-informatics, and aim
to expand our cooperation with Wageningen, Nijmegen and increase our role in NBIC. Our spin-off companies MagnaView
and SynerScope provide interesting use cases from practice, including visualization of multivariate data for professionals and
fraud detection for banking. Our research on moving object visualization will continue in METIS, a follow-up project of
POSEIDON, in cooperation with Thales, with a focus on uncertainty visualization. Furthermore, we aim to expand
cooperation here with our colleagues from the algoritmics group. Other challenges come from for instance CBS
(demographic data), Kempenhaeghe (medicine use), and ASML (log data).
Also, we aim to expand our work in Visual Analytics: The science of analytical reasoning, supported by interactive visual
interfaces. Integration of other data analysis methodologies (statistics, data mining); heterogenous data; and consideration of
the complete data analysis process, from collection to presentation, are key aspects. We have participated in the EU
VisMaster project, which has set up a European research agenda for Visual Analytics; a proposal for a EU research project
is in preparation. Furthermore, we aim to contribute to FuturICT, an EU flagship project in preparation. We aim at extension
of cooperation with data-mining experts at TU/e. Also, we cooperate with dr. M. Worring, University of Amsterdam, on
interactive multimedia analysis, and aim to increase this; we continue cooperation with prof. W. van der Aalst on interactive
process mining.
Furthermore, our cooperation with the groups of prof. L. Florack (TU/e Mathematics) and dr. A. Vilanova (Department of
Biomedical Engineering) on medical visualization will be continued.
Key Publications 2009-2010
Willems, N., H. van de Wetering, J.J. van Wijk. Visualization of Vessel Movements.
Computer Graphics Forum, 28(3), 959-966, 2009.
L. Liu, R. van Liere, K. Nieuwenhuizen, Jean-Bernard Martens (2009). Comparing Aimed Movements in the Real World and
in Virtual Reality. In Proceedings IEEE Virtual Reality Conference 2009 (VR 2009), 14-18 March 2009, Lafayette, Louisiana,
USA, 219-222.
J.J. van Wijk (2009). Symmetric Tiling of Closed Surfaces: Visualization of Regular Maps. ACM Transactions on Graphics
28(3), Article 49, 12 pages. Proceedings ACM SIGGRAPH 2009, New Orleans.
R. Otten, A. Vilanova, H. van de Wetering (2010). Illustrative White Matter Fiber Bundles. Computer Graphics Forum, 29(3),
1013-1022.
M.A. Westenberg, J.B.T.M. Roerdink, O.P. Kuipers, S.A.F.T. van Hijum (2010). SpotXplore: a Cytoscape plugin for visual
exploration of hotspot expression in gene regulatory networks. Bioinformatics 26(22), 2922-2923.
J. Li, J.-B. Martens, J.J. van Wijk (2010). A model of symbol size discrimination in scatterplots. Proceedings of the 28th
International Conference on Human Factors in Computing Systems, ACM CHI 2010, Atlanta, Georgia, USA, April 10-15,
2553-2562.
D. Holten, J.J. van Wijk (2010). Evaluation of Cluster Identification Performance for Different PCP Variants. Computer
Graphics Forum 29(3), 793-802.
Y.B. Shrinivasan, J.J. van Wijk (2009). Supporting Exploration Awareness in Information Visualization. IEEE Computer
Graphics and Applications, 29(5), p. 24-33.
ASCI bi-annual Report 2009-2010
37
de Rooij, J.J. van Wijk, M. Worring (2010). MediaTable: Interactive Categorization of Multimedia Collections. IEEE Computer
Graphics and Applications 30(5), 42-51.
L. Astola, A. Jalba, E. Balmashnova, L. Florack (2011). Finsler Streamline Tracking with Single Tensor Orientation
Distribution Function for High Angular Resolution Diffusion Imaging. Journal of Mathematical Imaging and Vision 41(3), 170181.
3.16 Contribution of TUE-BMT
ASCI Annual Report 2009-2010 – Biomedical Image Analysis – Eindhoven University of Technology
Staff: Prof.dr.ir. B.M. ter Haar Romeny (project leader), dr. A. Vilanova, dr.ir. H.C. van Assen, dr. ir. B.Platel, prof.dr. L.M.J.
Florack, dr.ir. R. Duits, prof.dr.ir. M. Breeuwer (Philips Healthcare).
Background:
The group Biomedical Image Analysis focuses on generic mathematical approaches to solve image analysis problems in
cardiovascular and neurological applications, and advanced visualization. The group collaborates with the TU/e Magnetic
Resonance Lab, Philips Healthcare, the FC Donders Institute, the University of Zürich, the Maastricht, Utrecht, Nijmegen and
Leiden University Hospitals and the Epilepsy Center Kempenhaeghe. Education is an important aspect, being housed in the
largest BME Dept. in the Netherlands, with 500 students. A full range of courses is given, from 1 st – 5th year, and at PhD level
(ASCI course a8).
Research:
In collaboration with Philips Healthcare (Best) work on computer aided diagnosis focuses on dynamic contrast enhanced
MRI of breast tumors, low-dose catheter tracking, and cardiovascular dynamics from MRI tagging data to study local dense
ventricular optic flow and deformation for non-invasive ventricular infarct size estimation. The challenge is taken to segment
the thin atrial wall, to optimize cardiac ablation procedures.
Much effort has been given to the GPU-based visualization and analysis of tensor fields of DTI (Diffusion Tensor Imaging)
data, and High Angular Resolution Diffusion Imaging (HARDI). The interactive visualization of 4D flow data of turbulent aorta
blood flow is also GPU-based. The clinical branch at the Maastricht University Hospital focuses on precise navigation and
targeting for Deep Brain Stimulation, in close collaboration with the neurosurgery dept.
