README.md

Brainard Lab Experiment Preregistrations

Experiments in the Brainard Lab are usually preregistered. This page organizes links to these pre-registration documents by project. We sometimes make use of the open science foundation website for this purpose, but also find reasonable simply committing preregistration documents to this repository. In some cases, depending on our collaborators or funding agency requirements, we use other mechanisms of pre-registration such as clinicaltrials.gov.

This page contains links to experiments we preregistered prior to 2021.

ColorTracking (with Burge lab)

• 2021-09-30 Measuring the Temporal lag to Combinations of L- and S- Photoreceptor Modulations via a Continuous Tracking Paradigm, Exp 1. Data collection complete.
• 2021-10-27 Measuring the Temporal lag to Combinations of L- and S- Photoreceptor Modulations via a Continuous Tracking Paradigm, Exp 2. Data collection complete.
• 2021-12-14 Measuring the Temporal lag to Combinations of L- and S- Photoreceptor Modulations via a Continuous Tracking Paradigm, Exp 3. Data collection complete.
• 2022-02-12 Measuring the Temporal lag to Combinations of L- and S- Photoreceptor Modulations via a Continuous Tracking Paradigm, Exp 4. Data collection complete.
• 2022-03-15 Measuring the Temporal lag to Combinations of L- and S- Photoreceptor Modulations via a Continuous Tracking Paradigm, Exp 5.
• Status (2022-08-20: Data collection complete. Preliminary descriptions available in Michael Barnett's and Ben Chin's dissertations. Manuscript in preparation.

RayleighForcedChoice

• 2021-04-15_OLRayleighMatch_PreRegistration. Preregistration for initial data collection in this project. This file posted after 6 matches collected for Subject MELA_0034 and 2 matches collected for Subject MELA_0035.
• 2021-04-15_OLRayleighMatch_PreRegistration. Preregistration for data collection on three new subjects with refined procedure.
• Status (2022-08-20): Project potentially ongoing.

NaturalImageThresholds (with Cohen lab)

• 2021-08-12_NaturalImageThresholds_PreRegistration - Preregistration for initial data collection in this project. This preregistration was posted to ClinicalTrials.gov in advance of the start of data collection: NCT number: NCT05004649; protocol ID number 305435. The version there is archival.
• Status (2023-05-26): Data collection complete. Analysis and writeup ongoing. Data posted at [OSF](https://osf.io/yf3sr/. Summary results reported on ClinicalTrials.gov, associated with the NCT number above.

Optoretinography Reliability and Reciprocity (with Morgan lab)

• 2021-02-17 Test Reciprocity and Reliability of the Cone Optoretinogram. This preregistration is not yet public. It provided preliminary data that informed the 2021-08-30 preregistration below.
• 2021-08-30 Measuring Cone Optoretinogram Reciprocity and Repeatability using Adaptive Optics Scanning Laser Opthalmoscope. This preregistration is not yet public.
• 2021-09-15 Addendum on light power. This preregistration is not yet public.
• Status (2023-05-26): This work is now published in Warner, R. L., Brainard, D. H., Morgan J. I. W. (2022). Repeatability and reciprocity of the cone optoretinogram, Biomed. Opt. Express, 13, 6561-6573. https://opg.optica.org/boe/fulltext.cfm?uri=boe-13-12-6561&id=521886. We will make the preregistrations public soon.

Optoretinography Dependence on Eccentricity (with Morgan Lab)

• 2022-08-19 Nrmative Cone Optoretinography Across Retinal Eccentricity using Adaptive Optics Scanning Laser Ophthalmoscopy. This pregistration is not yet public.
• Status (2023-05-26): Data collection halted because of apparatus issues. Project will be restarted soon.

Single Cone Optoretinography (with Morgan Lab)

• 2023-05-22 Dose-Respose of the Single Cone Optoretinogram using Adaptive Optics Scanning Laser Ophthalmoscopyy. This pregistration is not yet public.

