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idTracker: tracking individuals in a group by automatic identification of unmarked animals

Nature Methods volume 11, pages 743–748 (2014)Cite this article

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Abstract

Animals in groups touch each other, move in paths that cross, and interact in complex ways. Current video tracking methods sometimes switch identities of unmarked individuals during these interactions. These errors propagate and result in random assignments after a few minutes unless manually corrected. We present idTracker, a multitracking algorithm that extracts a characteristic fingerprint from each animal in a video recording of a group. It then uses these fingerprints to identify every individual throughout the video. Tracking by identification prevents propagation of errors, and the correct identities can be maintained indefinitely. idTracker distinguishes animals even when humans cannot, such as for size-matched siblings, and reidentifies animals after they temporarily disappear from view or across different videos. It is robust, easy to use and general. We tested it on fish (Danio rerio and Oryzias latipes), flies (Drosophila melanogaster), ants (Messor structor) and mice (Mus musculus).

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Figure 1: idTracker maintains correct identities without propagation of errors.
Figure 2: Identification method.
Figure 3: Examples of applications of idTracker.
Figure 4: Analysis of social behavior using idTracker.

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Acknowledgements

We thank P. Bovolenta (Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas (CSIC)), A. Dussutour (Centre de Recherches sur la Cognition Animale, Centre National de la Recherche Scientifique, Toulouse University), A. Ferrús (Instituto Cajal, CSIC), A. Sorribes (Instituto Cajal, CSIC), G. Sumbre (Ecole Normale Supérieure) and J.L. Trejo (Instituto Cajal, CSIC) for providing animals. We also thank I. Arganda-Carreras, K. Branson, I. Couzin, J. Gautrais, R. Ottenhoff, H. Roosken, R. Tegelenbosch, W. van Dommelen and H. Wu for feedback; A. Bruce, A. King, E. Pope, G. Thelauraz, R. Goulard, U. Lopez and D. Calovi for testing in their labs; and R. Gil de Sagredo, G. Madirolas, A.C. Román and F. Romero-Ferrero for a critical reading of the paper. We acknowledge an FPU fellowship from Ministerio de Economía y Competitividad, Spain (to A.P.-E.), an FPI fellowship from Ministerio de Economía y Competitividad (to R.C.H.), a JAE fellowship from CSIC (to J.V.-P.), funding from Spanish Plan Nacional BFU2009-09967 and BFU2012-33448 from Ministerio de Economía y Competitividad (to G.G.d.P.) and funding from ERASysBio+ initiative supported under the European Union European Research Area Networks (ERA-NET) Plus scheme in the FP7 Seventh Framework Programme as EUI2009-04090 (to G.G.d.P., including contracts to S.A. and A.P.-E.).

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Author notes

  1. Sara Arganda

    Present address: Present address: Centre de Recherches sur la Cognition Animale, Centre National de la Recherche Scientifique, Université Paul Sabatier, Toulouse, France.,

Authors and Affiliations

  1. Instituto Cajal, Consejo Superior de Investigaciones Científicas, Madrid, Spain

    Alfonso Pérez-Escudero, Julián Vicente-Page, Robert C Hinz, Sara Arganda & Gonzalo G de Polavieja

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  1. Alfonso Pérez-Escudero
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Contributions

A.P.-E. designed the project, performed experiments, analyzed data, wrote and tested the software and wrote the paper; R.C.H. performed experiments, tested the software and analyzed data; J.V.-P. performed experiments, tested the software and analyzed data; S.A. performed experiments and tested the software, G.G.d.P. designed the project, advised and directed the project including experiments, software and data analysis and wrote the paper.

Corresponding authors

Correspondence to Alfonso Pérez-Escudero or Gonzalo G de Polavieja.

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Competing interests

Consejo Superior de Investigaciones Cientificas (CSIC) owns a patent describing this method (patent no. PCT/ES2013/070585). A.P.-E., G.G.d.P. and S.A. are listed as inventors of the patent and will receive a part of the revenues that it may generate. Noncommercial use of the method and the associated software is allowed free of charge

Supplementary information

Supplementary Text and Figures

Supplementary Figures 1–7, Supplementary Table 1 and Supplementary Notes 1–4 (PDF 16844 kb)

Supplementary Software

Source code of idTracker (Matlab and C) (ZIP 130 kb)

Supplementary Data

Raw data and scripts to reproduce the results in Figure 4 (ZIP 45931 kb)

idTracker: Visual Summary

This movie explains the main features and advantages of idTracker, outlines the method, and shows examples of multitracking of several species: zebrafish (Danio rerio), medaka fish (Oryzias latipes), fruitflies (Drosophila melanogaster), mice (Mus musculus) and ants. (MP4 20213 kb)

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Pérez-Escudero, A., Vicente-Page, J., Hinz, R. et al. idTracker: tracking individuals in a group by automatic identification of unmarked animals. Nat Methods 11, 743–748 (2014). https://doi.org/10.1038/nmeth.2994

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