LAYMAN’S REPORT With the contribution of the LIFE financial instrument of the European Union LIFE+ NATURE AND BIODIVERSITY WWw.AMIBIO-PROJECT.EU LIFE08 NAT/GR/000539 Support Total Budget: 1,664,282.00 Life+ Contribution: 830,641.00 Year of Finance: 2008 Start Date: 01−FEB−2010 End Date: 30−JUN −2013 AmiBio: Automatic acoustic Monitoring and Inventory of BIOdiversity Contact Us Nikos Fakotakis, Project Coordinator Wire Communications Laboratory, University of Patras, 26500 Rion-Patras, Greece E-mail: [email protected]Phone: +30 2610 996 496 http://www.amibio-project.eu/
Transcript
LAYMAN’S REPORT
With the contribution of the LIFE financial instrument of the European Union
LIFE+ NATURE AND BIODIVERSITY WWw.AMIBIO-PROJECT.EU LIFE08 NAT/GR/000539
Support Total Budget: 1,664,282.00
Life+ Contribution: 830,641.00
Year of Finance: 2008
Start Date: 01−FEB−2010
End Date: 30−JUN −2013
AmiBio: Automatic acoustic Monitoring and Inventory of BIOdiversity
Contact Us Nikos Fakotakis, Project Coordinator Wire Communications Laboratory,
A considerable number of species – including ourselves – communicate acoustically. Bird songs are
an inspiring aesthetic experience, including poets and composers. Experienced naturalists
(ornithologists) can interpret their voices to determine the species and even a bird´s mood. In 2010,
an interdisciplinary team of Greek engineers and German zoologists launched the Life+ Biodiversity
AmiBio project, to establish an automated system of acoustic biodiversity monitoring in the Natura
2000 site Hymmetus mountain near Athens, Attica, Greece.
The rugged mountain range reaches from sea level to 1,100 m, and consists of a complex mosaic of
Mediterranean habitats, including caves and a thermal freshwater lake. Besides an impressive di-
versity of plants, Hymmetus provides home for a wide variety of animals, including some insects
endemic for Attica, such as the katydid Poecilimon propinquus.
Nearly all birds, crickets, grasshoppers and katydids produce species-specific songs to recognise
their own conspecifics, and therefore can be detected acoustically. In fact, some grasshopper spe-
cies occurring at Hymmetus look so similar that zoologists use the fine structure of their songs to
distinguish these “cryptic” species.
In addition, mammals such as feral cats, dogs, and foxes but also bats, can frequently be heard at
the mountain. Because bats communicate in the ultrasound, “bat detectors” (special microphones
and software transforming their song) are needed by humans interested in bat observation.
AUTOMATIC ACOUSTIC MONITORING AND INVENTORYING OF BIODIVERSITY
Specimens and oscillograms of stridulation of Chorthippus bornhalmi (Harz, 1971) and Chorthippus brunneus (Thunberg, 1815)
What and where?
Opposite: The AmiBio concept illustrated: the sounds of a disturbed Marginated Tortoise Testudo marginata and a group of flushed Chukars Alectoris chukar are recorded by a remote ARU and wirelessly transmitted to the base station in Patras. The sonagrams show 5-second fragments and a frequency range of 22 kHz (frequency on the y-axis, time on the x-axis, and intensity coded by red-dish colours). Habitat photographs: Upper left view of Athens from the mountain, Right: phrygana plant formation and pine forest are typical habitats of the mountain, often interesperesed within the rough, rocky terrain (lower left). The Vougliameni thermal lake (lower right) is in stark contrast to the dominating dry, calcareous landscape.
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What and where?
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The AmiBio project concentrated on animals vocalising within human hearing range, between 100
and 20,000 Hz. A network of autonomous recording stations was distributed over the mountain,
starting with commercially available soundmeters which had to be maintained every three weeks
and were recording 15 minutes per hour. During the course of the project they were replaced by
more sophisticated stations, working in 24/7 mode, equipped with solar panels and on-board mo-
dems and antennas, permitting wireless transmission and remote control to/from a central station
at Patras University, using the COSMOTE 3G mobile telephony network. In addition, weather data
such as temperature, wind speed, wind direction, rain, and solar radiation were measured, and ul-
trasound microphones were used to detect bats and insects with very high-pitched songs.
After only a few weeks of operation, the stations transmitted a huge amount of data, and at the
end of the project (June 2013) our team gathered Terabytes of acoustic raw data. The zoologists
from ZFMK were able to select 12,000 “snippets” with songs from insects (460), birds (10,000) and
mammals (1,540). However, a comprehensive analysis of such a high volume of “Big Data” can only
be analysed by recognition algorithms. These “recognisers” consist of computer programs designed
to detect a certain song or call (e.g. a kingfisher call) and extract the snippet from a larger file. The
recogniser runs over all data files and stores the snippet together with time, date and locality within
the specially designed AmiBio database. As a result, we get a record of the song activity of certain
species. This means that one recogniser per monitored species was needed, which had to be pro-
grammed, trained and tested. For training, a set of well-defined sample songs were needed, which
were drawn from our rich pool of commercial recordings and from the even richer library of short
sound segments (snippets). Recognisers were developed for the calls of several bird and insect spe-
and for one bat and one amphibian species (Pseudepidalea viridis and Tadarida teniotis).
