Papers, citations and how to cite.

How to cite

If ethoscopes contributed to your work, please cite the ethoscope paper. Cite rethomics or ethoscopy as well if you used them for the analysis.

• For the ethoscope hardware and real-time tracking platform

  Geissmann Q, Garcia Rodriguez L, Beckwith EJ, French AS, Jamasb AR, Gilestro GF (2017). Ethoscopes: An open platform for high-throughput ethomics. PLOS Biology 15(10): e2003026.

  doi:10.1371/journal.pbio.2003026Copy BibTeX

  BibTeX

  @article{geissmann2017ethoscopes,
    author  = {Geissmann, Quentin and Garcia Rodriguez, Luis and Beckwith, Esteban J. and French, Alice S. and Jamasb, Arian R. and Gilestro, Giorgio F.},
    title   = {{Ethoscopes}: An open platform for high-throughput ethomics},
    journal = {PLOS Biology},
    year    = {2017},
    volume  = {15},
    number  = {10},
    pages   = {e2003026},
    doi     = {10.1371/journal.pbio.2003026}
  }
  

• For analysing ethoscope or DAM data in R with the rethomics packages

  Geissmann Q, Garcia Rodriguez L, Beckwith EJ, Gilestro GF (2019). Rethomics: An R framework to analyse high-throughput behavioural data. PLOS ONE 14(1): e0209331.

  doi:10.1371/journal.pone.0209331Copy BibTeX

  BibTeX

  @article{geissmann2019rethomics,
    author  = {Geissmann, Quentin and Garcia Rodriguez, Luis and Beckwith, Esteban J. and Gilestro, Giorgio F.},
    title   = {{Rethomics}: An {R} framework to analyse high-throughput behavioural data},
    journal = {PLOS ONE},
    year    = {2019},
    volume  = {14},
    number  = {1},
    pages   = {e0209331},
    doi     = {10.1371/journal.pone.0209331}
  }
  

• For analysing ethoscope data in Python with ethoscopy or the ethoscope-lab container

  Blackhurst L, Gilestro GF (2023). Ethoscopy and ethoscope-lab: a framework for behavioural analysis to lower entrance barrier and aid reproducibility. Bioinformatics Advances 3(1): vbad132.

  doi:10.1093/bioadv/vbad132Copy BibTeX

  BibTeX

  @article{blackhurst2023ethoscopy,
    author  = {Blackhurst, Laurence and Gilestro, Giorgio F.},
    title   = {{Ethoscopy} and ethoscope-lab: a framework for behavioural analysis to lower entrance barrier and aid reproducibility},
    journal = {Bioinformatics Advances},
    year    = {2023},
    volume  = {3},
    number  = {1},
    pages   = {vbad132},
    doi     = {10.1093/bioadv/vbad132}
  }
  

• For behavioural fingerprinting with coccinella (ethoscope + HCTSA/catch22)

  Jones H, Willis JA, Firth LC, Giachello CNG, Gilestro GF (2023). A reductionist paradigm for high-throughput behavioural fingerprinting in Drosophila melanogaster. eLife 12: RP86695.

  doi:10.7554/eLife.86695Copy BibTeX

  BibTeX

  @article{jones2023reductionist,
    author  = {Jones, Hannah and Willis, Jenny A. and Firth, Lucy C. and Giachello, Carlo N. G. and Gilestro, Giorgio F.},
    title   = {A reductionist paradigm for high-throughput behavioural fingerprinting in {Drosophila melanogaster}},
    journal = {eLife},
    year    = {2023},
    volume  = {12},
    pages   = {RP86695},
    doi     = {10.7554/eLife.86695}
  }
  

• For the archived 3D-printable hardware design files (version 2017)

  Geissmann Q, Garcia L, Gilestro G (2017). Ethoscope Core Files. Zenodo.

  doi:10.5281/zenodo.831154Copy BibTeX

  BibTeX

  @misc{geissmann2017ethoscopecore,
    author    = {Geissmann, Quentin and Garcia, Luis and Gilestro, Giorgio},
    title     = {{Ethoscope Core Files}},
    publisher = {Zenodo},
    year      = {2017},
    doi       = {10.5281/zenodo.831154},
    url       = {https://doi.org/10.5281/zenodo.831154}
  }
  

Citations

Labs that used ethoscopes

Papers from other groups whose methods describe ethoscope experiments. The list comes from a search of open-access full text, so it is incomplete: if your paper is missing, tell us on GitHub Discussions.

1. 2026

   Sleep facilitates pattern separation through SK channel-mediated sparse coding

   Chen CC, Huang YC, Ortega A et al. · Current Biology 36(7): 1633-1643.e6

   Liu lab · VIB-KU Leuven Center for Brain & Disease Research · Belgium

2. 2026

   Behavioral screening defines the molecular Parkinsonism-related subgroups in Drosophila

   Kaempf N, Valadas JS, Robberechts P et al. · Nature Communications 17(1): 3761

   Verstreken lab · VIB-KU Leuven Center for Brain & Disease Research · Belgium

3. 2025

   Sensory quiescence induces a cell-non-autonomous integrated stress response curbed by condensate formation of the ATF4 and XRP1 effectors

