DOI: 10.6084/m9.figshare.30369064
title: Data from: A multi-region recurrent circuit for evidence accumulation in rats

description: Description of the dataAll data are stored in MATLAB (.mat) files. There are 12 files in total, each corresponding to a 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 information about trial events.Key fields include:<i>AP</i>, <i>ML</i>, <i>DV</i>: Anterior-posterior (AP), medial-lateral (ML), and dorsal-ventral (DV) distance of each unit relative to the bregma skull landmark<i>bank</i>: The recording electrodes of Neuropixels 1.0 probes are organized into different banks, and this indicates the bank of each unit.<i>penetration</i>: A struct containing neuropixels targeting information and regions targeted.DMS : anterior dorsal striatumFOF, M2 : frontal orienting fieldsNAc : Nucleus accumbensVS : ventral striatum<i>regions</i>: brain region of each unit, as an index of penetrations.regions<i>hemisphere</i>: hemisphere of each unit<i>clusterNotes</i>: notes added during manual curation of spike sorted clusters<i>distance_from_tip</i> : distance of each unit from the tip of the Neuropixels 1.0 probe, in cms<i>electrode</i>: Neuropixels 1.0 recording site of each unit<i>rat</i>: name of the rat subject<i>raw_spike_time_s</i> : cell array containing the spike times of each unit<i>recorded</i>: 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)<i>sessid</i> : identification of the session in the BControl behavioral control platformMetrics of cluster isolation quality:<i>unitCount</i>: total number of spikes<i>unitISIRatio</i>: The ratio of the number of interspike intervals (ISI) less than 2ms to the number of interspike interval less than 20ms<i>unitIsoDist</i> : Isolation distance: This is another quality metric of spikesorted clusters described in Neymotion et al., 2011 J. Neurosci (PMID: 22072690)<i>unitLRatio</i> : L-ratio<i>unitVppRaw</i>: Peak-to-peak voltage (uV) of the mean raw waveform at the recording electrode with the largest amplitude<i>waveform</i> : mean raw waveform at the peak recording site. This has the format of number-of-units by number-of-samples.<i>meanWfGlobalRaw</i> : mean raw waveform across all recording sites<i>frac_isi_violation</i>: Fraction of spikes for which ISI violations were recorded for each unit.Trials: this is a MATLAB structure with information about the task and behavior on each of N trials. Key fields include:<i>rat</i> : name of the rat subject<i>sess_date</i> : session date<i>sessid</i> : session ID in the BControl system<i>violated</i> : whether the rat prematurely ended nose fixation<i>is_probe_trial</i> : whether the duration of the click train stimulus is fixed at 1s rather than randomly sampled from a uniform distribution.<i>is_hit</i> : a boolean vector of length N stating whether reward was delivered on each trial.<i>sides</i> : the left or right side port where the reward was baited<i>gamma</i> : 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)<i>trial_type</i> : a character vector of length N indicating the type of trial ("a" = accumulation, "f" = free choice, "s" = side LED)<i>reward_loc</i> : left or right side port where the reward was baited<i>pokedR</i> : a boolean vector of length N indicating the animal's choice on each trial<i>stim_dur_s_theoretical</i> : a vector of length N stating the stimulus durations of each trial including temporal delay before the first click is sampled.<i>leftBups</i>,<i>rightBups</i> : a cell array of length N listing the times (in seconds relative to stimulus onset, i.e., <i>stateTimes.clicks_on</i>) of the left and right clicks on each trial<i>click_diff</i> : the difference between the total number of right and left clicks<i>stim_dur_s_actual :</i> duration (in seconds) of the click train stimulus<i>click_diff_hz</i> : the difference between the total number right and left clicks, divided by the duration of the click train stimulus<i>stateTimes</i> : 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.<i>sending_trialnum</i>: beginning of the in which the trial number (encoded as an eight bit number) is emitted through the digital output<i>wait_for_cpoke</i>: beginning of the a state that waits for the animal to poke into the center port<i>cpoke_in</i>: beginning of the state in which the animal inserts its nose into the center poke.<i>cpoke_req_end</i>: end of the required time when the animal must insert its nose into the center poke<i>break</i>: beginning of the violation state, which corresponds to the animal removing its nose from the center port before the minimum required time is up<i>clicks_on</i>: beginning of the sound wave<i>clicks_off</i>: end of the sound wave<i>wait_for_spoke</i>: beginning of the state waiting for the animal to poke either the left or right port<i>feedback</i>: beginning of either a reward or error state<i>error</i>: beginning of an error state<i>left_reward</i>: beginning of a reward state occurring at the left port<i>right_reward</i>: beginning of a reward state occurring at the right port<i>spoke</i>: beginning of the state when the animal pokes left or right<i>cpoke_out</i>: inferred time when the animal removes its nose from the center port and begins its movement toward a side port<i>cleaned_up</i>: beginning of the final state in each trial during which waves are turned off<i>laser_on</i> : onset time of the photostimulus<i>laser_off</i> : offset time of the photostimulus<i>laser_pulses</i> : timestamps of individual pulses within the photostimulusCode/softwarehttps://github.com/Brody-Lab/fof_ads_interactions