A multi-scale framework has been established over the years for doing high-order differential geometry on high-dimensional
images, with applications as adaptive ‘geometry-driven’ edge preserving enhancement, multi-scale optic flow extraction, and
deep structure analysis for content-based image retrieval. This visual perception-inspired framework is expanded to multiorientation analysis in 2D and 3D, giving rise to powerful contextual operators.
The mathematical analysis of (higher order) tensor fields, either for DTI, HARDI or strain tensor fields in cardiac deformation,
includes methods from Finsler geometry, numerical methods for geodesic ray tracing, and a new Lie-group based theory on
3D orientation ‘scores’. A new start-up company (InViso) is etablished to implement these methods in massively parallel
FPGA-based hardware. This project is rewarded a 200 K€ STW valorization grant.
To inspect and interact with these complex tensor fields a sophisticated and flexible GPU-based visualization tool is
developed, ‘DTItool’, which enables the interactive manipulation of all relevant parameters, 3D orientation glyphs, and
tractography. The tool is used in many collaborating labs.
The current and near-future focus of research is on:
 cardiovascular applications, primarily with X-Ray and MRI, exploiting multi-valued images for local strain analysis of
ventricular deformation from tagged MRI sequences, and 4D flow visualization;
 neuro applications, primarily focusing on DTI and HARDI exploited in tractography for brain connectivity and muscle
fibre orientation analysis.
 GPU-based visualization of multi-valued information. The hardly investigated visualization of uncertainties is an
important research topic. Applications include the surgical preparation for safe epilepsy surgery with fiber visualization
to spare the optic radiation, and brain tractography in relation to other brain imaging modalities (fMRI, EEG). The many
parameters of cardiac function are integrated into a clinically more effective comprehensive visualization.
 generic and advanced mathematical methods for multi-valued image analysis, for segmentation, enhancement,
morphological and contextual operations, and tractography of crossing and splitting fibers..
In 2010 the research collaboration IST/e (Image Science & Technology / Eindhoven) has been established as a TU/e High
Potential program, with a grant of 1 M€ of the TU/e board, with partners the Depts. of Mathematics & Computing Science
(Florack, van Wijk) and Biomedical Engineering (ter Haar Romeny, Nicolay).
Publications 2009-2010 (selection):
ASCI bi-annual Report 2009-2010
38
2010
 Duits, R. & Franken, E.M. (2010). Left-invariant parabolic evolutions on SE(2) and contour enhancement via invertible
orientation scores. Part I: Linear left-invariant diffusion equations on SE(2). Quarterly of Applied Mathematics, 68(2),
255-292. Part II: Non-linear left-invariant diffusions on invertible orientation scores. Quarterly of Applied Mathematics,
68(2), 293-331.
 Florack, L.M.J., Balmachnov - Sizykh, E.G., Astola, L.J. & Brunenberg, E.J.L. (2010). A new tensorial framework for
single-shell high angular resolution diffusion imaging. Journal of Mathematical Imaging and Vision, 38(3), 171-181.
 Pelt, R.F.P. van, Olivan Bescos, J., Breeuwer, M., Clough, R.E., Gröller, E., Haar Romenij, B.M. ter & Vilanova, A.
(2010). Exploration of 4D MRI blood-flow using stylistic visualization. IEEE Transactions on Visualization and Computer
Graphics, 16(6), 1339-1347.
 Heisen, M., Fan, X., Buurman, J., Riel, N.A.W. van, Karczmar, G.S. & Haar Romenij, B.M. ter (2010). The influence of
temporal resolution in determining pharmacokinetic parameters from DCE-MRI data. Magnetic Resonance in Medicine,
63(3), 811-816.
 Neubauer, A.M., Garcia, J.A., Messenger, J.C., Hansis, E., Kim, M.S., Klein, A.J.P., Schoonenberg, G.A.F., Grass, M. &
Carroll, J.D. (2010). Clinical feasibility of a fully automated 3D reconstruction of rotational coronary X-ray angiograms.
Circulation: Cardiovascular Interventions, 3(2), 71-79.
2009
 Brecheisen, R., Vilanova, A., Platel, B. & Haar Romenij, B.M. ter (2009). Parameter sensitivity visualization for DTI fiber
tracking. IEEE Transactions on Visualization and Computer Graphics, 15(6), 1441-1448.
 Bouma, H., Sonnemans, J.J., Vilanova, A. & Gerritsen, F.A. (2009). Automatic detection of pulmonary embolism in CTA.
IEEE Transactions on Medical Imaging, 28(8), 1223-1230.
 Franken, E.M. & Duits, R. (2009). Crossing-preserving coherence-enhancing diffusion on invertible orientation scores.
International Journal of Computer Vision, 85(3), 253-278.
 Peeters, T.H.J.M., Vilanova, A. & Haar Romenij, B.M. ter (2009). Interactive fiber structure visualization of the heart.
Computer Graphics Forum, 28(8), 2140-2150.
 Ruijters, D., Haar Romenij, B.M. ter & Suetens, P. (2009). Vesselness-based 2D-3D registration of the coronary
arteries. International Journal of Computer Assisted Radiology and Surgery, 4(4), 391-397.
 Schoonenberg, G.A.F., Florent, R., Lelong, P., Wink, O., Ruijters, D., Carroll, J.D. & Haar Romenij, B.M. ter (2009).
Projection-based motion compensation and reconstruction of coronary segments and cardiac implantable devices using
rotational X-ray angiography. Medical Image Analysis, 13(5), 785-792.
