EOI.FP6.2002
Expression of Interest: Integrated Projects
INTRODUCING TOMORROW'S IMAGING TECHNOLOGY FOR LARGE-SCALE
MONITORING OF MICROSCOPIC, AQUATIC ORGANISMS
Acronym: IMAQUA
Thematic areas:
1.1.6.3 - Global change and ecosystems - Biodiversity and ecosystems
1.1.2.iv - Information Society Technology
1.1.5 - Food safety
Submitted by Prof. Hans du Buf
CINTAL - Technological Research Centre of the Algarve
Faro, Portugal
Abstract
Two European pilot projects, i.e. DiCANN (Dinoflagellate Categorisation by Artificial Neural
Network) and ADIAC (Automatic Diatom Identification and Classification) have shown that image
identification by computer can compete with human experts. In order to prepare field-tested tools
that can be applied in all areas in which large-scale monitoring of microscopic organisms must be
done, these projects must be continued in an integrated framework at a much bigger scale that
includes more organisms and applications. The proposed framework integrates experts in pattern
recognition, taxonomists and researchers with different applications, such as water quality
(drinking, recreation, harmful algal blooms, shellfish production), global change and biodiversity. It
addresses EU policies such as the Water Framework Directive (WFD), Integrated Coastal Zone
Management (ICZM) and Information Society Technologies. After the DiCANN and ADIAC
projects, Europe is already the leader. Now this technology must be developed and integrated at the
European scale.
Need and relevance
Global change, coastal zone management, biodiversity and water quality assessment require all
routine monitoring on a large scale. This involves much time-intensive work by highly-trained
analysts. Recent European projects aimed at studying the possibility of automating this routine
work in order to allow researchers to make more efficient use of their time and to concentrate on
their applications. These projects demonstrated that dinoflaggellates and diatoms can be identified
with a precision that can compete with that of human experts.
The next, logical step is to widen the scope of the small pilot projects, DiCANN and ADIAC, such
that (a) more organisms can be identified, (b) all relevant monitoring applications can be covered,
and (c) the technology can be applied throughout Europe. This involves further algorithm
development, professional software development, extending the taxonomic databases to provide
comprehensive cover of major habitat types, extensive field-testing of the technology, and, most
importantly, the establishment of technology portals in all countries such that all researchers can
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have access to the technology. These portals will play an essential role in the future, because they
serve to coordinate activities and provide hands-on experience to bootstrap new activities and
researchers. The most ambitious goal is to develop a centralised database that covers most taxa of
most habitats, such that taxa necessary for an application can be selected and identifications can be
started without the need of building a special database.
Only by developing computer-based technology, in combination with shared databases and a
common users platform, it will be possible to develop more efficient solutions for studying global
change, biodiversity and ecosystems. These requirements are essential for and directly relevant to
EU policies such as the Water Framework Directive (WFD) and Integrated Coastal Zone
Management (ICZM). In addition, the project integrates perfectly into Information Society
Technologies (IST) and other initiatives such as Marie Curie fellowships and the Erasmus
exchange programme.
Scale of ambition and critical mass
Ten years ago, before the DiCANN and ADIAC projects, automatic identification of microorganisms did not exist. Now, after these projects, Europe has developed the necessary technology,
albeit at a pilot scale. Instead of proposing small follow-up projects that would serve to finetune the
technology, we propose an ambitious framework that will make Europe the leader in both
development and application within this area. A large, co-ordinated effort is necessary, firstly to
develop a critical mass of pure and applied researchers to challenge established paradigms, second
to provide scope for the necessary synergisms to develop between experts, and third to introduce
the new technology at the European scale.
A major objective of the proposed work is to bring together scientists form very different
disciplines: biology, environment and computing science. The aim is to introduce to biologists the
advantages that technology can bring to the field of microscopy and taxonomy. By working directly
with the end users, i.e. biologists and enviromental scientists, computer scientists can tune the
technology to be user friendly and to provide real solutions to the real problems of the disciplines.
Furthermore, establishing simple data banking procedures and bringing together the information
produced by the various centres will bring benefits to all contributors and users.
If Europe is going to realise policies such as WFD and ICZM, there is an absolute need for (a)
standardised sampling and analysis procedures, (b) centralised databasing concerning all microorganisms and habitats, and (c) efficient tools to be applied, throughout Europe, on a routine basis.
