EurOCEAN 2000 - Vlaams Instituut voor de Zee

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ADIAC: DIATOMS GO DIGITAL
M. Bayer 2 , J. du Buf 3 , H. Bunke 4 , A. Ciobanu 3 , G. Cristobal 1
S. Fischer 4 , R. Head 7 , S. Juggins 7 , B. Ludes 6 , D. Mann 2
J. Pech-Pacheco 1 , J. Roerdink 5 , L. Santos 3 , M. Wilkinson 5
1 Instituto de Optica (CSIC), Madrid, Spain; 2 Royal Botanic Garden Edinburg, UK
3 University of Algarve, Faro, Portugal; 4 University of Bern, Switzerland
5 University of Groningen, The Netherlands; 6 University Louis Pasteur, Strasbourg, France
7 University of Newcastle upon Tyne, UK
ABSTRACT. ADIAC is the first MAST project to study the automatic identification of
diatom images by computer. Now, two years after the project's start, it is taking shape in all
planned tasks and as a whole. Very large image databases with taxonomic and ecological
information have been created. These are already online accessible to diatomists as a new and
electronic version of the classical atlasses. First software packages have been created for
feature extraction and classification (identification) of diatom contours, and work concerning
the extraction of features of the ornamentation is about to start. Also, first results on the
automatic scanning of strewn slides are available, and strategic research with end-users on
specific applications in order to develop exploitable products has started.
INTRODUCTION
ADIAC started two years ago, on May 1st 1998. It is a first pilot project to investigate the
possibility of identifying diatoms on the basis of image information, taking into account both
the contour and the ornamentation of valves. Most information is online available at
http://www.ualg.pt/adiac/ and mirrored at http://www.rbge.org.uk/ADIAC/ and this
information will be regularly updated until, or even after, the end of the project which is
foreseen in October 2001. Because a first pilot project cannot deliver a high-quality end
product that is applicable in all phycological areas, an integral part of the project is concerned
with the establishment of contacts with end users in order to define a follow-up project in
which real applications must be challenged. Such applications are routine tasks in e.g.
monitoring water quality, all relevant areas in geology or drowning cases in forensic research.
Possible end users can contact the Coordinator or other partners in order to see how their input
can optimise ADIAC's impact on their specific applications and requirements.
All ADIAC tasks have a direct link with automating the identification process: (1) scanning
strewn slides at low magnification on a microscope fitted with a motorised stage to detect
diatom positions prior to image capture at a high magnification, (2) to extract contours and
morphological features from these, (3) the same for the ornamentation, and (4) to identify
diatoms using information stored in image and taxonomic databases. The following Sections,
contributed by the different partners, provide a snapshot of all current activities.
DATABASES
The contribution of the Royal Botanic Garden Edinburgh consists primarily of providing
diatom images and taxonomic data, as well as taxonomic advice to the non-biology partners in
the project. They are assisted by UNEW and ULP. RBGE has been building large image
databases of several thousands of diatoms acquired directly from specimens on light