DOI: 10.5061/dryad.3tx95x6t8
title: Decoding olfactory bulb output: A Behavioural assessment of rate, synchrony, and respiratory phase coding

description: The olfactory system is a well-known model for studying the temporal
 encoding of sensory stimuli due to its rhythmic stimulus delivery through
 respiration. Sniff-locked activity is pervasive in the primary olfactory
 area, the olfactory bulb, and is considered critical to structuring the
 output of its computation. We tested the behavioural importance of these
 temporal features using simple closed-loop optogenetics embedded in custom
 behavioural paradigms. We found that mice perceive differences in evoked
 spike counts and discriminate between synchronous vs. asynchronous
 activations of the output neurons. Surprisingly, they failed to
 distinguish the timing of evoked activity relative to the sniff cycle.
 These results suggest that, beyond the first steps of olfactory
 processing, sniff rhythms play a more nuanced role, with greater reliance
 on the spike rate and synchrony for the neural encoding of the
 environment, consistent with gradual transformation of encoding format at
 successive stages of sensory processing.
description: # Decoding olfactory bulb output: A Behavioural assessment of rate,
 synchrony, and respiratory phase coding Dataset DOI:
 10.5061/dryad.3tx95x6t8 ## Description of the data and file structure Data
 contained here are the individual data points plotted in the main figures
 of the manuscript “Decoding Olfactory Bulb Output: A Behavioural
 Assessment of Rate, Synchrony, and Respiratory Phase Coding” to appear in
 the journal iScience. The data are organized in the same structure as the
 figures. ## Data and file structure: Individual data points are available
 in double-precision numeric arrays in the .txt format, except for the
 electrophysiology (Neuropixels) data, which uses a Matlab format. **Common
 abbreviations:** * auROC: area under receiver operator curve * LOT:
 lateral olfactory tract ### Files and variables #### File: Figure1.zip *
 “Fig1_NeuropixelData_Mouse1.mat”: Matlab data that contains (i) spiketimes
 in a structure “units.spiketimes” in sedonds; (ii) onset times for 8
 odours used stored in a structure “odours(x).Onset”, in seconds, where x
 is the xth odour used; (iii) onset times for inhalation
 (“InhalationOnset”), in seconds; (iv) times of water droplets in seconds
 (“Water”) where, on a rewarded trials, 2 droplets of water were dispensed;
 (v) times of licks in seconds (“Licks”). *
 “Fig1_NeuropixelData_Mouse2.mat”: as above but for a different mouse. *
 “Fig1_NeuropixelData_Mouse3.mat”: as above but for a different mouse. *
 “Fig1_NeuropixelData_Mouse4.mat”: as above but for a different mouse. *
 “Fig1_NeuropixelData_Mouse5.mat”: as above but for a different mouse. *
 “Fig1C_EB”: Processed data in .txt; 2D colormap showing the firing rate
 relative to baseline in response to ethyl butyrate (EB) presentation. The
 values are in Hz. * “Fig1C_Eug”: 2D colormap showing the firing rate
 relative to baseline in response to eugenol (Eug) presentation. The values
 are in Hz. * “Fig1C_MS”: 2D colormap showing the firing rate relative to
 baseline in response to methyl salicylate (MS) presentation. The values
 are in Hz. * “Fig1E_DecoderAccuracy_Rate_Observed”: accuracy from support
 vector machine trained to discriminate the identities of odours presented
 where the input data was the firing rates of recorded units. *
  “Fig1E_DecoderAccuracy_Rate_Shuffle”: accuracy from support vector
 machine trained to discriminate the identities of odours presented where
 the input data was the firing rates of recorded units where the trial
 order was randomly permutated. * “Fig1E_DecoderAccuracy_Timing_Observed”:
 accuracy from support vector machine trained to discriminate the
 identities of odours presented. The input data was the latency to 2 action
 potential generations after the inhalation onset for recorded units. *
 “Fig1E_DecoderAccuracy_Timing_Shuffle”: accuracy from support vector
 machine trained to discriminate the identities of odours presented. The
 input data was the latency to 2 action potential generations after the
 inhalation onset for recorded units but with the trial order randomly
 permutated. * “Fig1E_Window_size”: window size used to sample the input
 for the decoder. #### File: Figure2.zip * “Fig2D_SpikeProbability_1pulse”:
 2D colormap corresponding to the probability of spikes with respect to the
 onset of one light pulse. First dimension = units, second dimension =
 time. * “Fig2D_SpikeProbability_3pulses”: 2D colormap corresponding the
 probability of spikes with respect to the onset of the first pulse in a
 train of 3 light pulses. * “Fig2D_time_axis”: time axis in ms for the
 above two plots. * “Fig2E_EvokedSpikes_pulse1”: number of spikes evoked
 following the first light pulse in a train of 3 light pulses. *
 “Fig2E_EvokedSpikes_pulse2”: number of spikes evoked following the second
 light pulse in a train of 3 light pulses. * “Fig2E_EvokedSpikes_pulse3”:
 number of spikes evoked following the third light pulse in a train of 3
 light pulses. #### File: Figure3.zip * “Fig3D_Accuracy_5pulse_Detection”:
 Accuracy of detecting a 5-pulse optogenetic stimulation, expressed as
 auROC over time. * “Fig3D_Trials_5pulse_Detection: trial numbers for the
 accuracy plot for the 5-pulse detection task. *
 “Fig3D_Accuracy_Odour1_Discrimination”: Accuracy of discriminating between
 two odours prior to the 5-pulse detection task, expressed as auROC over
 time. * “Fig3D_Trials_odour1: trial numbers for the accuracy plot for
 odour discrimination. * “Fig3E_Accuracy_3pulse_Detection”: Accuracy of
 detecting a 3-pulse optogenetic stimulation, expressed as auROC over time.