3.17 Contribution of UL-LUMC
Leiden University Medical Center, division of Image Processing, laboratorium voor klinische en Experimentele
Beeldverwerking
Prof.dr.ir. Johan H.C. Reiber, Dr.ir. B.P.F. Lelieveldt, Prof.dr. R. Nelissen
ASCI enquete 2009-2010
Question 1: Name of the group
Division of Image Processing (Dutch abbreviation LKEB)
Dept of Radiology,
Leiden University Medical Center,
P.O. Box 9600
2300 RC Leiden
the Netherlands
www.lkeb.nl
Head in 2009-2010: Prof fr ir J.H.C. Reiber
Question 2: ASCI research theme
Processing, Interpretation and Visualization of Medical Images (Theme C)
Question 3: Short description of research
Contribution of LUMC-lkeb
The main goal of the Division of Image Processing is the research, implementation and validation of image processing
approaches, which allow the objective and reproducible assessment of objects in medical images. LKEB activities belong to
ASCI bi-annual Report 2009-2010
39
one of the seven main research fields of the LUMC under the headings “Vascular Medicine”, “Neuro-science” and
“Biomedical Imaging”. Part of the research involves computer vision research and algorithm development, whereas clinical
applications also play an important role. Applications focus on Neuro-imaging, Pulmonology, Orthopaedics, Cardiology and
molecular and cellular imaging. In 2009-2010, important research directions were:
Statistical shape modeling fitting to sparse image data
Statistical shape models are widely used to integrate a-priori knowledge about shape and image appearance into
segmentation algorithms. Research at LKEB is directed towards fitting statistical shape models to sparse image
observations. A 3D Active Shape Model has been developed, along with a number of techniques to fit these models to biplane X-ray data, and radially scanned echocardiographic imaging; Apart from segmentation, we have developed statistical
shape models for computer-aided diagnosis to detect cardiac shape- and motion abnormalities in MR images for patients
with a cardiac infarction, and for quantifying local shape changes caused by brain diseases.
Molecular image integration
In this project, we are investigating novel algorithms to combine complementary information in molecular, structural and
functional imaging. We address novel image processing challenges brought on by new molecular imaging modalities such as
bioluminenscence imaging and fluorescence imaging. We focus on whole body registration between optical and structural
data in follow-up studies, detection of changes and abnormalities in follow-up studies and on integrating information sources
over the scale range from molecule to organism.
Elastic image registration
We are also developing core technologies for non-rigid image registration. In collaboration with UMCU and Erasmus MC, we
are maintaining and extending the well-known registration software elastiX, where we focus on parallel optimization
algorithms to achieve near-real-time registration performance. The elastiX software has been downloaded > 6000 times, and
is regarded as a worldwide reference for image registration
Clinical Image Analysis Applications
Much of the research at LKEB is driven by questions from clinical partners. To this end, we are developing algorithms and
software for:
 Detection and quantification of pulmonary emphysema in CT Images
 Early detection of micro motion of prosthetic implants in bi-plane X-ray images
 Automatic analysis of coronary vessels in CT and intravascular ultrasound images
 Automatic analysis of coronary and left-ventricular angiograms
 Automatic analysis of cardiac function in MR and CT patient studies
 Automatic analysis of changes in brain structure with ageing and disease
 Automatic analysis of vascular MR data
 Automatic white matter lesion detection in MR images of the brain
Question 6: key publications
Peer-reviewed journal papers






M. Baiker, J. Milles, J. Dijkstra, T. Henning, A.W. Weber, I. Que, E.L. Kaijzel, C.W.G.M. Lowik, J.H.C. Reiber,
B.P.F. Lelieveldt, "Atlas-based whole-body segmentation of mice from low-contrast µCT data", Medical Image
Analysis, vol. 14(6), pp 723-737, 2010
M.Ma, M. van Stralen, J.H.C. Reiber, J.G. Bosch, B.P.F. Lelieveldt, "Model Driven Quantification of Left Ventricular
Function from Sparse Single-beat 3D Echocardiography", Medical Image Analysis, vol 14(4), pp 582-593, 2010.
P.Kok, M. Baiker, E.A. Hendriks, F.H. Post, J. Dijkstra, C.W.G.M. Löwik, B.P.F. Lelieveldt, C.P. Botha, "Articulated
Planar Reformatting for change visualization in small animal imaging", IEEE Transactions on Visualization and
Computer Graphics, vol. 16(6), 1396-1404, 2010
Suinesiaputra, A.F. Frangi, A.M. Kaandorp, H.J. Lamb, J.J. Bax, J.H.C. Reiber, B.P.F. Lelieveldt, “Automatic
Detection of Regional Wall Motion Abnormalities Based on a Statistical Model Applied to Multi-Slice Short-Axis
Cardiac MR Images”, IEEE Transactions on Medical Imaging, vol. 28(4), pp 595-607, 2009.
S Klein, M Staring, K Murphy, MA Viergever, J Pluim , Elastix: a toolbox for intensity-based medical image
registration, IEEE Transactions on Medical Imaging, 29 (1), 196-205 , 2010
Bovenkamp EG, Dijkstra J, Bosch JG, Reiber JH. “User-agent cooperation in multiagent IVUS image
segmentation”. IEEE Trans Med Imaging. 2009 Jan;28(1):94-105.
ASCI bi-annual Report 2009-2010
40

L. Ferrarini, I.M. Veer, E. Baerends, M.J. van Tol, L.R. Demanescu, N.J.A. van der Wee, D. Veltman, A. Aleman,
M.A. van Buchem, J.H.C. Reiber, S.A.R.B. Rombouts and J. Milles, “Hierarchical functional modularity in restingstate human brain”, Human Brain Mapping, 30(7):2220-2231, 2009.
Questions for five year research plan
Question 10: description of 5 year research plan
The next five years the research at LKEB will continue to focus on development of generic methodologies for quantification,
visualization and analysis techniques for biomedical images. Concrete clinical applications will involve:
 Pulmonology: analysis of pulmonary disease from follow up CT scans,
 Orthopaedics: pre-operative surgery simulation and post-operative evaluation of prosthesis fixation
 Vascular image analysis: quantification and risk stratification of vascular disease from several imaging modalities



Cardiac image analysis: quantification and information fusion to support cardiac diagnostics from large,
heterogeneous image data sets.
