Extracellular recordings from mouse superior colliculus during the optokinetic reflex
Data files
Jan 07, 2025 version files 90.61 GB
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README.md
18.81 KB
Abstract
This dataset contains extracellular recordings using Neuropixels 1.0 probes of neurons from the superior colliculus of mice viewing a drifting grating stimulus. The drifting grating stimulus included a "probe" phase every 0.5 to 1 s in which the contrast of the grating was briefly (50 ms) increased from 40% to 100%. The electrode was inserted at an extreme angle tangential to the medial-lateral axis of the brain so that most of the contacts were positioned in the zonal layer, the superficial gray layer, the optic layer, or the intermediate gray layer of the superior colliculus. The goal of this experiment was to understand how resetting saccades produced via the optokinetic reflex modulate visual responses in the superior colliculus.
README: Extracellular recordings from mouse superior colliculus during the optokinetic reflex
Please use this digital object identifier to cite the dataset: https://doi.org/10.5061/dryad.cnp5hqcfn
How to access data files
Data are stored in a hierarchical data format (hdf) with each data file corresponding to a single experimental session. Files are named with the convention: <year-month-day>mlati<animal number>_store.hdf
. "mlati" is an acronym that stands for medial (m)-lateral (l) axis (a) tangential (t) insertion (i). The animal number is a unique number associated with each animal used in the experiments. There are many free applications and software for accessing data stored as an hdf file including the graphical user interface HDFView and the Python package h5py.
Datasets contained within each data file
Datasets within each data file are grouped by the type of data or the data processing module used to produce the dataset. Here are descriptions of each dataset which include the path to the dataset, the dataset shape, and a brief description of the dataset. Please note that not all datasets are populated in every data file. Variability in the availability of datasets is indicated with italicized text.
Barcodes
Datasets related to the periodic TTL pulse train encoding a 32-bit integer (i.e., barcode) recorded by all data acquisition systems. The barcode was used for synchronizing event timing across systems.
barcodes/labjack/indices
(N) - The sample index from the LabJack recording that indicates the start of the barcode signal for each barcode recorded by the LabJack devicebarcodes/labjack/trains
(N x 100) - The sample from the LabJack recording for each rising edge in the TTL pulse train associated with each barcode recorded by the Labjack devicebarcodes/labjack/values
(N) - The integer value encoded by each barcode recorded by the LabJack devicebarcodes/neuropixels/indices
(N) - The sample index from the Neuropixels recording that indicates the start of the barcode signal for each barcode recorded by the Neuropixels data acquisition systembarcodes/neuropixels/trains
(N x 100) - The sample from the Neuropixels recording for each rising edge in the TTL pulse train associated with each barcode recorded by the Neuropixels data acquisition systembarcodes/neuropixels/values
(N) - The integer value encoded by each barcode recorded by the Neuropixels data acquisition system
Epochs
Manually-collected data used for segmenting the recording into distinct epochs based on visual stimuli. Please note, not all experiments included the same set of visual stimuli, so some of these datasets may be empty. For example, not all of the experiments included a sparse noise stimulus at the end of the recording, so the epochs/sn/post
dataset is empty in these data files.
epochs/bn/hr/hf
(2) - Start and stop sample from the LabJack recording for the epoch associated with the binary noise stimulus (high-resolution, high-frequency)epochs/bn/hr/lf
(2) - Start and stop sample from the LabJack recording for the epoch associated with the binary noise stimulus (high-resolution, low-frequency)epochs/bn/lr/hf
(2) - Start and stop sample from the LabJack recording for the epoch associated with the binary noise stimulus (low-resolution, high-frequency)epochs/bn/lr/lf
(2) - Start and stop sample from the LabJack recording for the epoch associated with the binary noise stimulus (low-resolution, low-frequency)epochs/dg
(2) - Start and stop sample from the LabJack recording for the epoch associated with the drifting grating stimulusepochs/fs
(2) - Start and stop sample from the LabJack recording for the epoch associated with the fictive saccades stimulusepochs/mb
(2) - Start and stop sample from the LabJack recording for the epoch associated with the moving bars stimulusepochs/sn/pre
(2) - Start and stop sample from the LabJack recording for the epoch associated with the sparse noise stimulus presented at the beginning of the experimentepochs/sn/post
(2) - Start and stop sample from the LabJack recording for the epoch associated with the sparse noise stimulus presented at the end of the experiment
Frames
Datasets related to video acquisition.
