ADIAC: Automatic Diatom Identification And Classification

Funded by the European MAST (Marine Science and Technology) programme, contract MAS3-CT97-0122

Keywords: phycology, taxonomy, ecology, image processing, pattern recognition, databasing

Note: This is a brief frontpage with a summary. 
For all details and public data go to: ADIAC 
These pages are mirrored at University of Algarve, Portugal.

ADIAC in a nutshell (only 5 minutes reading):

Diatoms are unicellular algae found in water and wherever there is humidity. There are thousands of different taxa, and their valves have different shapes and ornamentations. Because of their narrow ecological preferences, they can be used as ecological indicators for measuring pH and nutrient status in old sediments. They are studied in archaeology to trace ceramic and clothing fragments. In forensic research they are used to determine the cause of death in drowning cases. Diatoms are very good indicators of water quality.

The identification of diatoms is a very tedious work, because microscope slides must be prepared, scanned, photographed, and the diatoms found must be linked to described taxa. The latter is normally done by comparing their images with those in atlasses, which is quite difficult even for experts because of the very subtle variations of the shapes and ornamentations.

The ADIAC project aims at developing algorithms for an automatic identification of diatoms using image information, i.e. both shape and ornamentation. For this purpose the consortium, existing of diatomists, taxonomists, ecologists and pattern recognition experts, will create image databases and software for feature extraction, identification, as well as automatic microscope slide scanning including autofocusing. The ADIAC project is very innovative and can, in a near future, introduce a revolution in diatom research in all application areas.

Because ADIAC is a pilot study (it is the first project to systematically study the identification taking the ornamentation into account), active collaborations with both diatomists and pattern recognition experts are sought. Much if not all information, image databases and software, will be made freely available by means of these webpages. Please keep track of ADIAC, and contact the coordinator or the partners if you think you could contribute!

PRELIMINARY RESULTS:
After 3 years the public database contains approx 3400 images, whereas the non-public database contains approx 2500 more images.
The online diatom browser contains approx 2300 images of 500 taxa plus 250 synonyms, about 750 names in total.
IDENTIFICATION TESTS:
On a very difficult set of Sellaphora pupula with 6 demes, different contour feature sets and different classifiers can achieve identification rates from 75% to 90%.
On a large set of 781 images with 37 taxa, a combination of all feature sets and 10-fold cross-validation with the C4.5 decision tree yielded an identification rate of 89%. For detailed information go to ADIAC and Results section.

YOU CAN EXPERIMENT WITH AN ONLINE DEMO IDENTIFICATION:
Partner RUG has prepared a web demo version that allows to select an image that will then be identified using part of the database. The user cannot yet identify his own images (this requires a continuation project ADIAC-2), but the demo shows the results we can obtain and how diatom identification in the 21st century might look like. Click: ADIAC ONLINE DEMO

  • Total budget: 1,250,000 ECU
  • Main funding: 850,000 ECU - CEC DG XII MAST Programme, contract MAS3-CT97-0122
  • Start: May 1998; Duration: 3 years
  • Coordinator: Hans du Buf, University of Algarve, Faro, Vision Laboratory
  • Partners:

    • Stephen Droop - Royal Botanic Garden Edinburgh, Diatom Laboratory
    Stephen Juggins - University of Newcastle Upon Tyne, Dept of Geography
    Bertrand Ludes - University Louis Pasteur, Strasbourg, Inst for Legal Medicine
    Jos Roerdink - University of Groningen, Research Instit Math and Comp Science
    Horst Bunke - University of Berne, Inst Informatik u Angew Mathematik
    Gabriel Cristobal - CSIC Madrid, Inst de Optica, Imaging and Vision Dept

    Address etc of the Coordinator:

    Prof.dr.ir. J.M.H. du Buf
    Email: dubuf@ualg.pt
    Homepage: dubuf

    Dept. of Electronics and Computer Science - UCEH,
    University of Algarve,
    Campus de Gambelas, 8000 Faro, Portugal

    Tel (+351 89) 800900 extension 7761 (is new number!)
    Fax (+351 89) 818560

    Diatom images:

    The wallpaper of this page consists of a graphically manipulated diatom image.
    If you would like to see real diatom images, click on one of these:
    Diploneis heemskerkiana (1) this is a SEM image showing a 3D valve.
    Diploneis heemskerkiana (2) this is a brightfield image of the same diatom.
    More images can be found in the PUBLIC DATA webpages.

    LINKS (more links are included in the ADIAC pages):

    You can go to the ADIAC detailed webpages, or the DG XII's MAST pages including the MAST-CORDIS server. Aditional information concerning the Environment and Climate programme can be found at the EUROPA and CORDIS servers.
    Have a look at the University of Algarve, or the UAlg Vision Laboratory.

    This page has been visited Supposed to be a counter times since July 1998.

    Last update: February 1999 (Hans du Buf)