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Publications

Journal Article Preprint Epublish

PubMed: 40501763 DOI: 10.1101/2025.06.01.657312

eyeris: A flexible, extensible, and reproducible pupillometry preprocessing framework in R.

bioRxiv

Authors: Shawn T Schwartz, Haopei Yang, Alice M Xue, Mingjian He

Affiliations

  • Stanford University, Stanford, United States. Stanford Memory Laboratory, Stanford, United States. Stanford University Wu Tsai Neurosciences Institute, Stanford, United States. Stanford University Wu Tsai Human Performance Alliance, Stanford, United States. Stanford University Center for Mind, Brain, Computation and Technology, Stanford, United States.
  • Stanford University, Stanford, United States. Stanford Memory Laboratory, Stanford, United States.
  • Stanford University, Stanford, United States. Stanford Memory Laboratory, Stanford, United States. Stanford University Wu Tsai Neurosciences Institute, Stanford, United States. Stanford University Center for Mind, Brain, Computation and Technology, Stanford, United States.
  • Stanford University, Stanford, United States. Stanford Memory Laboratory, Stanford, United States. Stanford University Medicine, Stanford, United States.

Abstract

Pupillometry provides a non-invasive window into the mind and brain, particularly as a psychophysiological readout of autonomic and cognitive processes like arousal, attention, stress, and emotional states. Pupillometry research lacks a robust, standardized framework for data preprocessing, whereas in functional magnetic resonance imaging and electroencephalography, researchers have converged on tools such as fMRIPrep, EEGLAB and MNE-Python; these tools are considered the gold standard in the field. Many established pupillometry preprocessing packages and workflows fall short of serving the goal of enhancing reproducibility, especially since most existing solutions lack designs based on Findability, Accessibility, Interoperability, and Reusability (FAIR) principles. To promote FAIR and open science practices for pupillometry research, we developed eyeris, a complete pupillometry preprocessing suite designed to be intuitive, modular, performant, and extensible (https://github.com/shawntz/eyeris). Out-of-the-box, eyeris provides a recommended preprocessing workflow and considers signal processing best practices for tonic and phasic pupillometry. Moreover, eyeris further enables open and reproducible science workflows, as well as quality control workflows by following a well-established file management schema and generating interactive output reports for both record keeping/sharing and quality assurance of preprocessed pupil data prior to formal analysis. Taken together, eyeris provides a robust all-in-one transparent and adaptive solution for high-fidelity pupillometry preprocessing with the aim of further improving reproducibility in pupillometry research.

MeSH

Workflow, Pupil, Solutions, Research