frames/left/dropped
(N) - Mask which indicates frames missing from the left camera video recordingframes/left/intervals
(N) - Inter-frame intervals between video frames from the left camera video recordingframes/left/timestamps
(N) - Timestamps for each frame in the left camera video recordingframes/right/dropped
(N) - Mask which indicates frames missing from the right camera video recordingframes/right/intervals
(N) - Inter-frame intervals between video frames from the right camera video recordingframes/right/timestamps
(N) - Timestamps for each frame in the right camera video recording
LabJack
Datasets associated with the LabJack data acquisition device.
labjack/cameras/missing
(N) - Mask which indicates frames missing from the LabJack recordinglabjack/cameras/timestamps
(N) - Timestamp for each of N frames (including missing frames) from the LabJack recordinglabjack/matrix
(N x M) - Raw digital and analog signal recorded by the LabJack device where N is the number of samples and M is the number of channels (usually 9)labjack/timespace
(N) - Timestamps associated with each sample in the LabJack recording
Metrics
Metrics and indices associated with each unit.
metrics/ac
(N) - Amplitude cutoff metric for all units (N)metrics/dsi
(N) - Direction selectivity index for all units (N)metrics/fr
(N) - Mean firing rate for all units (N)metrics/lpi
(N) - Luminance polarity index for all units (N)metrics/pr
(N) - Presence ratio metric for all units (N)metrics/ql
(N) - Manually-curate quality label for all units (N)metrics/rpvr
(N) - Refractory period violation rate metric for all units (N)
Pose
Eye position datasets. Please note that for any of these datasets which have a second axis with a length of 4, the order of columns is x/horizontal eye position from the left eye, y/vertical eye position from the left eye, x/horizontal eye position from the right eye, y/vertical eye position from the right eye.
pose/uncorrected
(N x 4) - Eye position (in pixels) estimated with DeepLabCut for each frame of the video recording not correcting for dropped framespose/corrected
(N x 4) - Eye position (in pixels) after correcting for dropped framespose/decomposed
(N x 4) - Eye position (in pixels) after using PCA to project eye position onto the horizontal (azimuth) and vertical (elevation) axespose/filtered
(N x 4) - Eye position (in pixels) after smoothing the reoriented eye position datapose/interpolated
(N x 4) - Eye position (in pixels) after interpolating the values for missing and dropped framespose/missing/left
(N) - Mask which indicates the missing and dropped frames from the left camera video recordingpose/missing/right
(N) - Mask which indicates the missing and dropped frames from the right camera video recordingpose/reoriented
(N x 4) Eye position (in pixels) after reorienting the decomposed eye position so that is positively correlated with the raw eye position data
Prediction
Datasets related to classifying eye movements as saccades or non-saccadic eye movements and estimating the start and stop of saccades. Training data wasn't collected from all experiments, so it's possible some or all of these datasets will be empty in some data files.
prediction/saccades/direction/X
(N x M) - Putative saccade waveforms centered on the peak velocity where N is the number of saccades and M is the number of samples (i.e. video frames)prediction/saccades/direction/y
(N x 1) - Labels for putative saccades where -1 is temporal, +1 is nasal, and 0 is noise/non-saccadic eye movementsprediction/saccades/epochs/X
(N x M) - Putative saccade waveforms centered on the peak velocity where N is the number of saccades and M is the number of samples (i.e. video frames)prediction/saccades/epochs/y
(N x 2) - Start (first column) and stop (second column) offsets that specify distance from the time of peak velocity for each saccadeprediction/saccades/epochs/z
(N x 1) - The predicted label for each saccade
Receptive fields
Estimates of ON and OFF receptive fields using the sparse noise stimulus.
rf/on
(N x M x P) - ON receptive fields for each unit where N is the number of units, M is the number of subregions along the vertical axis of the display, and P is the number of subregions along the horizontal axis of the displayrf/off
(N x M x P) - OFF receptive fields for each unit where N is the number of units, M is the number of subregions along the vertical axis of the display, and P is the number of subregions along the horizontal axis of the display
Saccades
Datasets related to saccades. Please note that only datasets associated with saccades detected in the left eye are described here. Datasets associated with saccades detected in the right eye are also available.