   Shekhar S, Tracy C, Lidsky PV et al. · Nature Communications 16(1): 252

   Krämer lab · UT Southwestern Medical Center · United States

4. 2025

   Role of D-serine in intestinal ROS accumulation after sleep deprivation

   Zheng F, Liu S, Wei T et al. · Science Advances 11(29): eadr8592

   Zheng lab · Hefei University of Technology · China

5. 2024

   Single-cell transcriptomics reveals that glial cells integrate homeostatic and circadian processes to drive sleep–wake cycles

   Dopp J, Ortega A, Davie K et al. · Nature Neuroscience 27(2): 359-372

   Liu lab · VIB-KU Leuven Center for Brain & Disease Research · Belgium

6. 2024

   A candidate loss-of-function variant in SGIP1 causes synaptic dysfunction and recessive parkinsonism

   Decet M, Scott P, Kuenen S et al. · Cell Reports Medicine 5(10): 101749

   Verstreken lab · VIB-KU Leuven Center for Brain & Disease Research · Belgium

7. 2024

   Revealing the Bioactivities of Physalia physalis Venom Using Drosophila as a Model

   Tomkielska Z, Frias J, Simões N et al. · Toxins 16(11): 491

   Toubarro lab · Biotechnology Centre of Azores, University of the Azores · Portugal

8. 2023

   Neuronal identity defines α-synuclein and tau toxicity

   Praschberger R, Kuenen S, Schoovaerts N et al. · Neuron 111(10): 1577-1590.e11

   Verstreken lab · VIB-KU Leuven Center for Brain & Disease Research · Belgium

9. 2023

   Allnighter pseudokinase-mediated feedback links proteostasis and sleep in Drosophila

   Shekhar S, Moehlman AT, Park B et al. · Nature Communications 14(1): 2932

   Krämer lab · UT Southwestern Medical Center · United States

10. 2023

    Homeostatic control of deep sleep and molecular correlates of sleep pressure in Drosophila

    Chowdhury B, Abhilash L, Ortega A et al. · eLife 12: e91355

    Shafer lab · Advanced Science Research Center, City University of New York · United States

11. 2023

    Differential adhesion during development establishes individual neural stem cell niches and shapes adult behaviour in Drosophila

    Banach-Latapy A, Rincheval V, Briand D et al. · PLOS Biology 21(11): e3002352

    Spéder lab · Institut Pasteur, Université Paris Cité · France

12. 2022

    Redundant functions of the SLC5A transporters Rumpel, Bumpel, and Kumpel in ensheathing glial cells

    Yildirim K, Winkler B, Pogodalla N et al. · Biology Open 11(1): bio059128

    Klämbt lab · University of Münster · Germany

13. 2022

    Physiological and life history changes associated with seasonal adaptation in the cactophilic Drosophila mojavensis

    Shaible TM, Matzkin LM · Biology Open 11(10): bio059610

    Matzkin lab · University of Arizona · United States

14. 2022

    A ShK-like Domain from Steinernema carpocapsae with Bioinsecticidal Potential

    Frias J, Toubarro D, Bjerga GEK et al. · Toxins 14(11): 754

    Simões lab · Biotechnology Centre of Azores, University of the Azores · Portugal

15. 2022

    A serine-folate metabolic unit controls resistance and tolerance of infectionpreprint

    Grimes K, Beckwith EJ, Pearson WH et al. · bioRxiv

    Dionne lab · Imperial College London · United Kingdom

16. 2021

    Astroglial Calcium Signaling Encodes Sleep Need in Drosophila

    Blum ID, Keleş MF, Baz ES et al. · Current Biology 31(1): 150-162.e7

    Wu lab · Johns Hopkins University · United States

17. 2021

    Open-source computational framework for studying Drosophila behavioral phase

    Kostadinov B, Lee Pettibone H, Bell EV et al. · STAR Protocols 2(1): 100285

    Fernandez lab · Barnard College, Columbia University · United States

From the Gilestro lab

1. 2025

   Sleep Deprivation Primes Synaptic Vulnerability Without Inducing Oxidative Damage: A Mechanistic Reappraisalpreprint

   Guo L, Ferretti V, Gilestro GF · bioRxiv

   Ten days of ethoscope-based sleep deprivation.

2. 2024

   Divergent evolution of sleep in Drosophila species

   Joyce M, Falconio FA, Blackhurst L et al. · Nature Communications 15(1): 5091

   Sleep, arousal thresholds (air puffs) and rebound across Drosophila species, recorded with ethoscopes.

3. 2022

   Infection increases activity via Toll dependent and independent mechanisms in Drosophila melanogaster

   Vincent CM, Beckwith EJ, Simoes da Silva CJ et al. · PLOS Pathogens 18(9): e1010826

   Activity of infected flies recorded with ethoscopes and analysed with rethomics.

4. 2021

   Sensory processing during sleep in Drosophila melanogaster

   French AS, Geissmann Q, Beckwith EJ et al. · Nature 598(7881): 479-482

   Arousal of sleeping flies by sensory stimuli, recorded with ethoscopes.

5. 2019

   Most sleep does not serve a vital function: Evidence from Drosophila melanogaster

   Geissmann Q, Beckwith EJ, Gilestro GF · Science Advances 5(2): eaau9253

   Sleep recorded and chronically restricted in ethoscope sleep arenas.

6. 2017

   Regulation of sleep homeostasis by sexual arousal

   Beckwith EJ, Geissmann Q, French AS et al. · eLife 6: e27445

   Sleep recorded with ethoscopes; mechanical sleep deprivation with the ethoscope sleep-deprivation module.

All citing publications