Neurological image analysis: development of shape comparison methods to detect pathologies compared to an
atlas of normal subjects, and development of algorithms to monitor the progression of white matter lesions and
ageing effects.
Molecular image analysis: fusion of and tracking in complementary imaging data from the whole-body scale to the
molecular scale, with an emphasis on translational biomedical research.
3.18 Contribution of UT-EWI-DACS
1. DACS Mission
DACS focuses on the design and analysis of dependable networked systems. A system is called dependable, whenever
reliance can justifiably be placed on the services it delivers. Tailored to communication systems, which can be wired,
wireless, or embedded in other systems, this means that we aim:
“to contribute to the design and implementation of dependable networked systems, as well as to
methods and techniques to support the design and dimensioning of such systems, such that they are
dependable, in all phases of their lifecycle.”
We thereby interpret the term dependability as encompassing availability, reliability, performance (quality of service) and
security.
2. DACS Strategy
Three phases in system design. We distinguish three phases in the design of dependable networked systems. In the first
(exploratory) phase the emphasis lies on the development of system models and the model-based evaluation of key system
characteristics. In the second, more concrete phase the emphasis lies on designing and/or standardizing systems
architectures, protocols, and algorithms, as well as on implementing prototype systems. In the third, operational phase the
systems have been implemented and the emphasis lies on operationally managing them. As an example of these three
phases, consider the Internet backbone. During 1965-1985, research concentrated on a variety of networking models
(circuit-switching vs. packet-switching, various local area access mechanisms). In the period 1980-1995, research focus
shifted toward designing, implementing and standardizing protocols (TCP/IP, Ethernet). Since the beginning of the 1990s, an
ever more important challenge is to keep the Internet up and running (dependability), and solve problems related to
(performance) management, security and scalability. A similar transition in focus can be seen for wireless communication
system. The figure below illustrates, through a horizontal structuring, the above three phases in system design.
ASCI bi-annual Report 2009-2010
41
phase
Operational
DA
CS
Dependability
Protocol design
FO
CU
S
Model based
technology
Wired
Wireless
Embedded
Three technologies for dependable networked systems. Research within DACS covers the whole spectrum of network
technologies: from well-established technologies (like the wired Internet), via technologies that are under development (such
as wireless networks) to emerging technologies (like embedded network systems).
In the case of well-established technologies, research concentrates on operational aspects, here, in particular, of the wired
Internet. Specific topics include bandwidth allocation, accounting, self-management of lambda switches and protection
against scans, denial-of-service attacks and phishing. Taking and interpreting measurements plays an important role in this
research.
For technologies under development, research focuses on the design, evaluation, and prototype implementation of new
protocols and algorithms for wireless and ad-hoc networks. Topics include algorithms for context- and power-aware routing
in ad-hoc networks, and, lately, more and more on car-to-car communications and wireless sensor networks. These types of
networking systems are exponents of embedded networking technologies as well.
The remaining research on embedded networking technologies focuses on system specification and evaluation techniques
to describe such systems, and the resource constraints (performance, dependability, energy usage) they have to operate
under. This includes the development of new stochastic model checking techniques and the application thereof to predict
dependability and performance properties.
The figure above also shows these three technology domains (where a clear cut separation can, of course, never be made).
When technologies mature over time, a shift in phase and type of activity is foreseen. Inherent to university research, DACS
moves on the increasing side of the wave (to the right). Note that the presented structure is based on technical content, not
an organizational sub-structuring of the group. There is strong collaboration between the various group members, and
projects generally cover multiple issues.
3. Key journal publications for 2009-2010
van Brandenburg, R. and van Deventer, M.O. and Karagiannis, G. and Schenk, M.
Towards personalized TV for concurrent use; challenges and opportunities for IMS-based IPTV
In: Journal of Internet Engineering
December 2010
van Wanrooij, W. and Pras, A.
Filtering spam from bad neighborhoods
In: International Journal of Network Management
15 November 2010
Klink, D. and Remke, A.K.I. and Haverkort, B.R.H.M. and Katoen, J.P.
Time-bounded reachability in tree-structured QBDs by abstraction
In: Performance evaluation
31 May 2010
Jongerden, M.R. and Mereacre, A. and Bohnenkamp, H.C. and Haverkort, B.R.H.M. and Katoen, J.P.
Computing Optimal Schedules of Battery Usage in Embedded Systems
ASCI bi-annual Report 2009-2010
42
In: IEEE Transactions on Industrial Informatics
2010
Menth, M. and Lehrieder, F. and Briscoe, B. and Eardley, P. and Moncaster, T. and Babiarz, J. and Charny, A. and
Zhang, Sinyang and Taylor, T. and Chan, Kwok-Ho and Satoh, Daisuke and Geib, R. and Karagiannis, G.
A Survey of PCN-Based Admission Control and Flow Termination
In: IEEE Communications Surveys & Tutorials
2010
Sperotto, A. and Schaffrath, G. and Sadre, R. and Morariu, C. and Pras, A. and Stiller, B.
An Overview of IP Flow-Based Intrusion Detection
In: IEEE Communications Surveys & Tutorials
2010
Andrey, L. and Festor, O. and Lahmadi, A. and Pras, A. and Schoenwaelder, J.
Survey of SNMP performance analysis studies
In: International Journal of Network Management
November 2009
Liu, Fei and Heijenk, G.J.
3.19 Contribution of UT-EWI-CAES
University of Twente, Faculty of Electrical Engineering, Mathematics an Computer Science, Computer Architecture, Design &
Test for Embedded Systems
Prof.dr.ir. G.J.M. Smit, Dr.ir. A.B.J. Kokkeler, Ir. E. Molenkamp
Program Design
The main emphasis of the group is on efficient architectures for dependable networked embedded systems. Within this
theme the chair performs research on three related key areas:
1) Efficient architectures for streaming applications,
2) Architectures for efficient energy management,
3) Dependability issues of embedded systems.
