CodyCBakerPhD
commented
9 months ago From new white paper sent by Saskia, all gratings are sinusoidal and used custom scripts based off of the PsychoPy software
Extra devices and OpticalSeries or experiment-level metadata
""" Monitor was positioned 15 cm from the mouse's eye, and spanned 120 degrees x 95 degrees of visual space without accounting for stimulus warping.
Each monitor was gamma corrected using a USB-650 Red Tide Spectrometer (Ocean Optics). Luminance was measured using a SpectroCAL MKII Spectroradiometer (Cambridge Research Systems). Monitors were used at a brightness setting of 30% and contrast at 50%, corresponding to mean luminance of 50 cd/m^2. """
Static gratings
(a) orientation_in_degrees
"Angle of the grating."
(b) spatial_frequency_in_cycles_per_degree
"Period of the grating in cycles/degree."
(c) phase
Not mentioned in white paper, but is in this data book for a summer workshop https://allenswdb.github.io/visual-coding-2p/vc2p-stimuli.html
https://observatory.brain-map.org/visualcoding/stimulus/static_gratings also has a handy little widget for it
"Relative position of the grating. Phase 0 and Phase 0.5 are 180° apart so that the peak of the grating of phase 0 lines up with the trough of phase 0.5."
TODO: I should really add a 'is_blank_sweep' boolean column to be consistent with the drifting parts; this is the explanation of the NaN values
Drifting gratings
"A full field drifting sinusoidal grating at a single spatial frequency (0.04 cycles/degree) and contrast (80%)."
The direction of motion is not mentioned by the white paper, but is mentioned in the data book: https://allenswdb.github.io/visual-coding-2p/vc2p-stimuli.html#drifting-gratings
"The drifting gratings stimulus consists of a sinusoidal grating that is presented on the monitor that moves orthogonal to the orientation of the grating, moving in one of 8 directions (called orientation) and at one of 5 temporal frequencies."
(a) orientation_in_degrees
"Angle of the grating."
(b) temporal_frequency_in_hz
"The speed at which the grating moves, in Hz."
(c) is_blank_sweep (bool)
"Mean luminance gray image; not a grating."
So I don't make up something inaccurate, best to consult them on what descriptions they would like to set for
static gratings
(a) orientation [even though this one is fairly obvious] (b) spatial_frequency (c) phase
drifting gratings
(a) orientation [of the line or direction of motion? AllenSDK seems to thnk latter...] (b) temporal_frequency (c) blank_sweep
Might also be nice to get some code that can generate what the subject saw given these parameters...