In addition, more general recognisers for birds, insects and abiotic events such as gunshots, motor,
dog, human voice, were implemented within the monitoring stations. These “light recognisers” de-
livered an immediate signal, which means that instead of a sound file a short text code of the de-
tected events was transmitted with priority to the base station. The AmiBio administrative user in-
terface highlighted the respective event on a map, giving to the operator the possibility to screen
the sound recordings and evaluate the alarms.
In spite of this progress, there are still a lot of remaining tasks to improve the system: optimize
hardware with respect to power consumption and minimize station size, recognisers have to be-
come more robust and cover a wider spectrum of species, and sound archives from all over the
world have to be integrated within one overarching platform, similar to GBIF and Europeana.
AUTOMATIC ACOUSTIC MONITORING AND INVENTORYING OF BIODIVERSITY
Achievements
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Achievements
Audio aquisittion
Audio parameterization
Bird activity detection
Bird species classification
Recognized birds
Data storage
Bird vocalizations
Environmental noise
Top: Flowchart of AmiBio computer-assisted sound recognition software, using Hidden Markov Models, middle: Oscillogram and bottom: Sonagram of Common Kingfisher Alcedo atthis calls.
Solar-powered and real-time transmission stations, recording sounds and weather, were deployed in 24/7 mode at Hymettus.
Passive battery-powered soundmeter recording units (Wildlife Acoustics) were used in highly populated areas.
Workflow of AmiBio sound data acquisition, on-board audio processing and recognition. Raw data are stored at Museum Koenig and Patras University.
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DISSEMINATION ACTIVITIES
Awareness raising Establishment and maintenance of the project web site in English, Greek and German languages. Elaboration and dissemination of a newsletter as information tool addressing all stakeholders, including
the citizens living in the vicinity of Hymettus, relevant state authorities, bioacoustic researchers, biolo-gists. Twelve regular issues and three special issues have been published during the project life.
Organization of 3 information days, in June 2011 and June 2012 in Bonn, Germany, and in May 2012 in Athens, Greece.
Networking Activities Established working relations with other projects and initiatives in many countries in Europe, South
America, Africa, and Asia, by participating in more than 25 networking events. Connection of the biodiversity content collected in AmiBio project with OpenUp! ICT FP7 project and to
Europeana (www.europeana.eu) database.
Scientific dissemination Special session on biodiversity conservation held on 8 September 2012 during the IUCN World Conserva-
tion Congress, 6-15 September 2012, Jeju, South Korea. The special session was embedded in a “Knowledge Café” event with the motto “Bioacoustics for species monitoring - a new tool for Red List assessment?”
International AmiBio Work-shop “Recent Progress in Com-putational Bioacoustics”, held in June 2013 in Bonn, Ger-many. Scientists of eight coun-tries and four continents ac-tively participated in the event. A total of 16 scientific/technical talks were pre-sented. In addition a round table on “The future of auto-mated monitoring of biodiver-sity” was organized.
Scope The AmiBio “Afer LIFE Communication Plan” has the scope to underline the main activities that will be carried out by the project beneficiaries after the official project end in June 2013, in order to:
Disseminate, distribute and further exploit the project results
Promote the Life+ instrument as a source of financing within the range of environmental pro-tection and biodiversity conservation.
Planned Actions The following activities and actions are planned beyond the life-time (Feb. 2010 – Jun. 2013) of the AmiBio project : Maintenance of the project website for at least 5 years. The project information an dissemi-
nation materials, including brochures, flyers, newsletters, scientific papers, project reports, and selected sound recordings will remain available for the wider public, and will further pro-mote the AmiBio project results. The project website will be maintained by the UOP/WCL team.
Distribution of information brochures and flyers to future events that will be attended by the project beneficiaries, and especially by SPAY, to visitors of Hymettus mountain. Every year SPAY is organizing guided visits at Hymettus for adults, and especially for school children.
Presentation of the AmiBio system to stakeholders, including field visits and demonstration of an automatic monitoring station. SPAY is continuously in contact with a large variety of stake-holders, such as the municipalities in the vicinity of Hymettus, governmental institutions in-volved in environmental protection from all over Greece and abroad, and environment-policy decision makers.
The research-oriented AmiBio beneficiaries, namely, UOP, TEIC, and ZFMK, will continue to exploit the original sound repository, the detectors, and the innovative technology, to pre-pare, present, and publish scientific research results to national and international confer-ences and journals. Topics currently considered for international journals are: computational challenges of large datasets and real time monitoring, optimized detectors training workflow, and sound source localization.
The AmiBio system will remain deployed, it will continue to work and it will be maintained beyond project life-time, as all the beneficiaries have a high interest to exploit it, for as long as possible, for future demonstration of technology to stakeholders, for research activities and for assessment of life-time expectancy of system components.
