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Journal of Ornithology

, Volume 159, Issue 4, pp 1105–1111 | Cite as

“Ficedula”: an open-source MATLAB toolbox for cutting, segmenting and computer-aided clustering of bird song

  • Sándor Zsebők
  • György Blázi
  • Miklós Laczi
  • Gergely Nagy
  • Éva Vaskuti
  • László Zsolt Garamszegi
Technical Note

Abstract

Qualitative and quantitative assessments of bird song repertoires are important in studies related to song learning, sexual selection and cultural evolution. Despite methods for automatic analysis, it is still necessary to engage in manual cutting, segmenting and clustering of bird song elements in many cases. Here, we describe a program, the Ficedula Toolbox, which has been made available for free to the bird song research community and has recently come into extensive use. The main advantages of this package are the opportunity to conduct all processing steps in one framework and the option of carrying out computer-aided manual clustering. Output files are ready for further analyses, such as estimation of repertoire size, sequential analysis and repertoire overlap calculation. With this program, findings based on empirical data from the Collared Flycatcher (Ficedula albicollis) song show high inter-observer similarity, and thus, reproducible results. The toolbox may be especially applicable to the analysis of song in species with moderately high repertoires.

Keywords

Bird song analysis Computer-aided manual clustering Syllable repertoire size Repertoire overlap Sound analysis software 

Zusammenfassung

“Ficedula”—eine open-source MATLAB toolbox für Schnitt, Segmentierung und computerunterstütztes Clustering von Vogelgesang

Die qualitative und quantitative Bewertung von Gesangsrepertoires von Vögeln ist wesentlich in Studien im Zusammenhang mit Themen wie Gesangslernen, sexuelle Selektion und kulturelle Evolution. Trotz automatischer Analysemöglichkeiten ist es in vielen Fällen immer noch nötig, die Gesänge manuell zu Schneiden, zu Segmentierung und zu Clustern. Hier beschreiben wir das Programm „Ficedula Toolbox“, welches für Vogelgesangsforscher frei verfügbar gemacht wurde und das neuerdings in größerem Umfang genutzt wird. Die größten Vorteile dieses Paketes sind zum einen die Möglichkeit, alle Verarbeitungsschritte in einem System vorzunehmen und zum anderen die Option der Durchführung von computerunterstütztem manuellen Clustern. Die Ausgabedateien sind bereit für weitere Auswertungen, wie beispielsweise die Bestimmung des Repertoireumfangs, sequentielle Analysen und die Berechnung von Repertoireüberlappungen. Mit Hilfe dieses Programms zeigen die Ergebnisse, basierend auf empirischen Daten zum Halsbandschnäpper-Gesang (Ficedula albicollis) eine große Ähnlichkeit zwischen den Beobachtern und daher reproduzierbare Resultate. Die Nutzung dieser Toolbox könnte insbesondere für Arten mit einem moderat hohen Gesangsrepertoire von Vorteil sein.

Notes

Acknowledgements

We are grateful to the members of the Behavioural Ecology Research Group for assistance during the fieldwork, Erdők a Közjóért Alapítvány and Pilisi Parkerdő Zrt. Permission for the fieldwork was given by the Middle-Danube-Valley Inspectorate for Environmental Protection, Nature Conservation and Water Management.

Compliance with ethical standards

Conflict of interest

This study was supported by funds from the Ministry of Economy and Competitiveness, Spain (CGL2015-70639-P) and the National Research, Development and Innovation Office Hungary (NKFIH, K-115970 and PD-115730).

Ethical approval

All applicable international, national and/or institutional guidelines for the care and use of animals were followed.

Supplementary material

10336_2018_1581_MOESM1_ESM.docx (5.7 mb)
Supplementary material 1 (DOCX 5790 kb)

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Copyright information

© Dt. Ornithologen-Gesellschaft e.V. 2018

Authors and Affiliations

  1. 1.Behavioural Ecology Group, Department of Systematic Zoology and EcologyEötvös Loránd UniversityBudapestHungary
  2. 2.The Barn Owl FoundationOrosztonyHungary
  3. 3.Department of Evolutionary EcologyEstación Biológica de Doñana-CSICSevilleSpain
  4. 4.MTA-ELTE, Theoretical Biology and Evolutionary Ecology Research Group, Department of Plant Systematics, Ecology and Theoretical BiologyEötvös UniversityBudapestHungary

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