DOI: 10.5061/dryad.sj3tx96dm
title: Data from: Transitions in dynamical regime and neural mode underlie perceptual decision-making

description: Perceptual decision-making is the process by which an animal uses sensory
 stimuli to choose an action or mental proposition. This process is thought
 to be mediated by neurons organized as attractor networks. However,
 whether attractor dynamics underlie decision behavior and the complex
 neuronal responses remains unclear. Here we use simultaneous recordings
 from hundreds of neurons, together with an unsupervised, deep
 learning-based method, to discover decision-related neural dynamics in
 frontal cortex and striatum of rats while the subjects accumulate
 pulsatile auditory evidence. The data set consists of spike times from
 simultaneously recorded neurons, along with the timing of the sensory
 stimuli and the rat's actions for each trial. Recordings were made
 from 12 rats across 115 daily sessions, 84-663 units recorded per session
 (median: 327) and 157 to 854 trials completed per session (median: 455).
 We found that trajectories evolved along two sequential regimes, the first
 dominated by sensory inputs, and the second dominated by the autonomous
 dynamics, with flow in a direction (i.e., “neural mode”) largely
 orthogonal to that in the first regime. We propose that the second regime
 corresponds to decision commitment. We developed a simplified model that
 approximates the coupled transition in dynamics and neural mode and allows
 precise inference, from each trial’s large-scale neural population
 activity, of a putative internal decision commitment time in that trial.
 The simplified model captures diverse and complex single-neuron temporal
 profiles, such as ramping and stepping. It also captures trial-averaged
 curved trajectories, and reveals distinctions between brain regions. The
 putative neurally-inferred commitment times (“nTc”) occurred at times
 broadly distributed across trials, and not time-locked to stimulus onset,
 offset, or response onset. Nevertheless, when trials were aligned to nTc,
 behavioral analysis showed that, as predicted by a decision commitment
 time, sensory evidence before nTc affected the subjects’ decision, but
 evidence after nTc did not. Our results show that the formation of a
 perceptual choice involves a rapid, coordinated transition in both the
 dynamical regime and the neural mode of the decision process, and suggest
 the moment of commitment to be a useful entry point for dissecting
 mechanisms underlying rapid changes in internal state.
description: Action potentials were recorded using Neuropixel 1.0 probes and
 sorted using Kilosort 2.0. Clusters were manually curated.
description: # Data from: Transitions in dynamical regime and neural mode underlie
 perceptual decision-making
 [https://doi.org/10.5061/dryad.sj3tx96dm](https://doi.org/10.5061/dryad.sj3tx96dm) ## Description of the data and file structure All data are stored in MATLAB (.mat) files. There are 115 files in total, each corresponding to a single daily recording session from a rat performing an auditory decision-making task. Each file is named as “subjectID_YYYY_MM_DD.mat,” based on the subject ID and the recording date. Each file contains spike times for all recorded units, along with the timing of the stimuli (e.g., auditory clicks) and the animal’s actions (e.g., nose-poking into the center port) for every trial. The following two variables are included in each file: ### **Cells** This is a MATLAB "struct" containing the spike times and the identifying information of each recorded unit. It contains the following fields: * *anatom_loc_mm *: Anterior-posterior (AP), medial-lateral (ML), and dorsal-ventral (DV) distance of each unit relative to the bregma skull landmark * *bank *: The recording electrodes of Neuropixels 1.0 probes are organized into different banks, and this indicates the bank of each unit. * *cell*_*area *: brain region of each unit * dmFC : dorsomedial frontal cortex, overlapping the areas "M2" and "Cg1" in the Paxinos and Watson Rat Brain Atlas (6th edition) * mPFC : medial prefrontal cortex (PW areas "PrL" and "IL") * dStr : dorsal striatum (PW area "CPu") * vStr : ventral striatum * M1 : primary motor cortex * FOF : frontal orienting fields * *cell_hemi *: hemisphere of each unit * *clusterNotes *: notes added during manual curation of spike sorted clusters * *dist_from_tip_um :* distance of each unit from the tip of the Neuropixels 1.0 probe, in microns * *electrode *: Neuropixels 1.0 recording site of each unit * *is_single *: whether a unit is considered by Kilosort2 as a single unit, as opposed to a multiunit cluster * *meta *: metadata * *meta.ap_meta* : contains information about the Neuropixels 1.0 recording saved by the SpikeGLX acquisition application * *rat *: name of the rat subject * *raw_spike_time_s :* cell array containing the spike times of each unit * *recorded *: cell array indicating whether usable spiking data could be recorded for each unit on each trial (i.e., the signal was not obscured by artifacts) * *recording_site *: channel where the largest waveform of each unit was recorded * *sessid :* identification of the session in the BControl behavioral control platform Metrics of cluster isolation quality: * *unitCount *: total number of spikes  * *unitISIRatio *: The ratio of the number of interspike intervals (ISI) less than 2ms to the number of interspike interval less than 20ms * *unitIsoDist :* Isolation distance: This is another quality metric of spikesorted clusters described in Neymotion et al., 2011 J. Neurosci (PMID: 22072690) * *unitLRatio :* L-ratio * *unitVppRaw *: Peak-to-peak voltage (uV) of the mean raw waveform at the recording electrode with the largest amplitude * *waveform*.