1. Neuroscience
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Correcting for physical distortions in visual stimuli improves reproducibility in zebrafish neuroscience

  1. Timothy W Dunn  Is a corresponding author
  2. James E Fitzgerald  Is a corresponding author
  1. Duke University, United States
  2. Janelia Research Campus, Howard Hughes Medical Institute, United States
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Cite this article as: eLife 2020;9:e53684 doi: 10.7554/eLife.53684


Breakthrough technologies for monitoring and manipulating single-neuron activity provide unprecedented opportunities for whole-brain neuroscience in larval zebrafish1–9. Understanding the neural mechanisms of visually guided behavior also requires precise stimulus control, but little prior research has accounted for physical distortions that result from refraction and reflection at an air-water interface that usually separates the projected stimulus from the fish10–12. Here we provide a computational tool that transforms between projected and received stimuli in order to detect and control these distortions. The tool considers the most commonly encountered interface geometry, and we show that this and other common configurations produce stereotyped distortions. By correcting these distortions, we reduced discrepancies in the literature concerning stimuli that evoke escape behavior13,14, and we expect this tool will help reconcile other confusing aspects of the literature. This tool also aids experimental design, and we illustrate the dangers that uncorrected stimuli pose to receptive field mapping experiments.

Article and author information

Author details

  1. Timothy W Dunn

    Duke Forge, Department of Statistical Science, Duke University, Durham, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
  2. James E Fitzgerald

    Computation and Theory, Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, United States
    For correspondence
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-0949-4188


Duke Forge

  • Timothy W Dunn

Duke AI Health

  • Timothy W Dunn

Howard Hughes Medical Institute

  • James E Fitzgerald

National Institutes of Health (U01 NS090449)

  • Timothy W Dunn
  • James E Fitzgerald

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Claire Wyart, Institut du Cerveau et la Moelle épinière, Hôpital Pitié-Salpêtrière, Sorbonne Universités, UPMC Univ Paris 06, Inserm, CNRS, France

Publication history

  1. Received: November 16, 2019
  2. Accepted: March 23, 2020
  3. Accepted Manuscript published: March 24, 2020 (version 1)
  4. Version of Record published: April 16, 2020 (version 2)


© 2020, Dunn & Fitzgerald

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.


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