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

Abstract

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
    timothy.dunn@duke.edu
    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
    fitzgeraldj@janelia.hhmi.org
    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

Funding

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.

Copyright

© 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.

Metrics

  • 1,232
    views
  • 185
    downloads
  • 9
    citations

Views, downloads and citations are aggregated across all versions of this paper published by eLife.

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
(2020)
Correcting for physical distortions in visual stimuli improves reproducibility in zebrafish neuroscience
eLife 9:e53684.
https://doi.org/10.7554/eLife.53684

Share this article

https://doi.org/10.7554/eLife.53684