Energy-efficiency and dependability are the main drivers of our research. Energy-efficiency is important for streaming
applications found in battery powered mobile devices, and for high-performance systems. The effort on energy efficient
architectures focuses on reconfigurable processors for streaming applications, e.g. found in battery powered mobile devices
(e.g. portable multimedia players) or sensor networks. However, within high performance embedded computing (e.g. medical
imaging, radar processing), extrapolating the current trend of using general purpose processors for future systems predicts
excessive power consumption. MPSoC (Multi Processor Systems-on-Chip) devices for streaming applications are prime
candidates for use in this application domain as well. Dependability plays an important role in sensor networks (nodes may
fail or run out of energy unexpectedly). In MPSoC (Multi Processor Systems-on-Chip) systems for streaming applications
dependability techniques also play an important role.
Results in 2009
Efficient Architectures for Streaming Applications (Dr. A.B.J. Kokkeler, Dr. J. Kuper, Prof. G.J.M. Smit, Prof. M. Bekooij)
Research on techniques for analysis and synthesis of predictable multi-processor systems continued in cooperation with
NXP. This resulted e.g. in new techniques for modeling run-time arbitration and fast calculation of buffer capacities for multicore architectures that was published in ACM TECS (2010 issue). The predicatable NoC developed by Wolkotte was
published in IEEE Transactions on VLSI. The results of run-time spatial mapping (Hölzenspies and ter Braak) resulted in a
publication in the Journal of Parallel Programming and a paper on DATE2010.
This theme resulted in four Ph.D. theses in 2009 of Maarten Wiggers “Aperiodic Multiprocessor Scheduling for Real-Time
Stream Processing Applications” , Pascal Wolkotte “Exploration within the Network-on-Chip Paradigm”, Qiwei Zhang
“Cognitive Radio on a Reconfigurable MPSoC Platform”, and Mohammed Khatib “MEMS-Based Storage Devices Integration in Energy-Constrained Mobile Systems”.
Architectures for efficient energy management (Prof. G.J.M. Smit)
Besides the development of efficient architectures, the use of these architectures to increase energy efficiency in a more
general sense, is a subject of research. Distributed micro-generation techniques (micro-CHP, solar cells, micro windmills)
play an important role in this research. Because of the reduced peak load a power plant can generate energy more
efficiently. The research topics resulted in a number of conference papers and a journal publication is in preparation. Smit
was one of the initiators of the STW/NWO/ICTRegie programme SES (Smart Energy Systems), a programme with a budget
of 6 M Euro.
ASCI bi-annual Report 2009-2010
43
Efficient dependable networked embedded systems (Dr. H.G. Kerkhoff)
The research in dependable systems, including mixed-signal IPs and sensors, is centred on the design and implementation
of architectures, IPs and circuits for dependable networked embedded systems. The key research challenge is to foster
dependability (i.e. availability, reliability, integrity and maintainability) as embedded systems are business or safety critical in
many applications. The group made the dependability managerfor the RFD chip in the FP7 the CRISP project.
This theme resulted in a number of conference publications and a publication in the Microelectronics journal.
Results in 2010
Efficient Architectures for Streaming Applications (Dr. A.B.J. Kokkeler, Dr. J. Kuper, Prof. G.J.M. Smit, Prof. M. Bekooij)
Research on techniques for analysis and synthesis of predictable multi-processor systems continued in cooperation with
NXP. This resulted e.g. in new techniques for modeling run-time arbitration and fast calculation of buffer capacities for multicore architectures that was published in ACM TECS. The results of run-time spatial mapping (Hölzenspies and ter Braak)
resulted in a publication in the Journal of Parallel Programming and a paper on DATE2010. Smit and ter Braak gave a
tutorial at the SoC conference in Tampere. Wiggers and Bekooij gave a tutorial at the Embedded Systems week. One of the
post-docs Maarten Wiggers has set up a cooperation with UC Berkeley with the group of prof. Edward Lee. This has resulted
in two papers in 2010 / 2011. In 2010 the group also contributed to three “kenniswerkers” projects: AIPRO together with Océ,
and RFTT together with Nedap. Projects that started in 2010 are STARS (BSIK FES2008 on reconfigurable sensor systems),
STW project SeaSTAR (on underwater communication), Pieken in de Delta project DTFC (on test platforms), EFRO project
TSR (reading RFID tags from a long distance), FP7 projects So(o)S and ADVANCE (on programming multi-core
architectures) This theme resulted in three Ph.D. theses in 2010 of Philip Hölzenspies “On run-time exploitation of
concurrency”, Marcel van de Burgwal “Interfacing Networks-on-Chip: Hardware meeting Software” and Leon Evers “Concise
and flexible programming of wireless sensor networks”.
Architectures for efficient energy management (Prof. G.J.M. Smit)
Besides the development of efficient architectures, the use of these architectures to increase energy efficiency in a more
general sense is a subject of research. Distributed micro-generation techniques (micro-CHP, solar cells, micro windmills)
play an important role in this research. Because of the reduced peak load a power plant can generate energy more
efficiently. The research topics resulted in a number of conference papers and a journal publication is IEEE Transactions on
Smart Grid. Smit was one of the initiators of the STW/NWO/ICTRegie programme SES (Smart Energy Systems). The group
contributed to four project proposals for SES; all four proposals were accepted.