This Integrated Project serves to:
1. Establish collaborations between major players in aquatic microbiology
2. Establish electronic databases that serve most key applications and habitats
3. Develop, test and optimise the technology
4. Apply the technology to key issues, from predicting harmful algal blooms
to coastal zone management
5. Train young researchers in using, and developing, computer technology
The main aim is to bring together all players and all applications, such that all are involved in the
development and all will use the technology. This integration at the largest scale is the best
guarantee that the technology will be useful for all. This needs to be done now in order to have the
technology up and running in 5-6 years from now, to guarantee that European policies can be
realised, and to assure that European research in this area maintains its cutting edge.
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Integration
The structure of the project may look simple but requires many interactions:
1. To collect representative samples at different habitats (applications)
2. To validate the samples by expert taxonomists
3. To construct databases with additional information (taxonomy, ecology)
4. To develop feature extraction algorithms for different organisms
5. To develop an identification scheme using multiple classifiers
6. To test algorithms using the databases
7. To develop professional software tools
8. To field-test the tools on new samples
The dimension of this project requires the establishment of different, pan-European, but
multidisciplinary task forces that address these logical units. This will involve a number of core
activities that also coordinate the project, plus satellite activities for collecting data etc., which can
be dynamic. The basic idea is to create specific or common feature extraction engines optimised for
images of different organisms (diatoms, dinoflagellates, coccoliths etc), and to apply these in
conjunction with one identification engine (classifier). One important requirement is that the
databases should contain sufficient samples for training the identifier, at least 20 samples per taxon.
This is the work to be done under points 1, 2 and 3. Points 4, 5 and 6 address experts in computer
vision, but require much input from biologists. Point 7 can also be done by experts in computer
vision, but requires feedback from field workers who are going to use the tools (user friendliness,
robustness). The most important difference with the previous projects DiCANN and ADIAC is the
fact that the biologists, i.e. field workers and taxonomists, are the key players: they must specify
what they want. This needs to be done right from the start of the project, and this must be
guaranteed throughout the project.
By definition, the project is a dissemination vehicle that addresses, apart from the wider audience
through scientific publications, direct colleagues in many laboratories and institutes through the
training of young researchers. At the same time it is a demonstration of the technology's
applicability, because expert knowledge is included and prior studies were rather successful, i.e. a
further development will lead to even better results: ID rates close to 100%.
The most important aspect is the training of young researchers, most importantly biologists but also
in pattern recognition. On the basis of the established experience in the DiCANN and ADIAC
projects, rigorous procedures must be applied in collecting and imaging samples, plus additional
data for the databases like taxonomic and ecological information. They must learn how to integrate
the tools into statistical analyses in order to develop the efficiency necessary for large-scale
monitoring tasks. They will also play key functions in establishing the techology portals, i.e. at
least one centre of excellence in each participating country that serves to disseminate the
technology and to provide a backup for all other end users.
With respect to necessary resources, hardware is not a point because of fast PCs, cheap disks, and
accessible scientific-grade CCD cameras. Most partners have already suitable microscopes. There
is one point that has not been mentioned before: methods have already been developed (ADIAC) to
automate slide scanning, but this requires a completely computer-controlled microscope. These are
very expensive, but it is possible that one microscope in each portal can be shared by many users.
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The main costs of this project are related to the training of young researchers, PhD students and
postdocs, including expenses involved with many partner visits, which are expected to have a
duration of up to several months. The project will foster many new grants and partner visits (Marie
Curie postdoc fellowships, exchange of PhD students within the Erasmus programme). In addition,
a successful integration implies many meetings in order to exchange experiences and to evaluate
the progress. It is anticipated that, apart from personnel contacts established during partner visits,
meetings will be organised every 6 months.