Repeatability of sensitivity thresholds in normal controls (with Morgan and Tuten labs)

• 2023-08-08 Fepeatability of foveal sensitivity measurements within and across sessions as measured with adaptive optics (AO) microperimetry in normal control subjects. This pregistration is not yet public.

Adaptive Optics Image Quality (with Morgan lab)

• 2020-12-04 Automated assessment of image quality in AO split detection images using edge quantification
• Status: Project complete. Published in Chen, M., Jiang, Y. Y., Gee J. C., Brainard, D. H., Morgan, J. I. W. (2022), Automated assessment of photoreceptor visibility in adaptive optics split-detection images using edge detection. Trans. Vis. Sci. Tech., 11(5):25. doi: https://doi.org/10.1167/tvst.11.5.25.

Adaptive optics psychophysics: two spot summation (with Morgan and Tuten labs)

• 2022-02-01_AO Two Spot Summation - Preregistration for two-spot summation with same and different spot polarities, as a function of spot separation.
• 2022-02-04_AO Two Spot Summation, Addendum 1 - Addendum 1, two-spot summation with same and different spot polarities, as a function of spot separation.
• 2022-03-26_AO Two Spot Summation, Addendum 2 - Addendum 2, two-spot summation with same and different spot polarities, as a function of spot separation.
• Status (2025-07-23). Project unlikely to complete at Penn.

Color discrimination ellipses in the iosluminant plane (with Williams and Guan labs)

• 2024-11-18-ELPS_1_PreRegistration - Preregistration for ELPS project Exp 1.
• 2025-02-25-ELPS_2_PreRegistration - Preregistration for ELPS project Exp 2.
• 2025-03-04-ELPS_2a_PreRegistration - Preregistration for ELPS project Exp 2a.
• 2025-04-21-ELPS_3_PreRegistration - Preregistration for ELPS project Exp 3.
• Status (2025-07-23). Preprint at Hong, F., Bouhassira, R., Chow, J., Sanders, C., Shvartsman, M., Guan, P., Williams, A. H., & Brainard, D. H. (2025). Comprehensive characterization of human color discrimination thresholds. bioRxiv, 2025.2007.2016.665219. https://doi.org/10.1101/2025.07.16.665219.

Color discrimination adaptation in the iosluminant plane (with Williams and Guan labs)

• 2025-10-17-ELPS_1_PreRegistration - Preregistration for ELPS adaptation project Exp 1.
• 2026-02-21-ELPS_2_PreRegistration - Preregistration for ELPS adaptation project Exp 2.
• 2026-04-08-ELPS_3_PreRegistration - Preregistration for ELPS adaptation, simulations and additional trials.

Color discrimination in deuteranopes (with Williams and Guan labs)

• 2025-11-15-ELPS_1_PreRegistration - Preregistration for ELPS deuteranope Exp 1.
• 2026-02-02-ELPS_2_PreRegistration - Addendum 1.
• 2026-03-22-ELPS_3_PreRegistration - Ellipsoid control exp. After a practice session with a deuteranope [2026-03-22], we adjusted the scalars for the AEPsyc-generated Sobel trials from the values of [0.15, 0.45, 0.75] specified in this document to [0.09, 0.15, 0.3] because the trials seemed easy for the participant. The scalars for the pregenerated Sobel trials (aka fallback trials) were not adjusted.

Color discrimination ellipsoids in full 3D color space (with Williams and Guan labs)

• 2026-02-02-ELPS_1_PreRegistration - Preregistration for ELPS ellipsoids in 3D color space.
• 2026-02-28-ELPS_2_PreRegistration - Initial analysis plan.
• 2026-04-05-ELPS_3_PreRegistration - Initial hyperparameters for comparison with validation.
• 2026-04-12-ELPS_4_PreRegistration - Comparison with CIELAB DE analyses. The preregistration refers to this html document. The link will take you to github and you can download the html, rename the file created to have extension .html as it may show up as .txt, and view in your browser.