*mean_uV :* mean raw waveform at the peak recording site. This has the format of number-of-units by number-of-samples. See *meta.ap_meta.imSampRate* for the sampling rate (typically 30000 Hz). * *waveform.meanWfGlobalRaw* : mean raw waveform across all recording sites * *waveform.width_ms :* Duration between the peak and trough of the average waveform (ms) ### Trials A structure with information about the task and behavior on each of N trials. Key fields include: * *rat* : name of the rat subject * *sess_date* : session date * *sessid :* session ID in the BControl system * *violated* : whether the rat prematurely ended nose fixation * *is_probe*_*trial* : whether the duration of the click train stimulus is fixed at 1s rather than randomly sampled from a uniform distribution. * *responded* : whether the animal entered a side port within ten seconds from when it was permitted to respond * *response_time_s* : time between when the animal removed its nose from fixation port and when it was allowed to do so * *is_hit* : a boolean vector of length N stating whether reward was delivered on each trial. * *sides* : the left or right side port where the reward was baited * *gamma* : a vector of length N stating what the signal level was on each trial (the log of the ratio of right / left click generative rates) * *trial_type* : a character vector of length N indicating the type of trial ("a" = accumulation, "f" = free choice, "s" = side LED) * *pharma* : information about pharmacological manipulation on each trial * *manip* : the chemical ("saline" or "muscimol") that was infused * *doseNG* : mass of the infused agent, in nanograms * *injector_mm* : length of the injector * *laser* : information about the photostimulus * *isOn* : whether a photostimulus occurred * *pulseMS* : duration (in milliseconds) of each photostimulus pulse * *freqHz* : frequency of the laser pulse in hertz; 0 indicates a non-periodic stimulus * *latencyMS* : latency (ms) of the photostimulus relative to the trial event that triggers the stimulus * *durMS* : total duration (ms) of the photostimulus * *triggerEvent* : event on each trial to which photostimulus onset is aligned * *brain_area* : the brain region targeted * *laterality* : indicated whether the photostimulus targeted the left hemisphere, the right hemisphere, or both. * *power_mW* : power of the photostimulus (mW) * *voltage* : the time course of the photostimulus is controlled a voltage signal * *line* : the channel in BControl through which the voltage is outputted * *clock_**speed*_*hz* : sampling rate of the BControl system * *is_sine_not_square* : whether a periodic photostimulus is sine wave rather than a square wave * *min_V* : minimum value of the voltage trace controlling the photostimulus * *max_V* : maximum voltage value * *on_ramp_dur_s* : duration (in seconds) of the power ramp up following photostimulus onset * *off_ramp_dur_s* : duration (in seconds) of the ramp down preceding photostimulus offset * *stim_per* : name of the trial period when the photostimulus occurred * *is_anesthetized* : whether the animal was anesthetized * *reward_loc* : left or right side port where the reward was baited * *pokedR* : a boolean vector of length N indicating the animal's choice on each trial * *stim_dur_s* : a vector of length N stating the stimulus durations of each trial * *leftBups*,*rightBups* : a cell array of length N listing the times (in seconds relative to stimulus onset, i.e., *stateTimes.clicks_on*) of the left and right clicks on each trial * *click_diff* : the difference between the total number of right and left clicks * *stim_dur_s :* duration (in seconds) of the click train stimulus * *click_diff_hz* : the difference between the total number right and left clicks, divided by the duration of the click train stimulus * *click_diff_norm* : the normalized difference between the clicks, computed as (#right clicks - #left clicks) divided by the total number of clicks * *stateTimes* : a structure with fields of length N for each task event, giving the times according to the BControl clock, when they occurred on each trial. * *sending_trialnum*: beginning of the in which the trial number (encoded as an eight bit number) is emitted through the digital output * *wait_for_cpoke*: beginning of the a state that waits for the animal to poke into the center port * *cpoke_in*: beginning of the state in which the animal inserts its nose into the center poke. * *cpoke_req_end*: end of the required time when the animal must insert its nose into the center poke * *break*: beginning of the violation state, which corresponds to the animal removing its nose from the center port before the minimum required time is up * *clicks_on*: beginning of the sound wave * *clicks_off*: end of the sound wave * *wait_for_spoke*: beginning of the state waiting for the animal to poke either the left or right port * *feedback*: beginning of either a reward or error state * *error*: beginning of an error state * *left_reward*: beginning of a reward state occurring at the left port * *right_reward*: beginning of a reward state occurring at the right port * *spoke*: beginning of the state when the animal pokes left or right * *cpoke_out*:[ ](https://github.com/Brody-Lab/labwide_PBups_analysis/blob/master/get_cpoke_out_time.m)inferred time when the animal removes its nose from the center port and begins its movement toward a side port * *cleaned_up*: beginning of the final state in each trial during which waves are turned off * *laser_on* : onset time of the photostimulus * *laser_off* : offset time of the photostimulus * *laser_pulses* : timestamps of individual pulses within the photostimulus ## Code/software [https://github.com/Brody-Lab/decision_dynamics_commitment](https://github.com/Brody-Lab/decision_dynamics_commitment)