Based on the knowledge and experience gained in the AmiBio project, UOP and SPAY con-tinue to disseminate and develop the innovative technology, and promote its applicability to other projects, such as DRYMOS – New Skills for New Jobs in the Forest Sector. In this con-text, UOP is currently integrating/adapting the “light” sound detectors, implemented in AmiBio project, in a mobile phone application, which will be further promoted / disseminated as an innovative tool for identification of forest animal life.
The AmiBio original sound recordings will be stored beyond the project-life, using the ZFMK dedicated infrastructure (LTO magnetic tape mass-storage), which can provide long-term storage for up to 30 years. ZFMK team will continue the work of classification and identifica-tion of the sounds, and their world-wide dissemination.
ZFMK will disseminate ID-confirmed sound files via GBIF to the scientific community and via Europeana to the broader public.
After-Life
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THE UNIVERSITY OF PATRAS, WIRE COMMUNICATIONS LABORATORY (WCL) Wire Communication Laboratory at the University of Patras is the coordinator and the main contributor to the AmiBio project, providing the overall framework for acquisition, communication and processing of environ-mental and bioacoustic information from the target areas at Hymettus. The WCL participates in AmiBio through its Artificial Intelligence Group (AIG), which has proven expertise on speech and audio processing and machine learning technologies. The recent technological advances in automatic identification of species and detection of
pests from their sound emissions, constitute the foundation for the development of an automated bioacoustics surveillance system in open-air environments, such as those at Hymettus. The AIG is an international team of Greek, Bulgarian, Romanian and English research staff, which has academic degrees in electrical engineering, computer science, physics and mathematics, with over than 350 scientific publications in both basic and applied research. The know-how in the area of Artificial Intelli-gence, and specifically on topics such as: Acoustic Biodiversity Monitoring, Sound Event Recognition, Rule Based Systems, Knowledge Representation, Search Methods, Machine Learning, Intelligent Human-Machine Interaction, are of great support for the development of autonomous technology for biodiversity monitoring, intelligent information filtering, and manage-ment of danger, emergency or crisis events.
THE TECHNOLOGICAL EDUCATIONAL INSTITUTE OF CRETE
The technology at the core of the AMIBIO project essentially is automatic processing of generalized audio sig-nals. As the problem is an emerging one, new techniques need to be developed and tested extensively so as to evaluate the applicability of the proposed technique with respect to biodiversity assessment task. This com-prises the basic responsibility of TEIC in the AMIBIO project. TEIC has established strong collaborative research
links with a large number of European and international Universities, research institutes and industrial companies. Its mission includes Under- and Post-Graduate Education, LLL and RTD in Engineering/Informatics, Agriculture/Environment, Health/Welfare, Management/Economics, spanning 18 Undergraduate and 3 MSc Courses, with 17.500 students. Ca. 50 PhD students carry out their research at TEIC. Staff includes ca. 750 FTE for teaching/research, 210 clerical and 75 technical. Projects span information and communication technologies, anti-pollution materials, renewable energy sources, laser technologies for the production of clean energy, waste recycling, seismology and geophysics, acoustics, biotechnology and quality in agriculture and the environment, natural resources, sociological affairs, environmental pollution and remedies.
THE ASSOCIATION FOR THE PROTECTION AND DEVELOPMENT OF HYMETTUS MOUNTAIN
SPAY is an association of the 15 municipalities that surround the mountain Hymettus. The scope of the association is to take action in protecting the mountain forest from fire and other dangers and to coordinate similar actions from the municipalities-members. Also to coordinate the actions of the volunteer organizations in the event of fire in assistance to the fire brigade. Major part of the associa-
tion activities is the reforestation of the burned areas and the irrigation of the newly plants. Since the equilibrium of trees and animals living in the mountain is vital for the survival of the forest, the project is giving the opportunity to study the animal life on the mountain, in order to assist as to the measures to be taking for the protection of the forest.
THE ZOOLOGICAL RESEARCH MUSEUM ALEXANDER KOENIG
Automated acoustic monitoring of wild animal species at Hymettus would not be possible without a good knowledge of the biodiversity present there. Species have to be inventoried and recordings of their vocalizations have to be gathered, identified, tagged, and archived in order to calibrate the sound identification software. These tasks are the main responsibilities
of the Zoological Research Museum A. Koenig (ZFMK, Bonn, Germany) in the AmiBio Project. Founded as a private research and exhibition institute by Alexander Koenig (1858-1940), it is one of the major natural history research museums in Germany and a member of the Leibniz Association (WGL). The museum has earned its reputation as a leader in the documentation, research, and interpretation of biodiversity. Its scientific collections comprise an estimated 350,000 specimens of vertebrates (80,000 mammals; 136,700 birds; 40,000 fishes; more than 77,000 reptiles and amphibians) and several million specimens of insects. These collections form the basis for the diversity of research conducted by the museum. The national and interna-tional significance of the institution’s research, and hence its trend-setting work, conforms to national interests. The museum maintains 49 permanent positions (14 of which are held by scientists), as well as 130 additional employees (comprising 15 researchers in externally funded projects, 100 doctoral, masters, and undergraduate students, and 15 volunteers). The ZFMK is promoting biodiversity conservation by combining technological innovation with expertise in species identification.