saccades/predicted/left/direction
(N) - Direction of saccades detected in the left eyesaccades/predicted/left/dop
(N) - Direction of motion of the closest probe stimulus for each saccade detected in the left eyesaccades/predicted/left/epochs
(N x 2) - Start (first column) and stop (second column) time (in frame indices) for each saccade detected in the left eyesaccades/predicted/left/gmds
(N) - Direction of the drifting grating stimulus during each saccade detected in the left eye where -1 is counter-clockwise motion, +1 is clockwise motion, and 0 is no drifting gratingsaccades/predicted/left/indices
(N) - Time of peak velocity (in video frame indices) for each saccade detected in the left eyesaccades/predicted/left/labels
(N) - Direction of each saccade detected in the left eye where -1 is temporal and +1 is nasalsaccades/predicted/left/timestamps
(N x 2) - Start (first column) and stop (second column) time (in seconds) for each saccade detected in the left eyesaccades/predicted/left/ttp
(N) - Distance (in seconds) between each saccade and the closest probe stimulussaccades/predicted/left/waveforms
(N x M) - Saccade waveforms for each saccade where N is the number of saccades and M is the number of samples (in video frames)saccades/putative/left/indices
(N) - Time of peak velocity (in video frame indices) for each putative saccade detected in the left eyesaccades/putative/left/waveforms
(N x M) Saccade waveforms for each putative saccade where N is the number of putative saccades and M is the number of samples (in video frames)
Spikes
Datasets related to extracellular spikes.
spikes/clusters
(N x 1) - Unit identity associated with each spike where N is the number of spikesspikes/timestamps
- (N x 1) - Timestamp (in seconds) associated with each spike where N is the number of spikes
Stimuli
Datasets related to visual stimuli.
Binary noise stimulus
Datasets associated with the binary noise stimulus. Please note that only the datasets associated with the high-spatial resolution (hr) x high-temporal frequency (hf) version of this stimulus are described here. Datasets associated with the other combinations of spatial resolution and temporal frequency are also available. Low-temporal frequency is abbreviated "lf" and low-spatial resolution is abbreviated "lr."
stimuli/bn/hr/hf/fields
(N x M x P) - Matrix which indicates the field presented on each trial where N is the number of trials, M is the position along the vertical axis of the display, and P is the position along the horizontal axis of the displaystimuli/bn/hr/hf/grids
(N x M x P x 2) - Matrix which indicates the location (in degrees of visual angle) for each subregion in the field where N is the number of trials, M is the position along the vertical axis of the display, and P is the position along the horizontal axis of the displaystimuli/bn/hr/hf/missing
(N) - Mask which indicates which trials are missing where N is the number of trialsstimuli/bn/hr/hf/timestamps
(N) - Timestamps (in seconds) for the onset of each trialstimuli/bn/hr/hf/length
(1) - Side length of each subregion in degrees of visual angle. All subregions have the same side length.
Drifting grating stimulus
Datasets associated with the drifting grating stimulus.
stimuli/dg/grating/motion
(N) - Direction of motion for each block of the drifting grating stimulus where N is the number of blocksstimuli/dg/grating/timestamps
(N) - Timestamps (in seconds) for the onset of each block of the drifting grating stimulus where N is the number of blocksstimuli/dg/iti/timestamps
(N) - Timestamps (in seconds) for the end of each block of the drifting grating stimulus where N is the number of blocksstimuli/dg/motion/timestamps
(N) - Timestamps (in seconds) for the onset of motion of the drifting grating stimulus where N is the number of blocksstimuli/dg/probe/contrast
(N) - Contrast level (0 to 1) for each probe where N is the number of probesstimuli/dg/probe/dos
(N) - Direction of the closest saccade where -1 is temporal and +1 is nasalstimuli/dg/probe/motion
(N) - Direction of motion of the drifting grating stimulus for each probe where N is the number of probesstimuli/dg/probe/phase
(N) - Phase of the drifting grating stimulus for each probe where N is the number of probesstimuli/dg/probe/timestamps
(N) - Timestamp (in seconds) associated with each probe where N is the number of probesstimuli/dg/probe/tts
(N) - Latency from each probe to the closest saccade where N is the number of probes
Fictive saccades stimulus
Datasets associated with the fictive saccades stimulus.