Efficient dependable networked embedded systems (Dr. H.G. Kerkhoff)
The research in dependable systems, including mixed-signal IPs and sensors, is centred on the design and implementation
of architectures, IPs and circuits for dependable networked embedded systems. The key research challenge is to foster
dependability (i.e. availability, reliability, integrity and maintainability) as embedded systems are business or safety critical in
many applications. There was cooperation with NXP and Recore systems in the Catrene TOETS project with 3 PhD
students, all related to dependability in automotive applications. The group designed the dependability manager for the RFD
chip in the FP7 the CRISP project. In November 2010 we received samples of the RFD chip and the dependability manager
is working as expected. In the “Kenniswerkingsregeling”, there was the cooperation of postdoc Dr. Kerzerho with NXP
automotive in Nijmegen resulting in a redesign of an existing product to improve the resilience of a CAN transceiver. In the
Strategic Research Orientation DSN (Dependability Sensor Networks) with shared postdoc Dr. Senouci, a wireless hardware
platform is being developed for real-time dependability tests. In the cluster project EMPATIE, new algorithms were developed
for NXP Eindhoven for evaluating embedded data converters. In total 10 IEEE contributions in dependability were accepted
for European and international conferences.
Five key publications
[1]
Banerjee, A. and Wolkotte, P.T. and Mullins, R.D. and Moore, S.W. and Smit, G.J.M., “An Energy and Performance
Exploration of Network-on-Chip Architectures” IEEE Transactions on Very Large Scale Integration (VLSI) Systems, 17 (3),
2009, pp. 319-329. ISSN 1063-8210
[2]
van de Burgwal, M.D. and Wolkotte, P.T. and Smit, G.J.M. “Non-power-of-Two FFTs: Exploring the Flexibility of the
Montium TP” International Journal on Reconfigurable Computing, 2009. 678045. ISSN 1687-7195
[3]
Hölzenspies, P.K.F. and ter Braak, T.D. and Kuper, J. and Smit, G.J.M. and Hurink, J.L. “Run-time Spatial Mapping
of Streaming Applications to Heterogeneous Multi-Processor Systems” International Journal of Parallel Programming, 38 (1),
2009, pp. 68-83. ISSN 1573-7640
[4]
Oude Alink, M.S. and Kokkeler, A.B.J. and Klumperink, E.A.M. and Rovers, K.C. and Smit, G.J.M. and Nauta, B.
“Spurious-Free Dynamic Range of a Uniform Quantizer” IEEE transactions on circuits and systems II: Express Briefs,
Volume 56 (6), 2009, pp. 434-438. ISSN 1549-7747
ASCI bi-annual Report 2009-2010
44
[5]
Kerkhoff, H.G. and Zhang, Xiao “Fault co-simulation for test evaluation of heterogeneous integrated biological
systems” Microelectronics journal, Volume 40, Issue 7, 2009, ISSN 0026-2692
[6]
Wiggers, M.H. and Bekooij, M.J.G. and Smit, G.J.M. “Buffer Capacity Computation for Throughput-Constrained
Modal Task Graphs”, ACM Transactions on Embedded Computing Systems, 10 (2). Article 17. ISSN 1539-9087
[7]
Molderink, A. and Bakker, V. and Bosman, M.G.C. and Hurink, J.L. and Smit, G.J.M. “Management and Control of
Domestic Smart Grid Technology”, IEEE transaction on Smart Grid, 1 (2). pp. 109-119. ISSN 1949-3053
[8]
ter Braak, T.D. and Hölzenspies, P.K.F. and Kuper, J. and Hurink, J.L. and Smit, G.J.M. “Run-time Spatial
Resource Management for Real-Time Applications on Heterogeneous MPSoCs”, In: Proceedings of the Conference on
Design, Automation and Test in Europe (DATE 2010), 8-12 Mar 2010, Dresden. pp. 357-362. ISBN 978-3-9810801-6-2
[9]
Oude Alink, M.S. and Klumperink, E.A.M. and Soer, M.C.M. and Kokkeler, A.B.J. and Nauta, B., “A 50MHz-to1.5GHz Cross-Correlation CMOS Spectrum Analyzer for Cognitive Radio with 89dB SFDR in 1MHz RBW”, In: IEEE
Symposium on New Frontiers in Dynamic Spectrum Access Networks (DySPAN 2010), 6-9-April-2010, Signapore. IEEE
Press. ISBN 978-1-4244-5188[10]
Kerkhoff, H.G. and Zhang, Xiao “Design of an Infrastructural IP Dependability Manager for a Dependable
Reconfigurable Many-Core Processor”, In: Fifth IEEE International Symposium on Electronic Design, Test & Applications,
DELTA 2010, 13-15 Jan 2010, Ho Chi Minh City, Vietnam. pp. 270-275. IEEE Computer Society Press. ISBN 978-0-76953978-2
3.20 Contribution of EUR-UMCR
The Biomedical Imaging Group Rotterdam develops and validates advanced image analysis algorithms for a number of
applications. The research is organized in 6 research lines, cardiovascular image analysis, neuro image analysis, image
analysis in oncology, model-based image analysis, cellular and molecular image analysis, and image guided interventions.
