All experiments were run on an Apple Mac Mini computer (OS X, Version 10.9.5). Stimuli were presented on an EIZO FS2434 LCD monitor with resolution of 1920 x 1080 pixels and a frame rate of 16.67 milliseconds (ms). Viewing distance was fixed at 57 cm, using a chin rest. Participants responded by pressing keys on a standard keyboard. Stimulus events were controlled, and responses were recorded, using MATLAB (version R2013b, 8.2, The Mathworks Inc., Natick, MA, USA) with the Psychophysics toolbox extension (version 3.0.11; Brainard, 1997 (link); Pelli, 1997 (link)).
Psychophysics toolbox extension
Manufactured by MathWorks
Sourced in United States
The Psychophysics Toolbox extensions for MATLAB provide a collection of functions and tools for conducting psychophysical experiments. These extensions offer a flexible and efficient framework for stimuli presentation, response collection, and data analysis. The core function of the Psychophysics Toolbox is to facilitate the creation and control of visual, auditory, and other sensory stimuli within the MATLAB environment.
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7 protocols using psychophysics toolbox extension
1
Psychophysics Experiment Setup Protocol
2
Electrophysiological Recording in Monocular Deprivation
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Extracellular recordings of single unit activity and local field potentials were made using linear silicone probes with 16 recording sites spaced at 50 μm intervals (NeuroNexus probes, A1x16-3 mm-50-177). Craniotomies to expose the primary visual cortex (2 mm in diameter, 1 mm anterior and 3 mm lateral to lambda) were made above one (contralateral to the deprived eye in MD animals or both hemispheres (control animals). The electrode was lowered into the brain to a depth of 1000 μm in the V1B, and was allowed to settle for 20 min before recording. Electrophysiological recordings were performed under light isoflurane anesthesia (0.5–1%) supplemented with intramuscular administration of chlorprothixene (0.2 mg). Visual stimuli was generated using Psychophysics Toolbox extension (Brainard et al. 1997 (link)) for MATLAB (Mathworks) and sinusiodal drifting gratings were displayed on a 21” computer monitor centered 25 cm in front of the animal. Four days of MD was started between postnatal day 25 (P25) and P27. Eyelids were sutured shut under isoflurane anesthesia.
3
Behavioral and Computational Analyses
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We report how we determined our sample size, all data exclusions, all manipulations, and all measures in the study. All data and analysis code are available at the Open Science Framework (https://osf.io/d4q9h/). All behavioral and simulation analyses were conducted using MATLAB, version R2020a (Mathworks, 2020) and the Psychophysics Toolbox extension, version 3.0.16 (Kleiner et al., 2007) . Computational modeling analyses were conducted using R, version 4.0.2 (R Core Team, 2020). This study's design and analyses were not pre-registered.
4
Dichoptic Visual Stimulation Protocol
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The phase, motion, and dOKN test were conducted for all subjects in the same dimly lit room (illumination of 100 lux). The visual stimuli were generated and controlled by MATLAB with Psychophysics Toolbox extensions (MathWorks, Inc., Natick, MA) displayed on an ASUS 3D monitor (VG278, 144-Hz refresh rate, 1,920*1,080 resolution, Taiwan). The subjects’ heads were fixed with the help of a chin rest, and the viewing distance to the monitor (597 mm*336 mm, background brightness of 35 cd/m2) was 57 cm. During stimulation, NVIDIA 3D VISION LCD shutter glasses (Santa Clara, CA) were used to create a dichoptic viewing state on the subjects. An extra pair of refractive-corrected glasses were used in the subjects with refractive errors.
5
Smooth Pursuit Eye Movement Protocol
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The subjects were seated 70 cm in front of a CRT monitor (22 inch, Diamond Pro 2070SB, Mitsubishi, refresh rate of 100 Hz, background mean luminance 60 cd/m2) with the head stabilized by a chin rest and a forehead restraint. Eye position signals from the right eye were calibrated by requiring the subjects to fixate a target spot (diameter of 0.3 deg) at known horizontal and vertical eccentricities in binocular viewing condition. The visual stimuli and target motion were generated by Psychophysics Toolbox extensions on MATLAB (Mathworks, MA). Smooth pursuit was produced by a step‐ramp paradigm (Rashbass 1961 ) with a constant speed of 18.5 deg/sec. The pursuit stimuli (diameter of 2 deg) were random dot fields (each dot, 5 × 5 pixels) whose contrast was modulated by a Gaussian window with a space constant of 20 pixels. Dots had a density of 50% and dot lifetime was equal to presentation duration. The subjects first fixated on a central stationary target (diameter of 0.3 deg) that appeared on uniform gray background for 1.0–1.5 sec and a pursuit target appeared 1.4 deg left or right from the center. The target then started to move either leftward or rightward. The subjects were instructed to track a moving target with their eyes. Ten trials were conducted for each direction. The leftward and rightward directions for smooth pursuit were randomized.
6
Video-Based Eye Tracking System Protocol
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The observers sat 57 cm in front of a CRT monitor (22-inch, RDF223G, Mitsubishi, refresh rate: 60 Hz, spatial resolution: 800 × 600 pixels, background luminance: 60 cd/m 2 ) with head stabilized by a chin rest and a forehead restraint. Eye movements from the right eye were detected using a video-based eye tracking system (Matsuda et al. 2017; Miyamoto et al. 2020; Ono et al. 2019) . The eye position signals detected by the system were digitized at 1 kHz with 16-bit precision using CED-Micro 1401 hardware (Cambridge Electronic Designs, Cambridge, England). Prior to the task, the eye position signals were calibrated by requiring the observers to fixate a target spot (diameter of 0.3 deg) at known horizontal and vertical eccentricities in binocular viewing condition. The target consisted of a white Gaussian dot (SD: 0.15 deg) on a uniform black background. All the visual stimuli were generated by Psychophysics Toolbox extensions on MATLAB (Mathworks, MA, US).
7
Contrast Tuning for Oriented Gratings
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Stimuli consisted of luminance-defined sinusoidal gratings with fixed phase and a spatial frequency of 3.33 cpd, embedded in uniform random noise (60% Michelson contrast; see Fig. 1). Their size was 3 • and they were positioned on the horizontal meridian either 3.5 • to the right or to the left of the fixation cross (from the center of the grating). The gratings were oriented either horizontally (5 • ) or vertically (95 • ; 50% each). The contrast of the stimuli was adjusted individually for each participant in a weighted up-down adaptive procedure (Kaernbach, 1991 (link); see below for the description of the procedure). The resulting mean contrast of the gratings was 8.6% (range: 7-10.5%, SD 1.2%, Michelson contrast). MATLAB (The Math-Works) in conjunction with the Psychophysics Toolbox extensions (Brainard, 1997; (link)Pelli, 1997) was used for creating and presenting the stimuli, and for recording responses. The experiment was presented on a 19 CRT (G90fB, ViewSonic, Walnut, CA) monitor (resolution 1024 × 768, refresh rate of 100 Hz).
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