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


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.

Data availability

No data were collected for this theoretical manuscript.

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.


  • 1,072
    Page views
  • 172
  • 4

Article citation count generated by polling the highest count across the following sources: Crossref, PubMed Central, Scopus.

Download links

A two-part list of links to download the article, or parts of the article, in various formats.

Downloads (link to download the article as PDF)

Open citations (links to open the citations from this article in various online reference manager services)

Cite this article (links to download the citations from this article in formats compatible with various reference manager tools)

  1. Timothy W Dunn
  2. James E Fitzgerald
Correcting for physical distortions in visual stimuli improves reproducibility in zebrafish neuroscience
eLife 9:e53684.

Further reading

    1. Neuroscience
    Claire Wyart

    Sensory neurons previously shown to optimize speed and balance in fish by providing information about the curvature of the spine show similar morphology and connectivity in mice.

    1. Neuroscience
    Catharina Zich, Andrew J Quinn ... Sven Bestmann
    Research Article

    Beta oscillations in human sensorimotor cortex are hallmark signatures of healthy and pathological movement. In single trials, beta oscillations include bursts of intermittent, transient periods of high-power activity. These burst events have been linked to a range of sensory and motor processes, but their precise spatial, spectral, and temporal structure remains unclear. Specifically, a role for beta burst activity in information coding and communication suggests spatiotemporal patterns, or travelling wave activity, along specific anatomical gradients. We here show in human magnetoencephalography recordings that burst activity in sensorimotor cortex occurs in planar spatiotemporal wave-like patterns that dominate along two axes either parallel or perpendicular to the central sulcus. Moreover, we find that the two propagation directions are characterised by distinct anatomical and physiological features. Finally, our results suggest that sensorimotor beta bursts occurring before and after a movement can be distinguished by their anatomical, spectral and spatiotemporal characteristics, indicating distinct functional roles.