Within the cardiovascular image analysis research line, the focus has been on (i) development and evaluation of plaque
detection and characterization in carotid arteries from CT and MRI data, to support improved diagnosis and prognosis in
stroke (ii) development of methods for functional and anatomical assessment of the heart chambers and coronaries from CT,
and (iii) development of motion estimation techniques from 4D imaging data, a.o. to study morphodynamics of cerebral
aneurysms, distensibility of carotid arteries, and coronary motion. Within the neuro group, the focus has been on the
development and application of new software tools to extract imaging biomarkers from MR brain data. Although volumetric
features are still a point of attention, we extended our work towards the measurement of shape features and connectivity
measures in the brain. Also the processing of large cohorts has been improved and more standardized, improving our
understanding of neurodegenerative disease, and providing reference data for clinical use. In the onco image analysis
research line focus has been on the development and validation of MRI based non-invasive biomarkers for (i) the
characterization of tumor tissue, and (ii) the evaluation of cancer treatment response and outcome. In the model based
medical image analysis research line several techniques for the quantitative analysis of a variety of medical images, have
been developed with a focus on statistical learning and modeling. Applications include (i) Segmentation and shape analysis
of brain structures from MR images, (ii) Characterization of blood vessel plaque components in MR and CT images using
registration and classification, (iii) Shape and motion modeling including landmark uncertainty estimates, and (iv)
Quantification of pulmonary disease by lung density, texture, and airway measures
Within the cellular and molecular image analysis group the focus has been on the development and evaluation of improved
methods for (i) particle detection and tracking in fluorescence microscopy, (ii) model-based cell segmentation, tracking, and
lineage reconstruction for the study of embryogenesis, and (iii) super-resolution image reconstruction with particular
application to molecular magnetic resonance imaging. Within the image guidance in interventions research line, the focus
has been on (i) modeling cardiac and coronary shape and motion from 4D CTA, and (ii) using these dynamic models for
registering cardiac CTA to coronary X-ray angiography images
In the next reporting period, within the cardiovascular image analysis research main focus areas will be on the detection and
quantification of progression of atherosclerotic disease, and prognostic value of cardiovascular imaging biomarkers, both in
the context of large scale longitudinal imaging studies. Within the neuro image analysis line we will focus on further
improving and extending the list of biomarkers of neurodegenerative disease, but also on the processing of larger and more
heterogeneous patient cohorts. In oncology we will focus on multi-modal image analysis for treatment planning, treatment
monitoring and outcome prediction to facilitate individualized patient care. In model-based image analysis the work on
computer-aided diagnosis of neurodegenerative, cardiovascular, and pulmonary disease will be extended and there will be a
special focus on the investigation of transfer learning techniques to improve analysis of image data acquired with different
scanning protocols.
In cellular and molecular image analysis we will focus on the development of methods for single molecule analysis, largescale object tracking, neuronal reconstruction, and learning-based image segmentation. Within the image guidance in
interventions research we will continue and extend the current cardiac work, and additionally start research in image
guidance in radiology, developing methods to improve guidance for o.a. US guided RFA and X-ray guided RFA and TACE.
ASCI bi-annual Report 2009-2010
45
Furthermore, in 2011, a new research line on image registration has been initiated. In the coming period, this research line
will focus mainly on registration of carotid vessel wall imaging data (to combine information from multiple modalities) and on
registration of MR brain scans (to facilitate atlas building and automated disease classification).
Main Publications:
1) M. Schaap, C.T. Metz, T. van Walsum, A.G. van der Giessen, A.C. Weustink, N.R.A. Mollet, C. Bauer, H. Bogunović, C.
Castro, X. Deng, E. Dikici, T. O'Donnell, M. Frenay, O. Friman, M. Hernández Hoyos, P.H. Kitslaar, K. Krissian, C. Kühnel,
M. A. Luengo-Oroz, M. Orkisz, Ö Smedby, M. Styner, A. Szymczak, H. Tek, C. Wang, S. K. Warfield, S. Zambal, Y. Zhang,
G. P. Krestin and W.J. Niessen. Standardized Evaluation Methodology and Reference Database for Evaluating Coronary
Artery Centerline Extraction Algorithms, Medical Image Analysis, 13(5):701-714, 2009.
2) T. den Heijer, F. van der Lijn, P. J. Koudstaal, A. Hofman, A. van der Lugt,
G. P. Krestin, W.J. Niessen and M.M.B. Breteler, A 10-year follow-up of
hippocampal volume on magnetic resonance imaging in early dementia and
cognitive decline, Brain, 2010
3) R. de Boer, H.A. Vrooman, M. A. Ikram, M. W. Vernooij, M.M.B. Breteler, A.
van der Lugt and W.J. Niessen, Accuracy and reproducibility study of
automatic MRI brain tissue segmentation methods, NeuroImage, 2010
4) C.T. Metz, S. Klein, M. Schaap, T. van Walsum and W.J. Niessen. Nonrigid registration of dynamic medical imaging data
using nD+t B-splines and a groupwise optimization approach, Medical Image Analysis, 2011
5) E. Meijering, O. Dzyubachyk, I. Smal, W. A. van Cappellen. Tracking in Cell and Developmental Biology. Seminars in Cell
and Developmental Biology, vol. 20, no. 8, October 2009, pp. 894-902.
6) O. Dzyubachyk, J. Essers, W. A. van Cappellen, C. Baldeyron, A. Inagaki, W. J. Niessen, E. Meijering. Automated
Analysis of Time-Lapse Fluorescence Microscopy Images: From Live Cell Images to Intracellular Foci. Bioinformatics, vol.
26, no. 19, October 2010, pp. 2424-2430.
7) L. Alic, M Van Vliet, C. F. van Dijke, A. M. M. Eggermont, J.F. Veenland and W.J. Niessen, Heterogeneity in DCE-MRI
parametric maps: a biomarker for treatment response?, Physics in Medicine and Biology, 2011 Mar 21;56(6):1601-16
8) L. Alic, J. Haeck, K. Bol, S. Klein, S. T. van Tiel, P. A. Wielopolski, M de Jong, W.J. Niessen, M Bernsen and J.F.
Veenland, Facilitating tumor functional assessment by spatially relating 3D tumor histology and in vivo MRI: Image
registration approach, PLoS ONE, PLoS ONE 6(8) :e22835
9) L. Sørensen, S. Shaker, and M. de Bruijne. Quantitative analysis of pulmonary emphysema using local binary
patterns. IEEE Transactions on Medical Imaging, 29(2):559-569, 2010.
10) H.C. Achterberg, F. van der Lijn, T. den Heijer, A. van der Lugt, M.M.B. Breteler, W.J. Niessen, and M. de Bruijne.
Prediction of dementia by hippocampal shape analysis. In Fei Wang, Pingkun Yan, Kenji Suzuki, and Dinggang Shen,
editors, Machine Learning in Medical Imaging, volume 6357 of Lecture Notes in Computer Science, pages 42-49. Springer,
2010.