stimuli/fs/probe/motion
(N) - Direction of motion of the drifting grating stimulus for each probe presented during the fictive saccades stimulus where N is the number of probesstimuli/fs/probe/timestamps
(N) - Timestamp (in seconds) associated with each probe presented during the fictive saccades stimulus where N is the number of probesstimuli/fs/saccade/motion
(N) - Direction of each fictive saccade where -1 is counter-clockwise motion and +1 is clockwise motionstimuli/fs/saccade/timestamps
(N) - Timestamps (in seconds) for the start of each fictive saccade
Moving bars stimulus
Datasets associated with the moving bars stimulus.
stimuli/mb/offset/timestamps
(N) - Timestamp (in seconds) for the onset of each moving bar where N is the number of trialsstimuli/mb/onset/timestamps
(N) - Timestamp (in seconds) for the offset of each moving bar where N is the number of trialsstimuli/mb/orientation
(N) - Orientation (in degrees) of the bar for each trial where N is the number of trials
Sparse noise stimulus
Datasets associated with the sparse noise stimulus. Please note only the datasets associated with the sparse noise stimulus presented at the beginning of the experiment (i.e., "pre"-experiment) are described here. Datasets associated with the sparse noise stimulus presented at the end of the experiment are also accessible by substituting "pre" with "post." For some experiments, the sparse noise stimulus was only presented at the beginning; there is no "post"-experiment presentation. For these experiments the "post"-experiment datasets associated with the sparse noise stimulus will be empty.
stimuli/sn/pre/coords
(N x 2) - The horizontal and vertical position (in degrees of visual angle) for the active subregion on each trial of the sparse noise stimulus where N is the number of trialsstimuli/sn/pre/fields
(N x M x P) - The field for each trial of the sparse noise stimulus where N is the number of trials, M is the position along the vertical axis of the display, and P is the position along the horizontal axis of the displaystimuli/sn/pre/missing
(N) - Mask which indicates which trials of the sparse noise stimulus are missingstimuli/sn/pre/signs
(N) - Mask which indicates the sign of the active subregion on each trial of the sparse noise stimulus where True is maximum luminance (i.e., ON) and False is minimum luminance (i.e. OFF)stimuli/sn/pre/timestamps
(N) - Timestamps for the onset of each trial of the sparse noise stimulus
Timestamping function parameters
Parameters for the function used to timestamp events. The timestamping function takes sample indices from the LabJack recording and transforms them into sample indices from the Neuropixels recordings accounting for temporal drift between the two data acquisition systems.
tfp/b
(1) - The slope of the timestamping functiontfp/fp
(N) - The barcode indices where N is the number of barcodestfp/m
(1) - The intercept of the timestamping functiontfp/xp
(N) - The timestamps (in seconds) for the barcodes recorded by the LabJack device where N is the number of barcodes
ZETA-test
ZETA-test results associated with each unit.
zeta/probe/left/latency
(N) - Latency from the probe to the response for probes presented during counter-clockwise motion of the drifting grating stimulus estimated with the ZETA-test for each unitzeta/probe/left/p
(N) - p-values from the ZETA-test for responses to probes presented during counter-clockwise motion of the drifting grating stimulus for each unitzeta/probe/right/latency
(N) - Latency from the probe to the response for probes presented during clockwise motion of the drifting grating stimulus estimated with the ZETA-test for each unitzeta/probe/right/p
(N) - p-values from the ZETA-test for responses to probes presented during clockwise motion of the drifting grating stimulus for each unitzeta/saccade/nasal/latency
(N) - Latency from the saccade onset to the response for nasal saccades estimated with the ZETA-test for each unitzeta/saccade/nasal/p
(N) - p-values from the ZETA-test for responses to nasal saccades for each unitzeta/saccade/temporal/latency
(N) - Latency from the saccade onset to the response for temporal saccades estimated with the ZETA-test for each unitzeta/saccade/temporal/p
(N) - p-values from the ZETA-test for responses to temporal saccades for each unit
Other datasets
There are other datasets that are leftover from the development of custom data analyses. For example, datasets keyed by paths starting with curves
, peths
, and population
are intermediate outputs from data analyses, may or may not be populated, and can be ignored.