Preliminary (confirmed) partnership
BIOLOGY AND APPLICATIONS:
Dr. Martyn Kelly
Dr. Joachim Huerlimann
Bowburn Consultancy
AquaPlus
Durham
Zug
UK
Switzerland
Dr. Michel Coste
CEMAGREF Water
Quality Research Unit
Cestas
France
Dr. Jean Prygiel
Agence de L´Eau ArtoisPicardie
Netherlands Institute of
Ecology - KNAW
Douai
France
Yerseke
The
Netherlands
Institute for Inland Water
Management and Waste
Water Treatment (RIZA)
Lelystad
The
Netherlands
Dr. Ana Cristina Cardoso Joint Research Centre –
IES
Dr. Lucien Hoffmann
Public Research Center
Gabriel Lippmann
Prof. Eugen Rott
Univ. of Innsbruck
Ispra
Italy
Luxembourg
Luxembourg
Innsbruck
Austria
Prof. Alice Newton
Univ. of Algarve
Faro
Portugal
Prof. Margarida Reis
Univ. of Algarve
Faro
Portugal
Dr. Fran Saborido-Rey
Institute of Marine
Research
Spanish Institute of
Oceanography - IEO
Institute of Marine
Sciences CMIMA-CSIC
Vigo
Spain
Vigo
Spain
Barcelona
Spain
Ghent Univ
Gent
Belgium
Univ. Athens
Athens
Greece
Brno
Czech republic
Dr. Lucas Stal
Dr. Arnold Veen
Dr. Beatriz Reguera
Dr. Celia Marrase,
Dr. Jordi Camp,
Dr. Lluisa Cros,
Dr. Carlos Pedros-Alio
Dr. Wim Vyverman
Dr. Daniel Daniliedis
Prof. Blahoslav Marsalek Czech Acad. of Sciences
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limnology, water quality
bioindication,
palaeolimnology, forensics
diatom taxonomy and
ecology, bioindication,
global change
monitoring, bioindication,
ecology, rivers, diatoms
ecophysiology and
diversity of benthic and
planktonic cyanobacteria
and diatoms
phyto- and zooplankton
surveys,
ISO 17025 phytoplankton
standardisation, quality
assurance
monitoring ecological
quality indicators, climate
taxonomy of cyanobacteria
(blue-green algae)
periphyton-based river
monitoring, taxonomy and
ecology
oceanography, coastal
zone monitoring
environmental
microbiology, ecology,
cyanobacteria
marine fisheries ecology,
monitoring
morphological variability
of microalgae
phytoplankton taxonomy
and ecology, monitoring
HABs
protistology and aquatic
ecology
diatom taxonomy and bio
monitoring
fluorescent probes for
metabolic quantification
Prof. David Mann
Royal Botanic Garden
Edinburgh
UK
Dr. Jeremy Young
Natural History Museum
London
UK
Dr. Steve Juggins,
Dr. Richard Telford
Univ. of Newcastle
Newcastle
upon Tyne
UK
Dr. Raymond Leakey,
Dr. Christine Campbell
Scottish Association for
Marine Sciences
Argyll
UK
Dr. Eva-Maria Noethig
Alfred Wegener Institute
for Polar and Marine
Research
Alfred Wegener Institute
for Polar and Marine
Research
Bremerhafen
Germany
Helgoland
Germany
Botanic Garden and
Museum Berlin-Dahlem
Max-Planck Institute for
Limnology
Berlin
Germany
Ploen
Germany
Dr. Serena Fonda Umani
Prof. Svetislav Krstic
Univ. of Trieste
Institute of Biology
Trieste
Skopje
Italy
Macedonia
Dr. Jacob Larsen,
Dr. Henrik Enevoldsen,
Dr. Gert Hansen
IOC Science and
Communication Centre on
Harmful Algae
Copenhagen
Denmark
Dr. Karen Wiltshire,
Dr. Mona Hoppenrath
Dr. Regine Jahn
Dr. Martin Beutler
taxonomy/identification of
freshwater and marine
algae
taxonomy/identification of
coccolithophores
freshwater and coastal
water quality, global
change
quantification of marine
phytoplankton, culture
collection
phyto- and
protozooplankton ecology
biological oceanography,
phytoplankton, taxonomy
of diatoms and
dinoflagellates
freshwater eucaryotic
microalgae, diatoms
primary productivity,
mathematical fit
algorithms
microplancton
diatom taxonomy,
monitoring
taxonomy and
identification of
dinoflagellates
PATTERN RECOGNITION AND SOFTWARE DEVELOPMENT:
Prof. Hans du Buf
Univ. of Algarve
Faro
Portugal
Prof. Phil Culverhouse
Univ. of Plymouth
Plymouth
UK
Prof. Hans Thierstein,
Dr. Joerg Bollmann,
Dr. Patrick Quinn
Prof. Horst Bunke
ETHZ
Zuerich
Switzerland
Univ. of Bern
Bern
Switzerland
Prof. David Marshall
Dr. Gabriel Cristobal
Cardiff Univ
CSIC
Cardiff
Madrid
UK
Spain
Dr. Fyllis Tafas
Univ. of Athens
Athens
Greece
Prof. Josef Bigun
Dr. Jon French
Halmstad Univ
University College
Halmstad
London
Sweden
UK
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computer vision and pattern recognition
(diatoms)
computer vision and pattern recognition
(dinoflagellates, zooplankton, fish
larvae)
automated microscopy and identification
(coccoliths, foraminifera)
computer vision and pattern recognition
(diatoms)
computer vision and pattern recognition
automatic slide scanning, pattern
recognition
very high speed optical scanning for
toxic dinoflagellates
pattern recognition
in situ imaging, water column profiling