3.21 Contribution of RUN-UMCR
Diagnostic Image Analysis Group (DIAG) Nijmegen
Radiology Department,
Radboud University Nijmegen Medical Centre
Prof Dr N Karssemeijer, Prof Dr B van Ginneken, Dr R Manniesing, Dr C Sanchez, Dr HJH Huisman
Research 2009-2010
The Diagnostic Image Analysis Group aims at developing computer algorithms to aid clinicians in the interpretation of
medical images and thereby improve the diagnostic process. Driven by clinically relevant application domains, innovative
ASCI bi-annual Report 2009-2010
46
methods are investigated to address challenging problems in image analysis, computer-aided detection, and computer-aided
diagnosis. While in previous years the group had a strong focus on breast and prostate imaging applications, research has
expanded to new areas as chest imaging and retinal imaging. An overview per theme is presented below.
Retinal imaging has rapidly grown within ophthalmology in the past twenty years. The availability of cheap cameras to take
direct images of the retina, fundus photography, makes it possible to examine the eye for the presence of many different eye
diseases with a simple, non-invasive method. Within DIAG, research has focused on automatic early detection of diabetic
retinopathy from fundus photographs. We are also applying the computer-aided detection and quantification techniques we
have developed to diagnosis and quantification of macular degeneration.
Breast imaging remains an active field of research of DIAG. Research focuses on developing automated image analysis
methods aimed at helping radiologists with detecting and diagnosing breast cancer. Analysis of mammograms is the most
important topic, as x-ray mammography is the technology by which the vast majority of cancers are detected. Computer
aided reading of mammograms is currently the largest application of CAD in practice. However, it has to be improved to
increase effectiveness. Research has been performed to improve algorithms, in particular those involving combination of
views and exams and exploitation of context. Apart from that, we are also trying to understand how radiologists can best
make use of CAD techniques. We performed observer studies to investigate how radiologist are influenced by CAD in their
decisions. Optimizing human performance with CAD appears to be far from trivial and requires better understanding of
cognitive processes leading to diagnostic decisions. In addition to projects in mammography, projects started in which multimodal breast imaging applications are developed. These involve combinations of MRI, whole breast ultrasound,
tomosynthesis, and mammography.
Lung imaging is a new area for DIAG. It has a large potential for development of clinically relevant applications as lung
diseases are among the most important causes of death. In 2020, it is expected that chronic obstructive pulmonary disease
(COPD) is the third cause of death, respiratory infections will be the fourth cause of death worldwide, followed by lung
cancer, the most deadly cancer. Tuberculosis will rank seven on this list. There are many other diseases of the lung, such as
interstitial lung disease, occupational lung disease and cystic fibrosis. For all these diseases, imaging is vital to learn more
about their nature, to detect them early and to follow up on their course and treatment. Research in DIAG focuses both on
the analysis of chest x-ray and chest CT. For x-ray we are developing tools to detect tuberculosis and lung cancer, and work
on algorithms to remove normal anatomical structures from the radiographs and to detect changes between baseline and
follow-up exams. For CT we are working on computer-aided detection of nodules, which can be small lung tumors, and we
have developed a toolkit for analysis of the lungs, the lobes, airways and vessel trees. With these techniques that are used in
many research projects with clinical collaborators, we are quantifying different aspects of various lung diseases.
Prostate imaging with MRI remains a major research themes. A diagnostic workstation under development in DIAG is used
in day-to-day clinical practice and clinical research projects. With Nijmegen being one of the world-wide leading centers in
prostate imaging the setting is ideal for innovative multi-disciplinary research. Research is aimed at development of
automated image analysis tools and computer aided diagnosis to support clinical workflow and quality of image
interpretation. Improved localization and staging of prostate cancer for targeted biopsies is a main direction of research.
More recently, advanced processing techniques are being developed aimed at screening applications, in which information
from multiple MRI sequences is optimally combined. In addition, a project is focusing on helping radiologist to identify and
diagnose lymph node metastases using USPIO enhanced MRI.
Publications
B. van Ginneken, S.G. Armato, B. de Hoop, S. van de Vorst, T. Duindam, M. Niemeijer, K. Murphy, A.M.R. Schilham, A.
Retico, M.E. Fantacci, N. Camarlinghi, F. Bagagli, I. Gori, T. Hara, H. Fujita, G. Gargano, R. Belloti, F.D. Carlo, R. Megna, S.
Tangaro, L. Bolanos, P. Cerello, S.C. Cheran, E.L. Torres and M. Prokop. "Comparing and combining algorithms for
computer-aided detection of pulmonary nodules in computed tomography scans: the ANODE09 study", Medical Image
Analysis 2010;14:707-722.
M. Samulski, R. Hupse, C. Boetes, R. Mus, G. den Heeten and N. Karssemeijer. "Using Computer Aided Detection in
Mammography as a Decision Support", European Radiology 2010;20(10):2323-2330.
P.C. Vos, T. Hambrock, J.O. Barentsz and H.J. Huisman. "Computer-assisted analysis of peripheral zone prostate lesions
using T2-weighted and dynamic contrast enhanced T1-weighted MRI", Physics in Medicine and Biology 2010;55(6):17191734.
ASCI bi-annual Report 2009-2010
47
R. Hupse and N. Karssemeijer. "Use of normal tissue context in computer-aided detection of masses in mammograms",
IEEE Transactions on Medical Imaging 2009;28(12):2033-2041.
N. Karssemeijer, A.M. Bluekens, D. Beijerinck, J.J. Deurenberg, M. Beekman, R. Visser, R. van Engen, A. Bartels-Kortland
and M.J. Broeders. "Breast cancer screening results 5 years after introduction of digital mammography in a population-based
screening program", Radiology 2009;253(2):353-358.
M. Velikova, M. Samulski, P.J.F. Lucas and N. Karssemeijer. "Improved mammographic CAD performance using multi-view
information: a Bayesian network framework", Physics in Medicine and Biology 2009;54(5):1131-1147.
ASCI bi-annual Report 2009-2010
48