 * “Fig3E_Trials_3pulse_Detection: trial numbers for the accuracy plot for
 the 3-pulse detection task. * “Fig3E_Accuracy_Odour1_Discrimination”:
 Accuracy of discriminating between two odours prior to the 3-pulse
 detection task, expressed as auROC over time. * “Fig3E_Trials_odour1:
 trial numbers for the accuracy plot for odour discrimination. *
 “Fig3F_Accuracy_1pulse_Detection”: Accuracy of detecting a 1-pulse
 optogenetic stimulation, expressed as auROC over time. *
 “Fig3F_Trials_1pulse_Detection: trial numbers for the accuracy plot for
 the 1-pulse detection task. * “Fig3F_Accuracy_Odour1_Discrimination”:
 Accuracy of discriminating between two odours prior to the 1-pulse
 detection task, expressed as auROC over time. * “Fig3F_Trials_odour1:
 trial numbers for the accuracy plot for odour discrimination. *
 “Fig3G_Trial2criterion_1pulseDetection”: number of trials taken to reach
 the accuracy level of 0.8 (auROC) for the 1-pulse detection task. *
 “Fig3G_Trial2criterion_3pulseDetection”: number of trials taken to reach
 the accuracy level of 0.8 (auROC) for the 3-pulse detection task. *
 “Fig3G_Trial2criterion_5pulseDetection”: number of trials taken to reach
 the accuracy level of 0.8 (auROC) for the 5-pulse detection task. ####
 File: Figure4.zip * “Fig4C_2vs1_Accuracy”: Accuracy of discriminating
 between 2 pulses vs. 1 pulse of optogenetic stimulation over time,
 expressed as auROC. * “Fig4C_2vs1_Blocks”: time axis for the above plot,
 in blocks of trials, where 1 block corresponds to 100 trials. *
 “Fig4C_3vs1_Accuracy”: Accuracy of discriminating between 3 pulses vs. 1
 pulse of optogenetic stimulation over time, expressed as auROC. *
 “Fig4C_3vs1_Blocks”: time axis for the above plot, in blocks of trials,
 where 1 block corresponds to 100 trials. * “Fig4C_4vs1_Accuracy”: Accuracy
 of discriminating between 4 pulses vs. 1 pulse of optogenetic stimulation
 over time, expressed as auROC. * “Fig4C_4vs1_Blocks”: time axis for the
 above plot, in blocks of trials, where 1 block corresponds to 100 trials.
 * “Fig4C_5vs1_Accuracy”: Accuracy of discriminating between 5 pulses vs. 1
 pulse of optogenetic stimulation over time, expressed as auROC. *
 “Fig4C_5vs1_Blocks”: time axis for the above plot, in blocks of trials,
 where 1 block corresponds to 100 trials. * “Fig4D_2vs1_OverallAccuracy”:
 Overall accuracy of discriminating between 2 pulses vs. 1 pulse of
 optogenetic stimulation across all days. * “Fig4D_3vs1_OverallAccuracy”:
 Overall accuracy of discriminating between 3 pulses vs. 1 pulse of
 optogenetic stimulation across all days. * “Fig4D_4vs1_OverallAccuracy”:
 Overall accuracy of discriminating between 4 pulses vs. 1 pulse of
 optogenetic stimulation across all days. * “Fig4D_5vs1_OverallAccuracy”:
 Overall accuracy of discriminating between 5 pulses vs. 1 pulse of
 optogenetic stimulation across all days. *
 “Fig4F_2vs1_Accuracy_VariableLatencies”: Accuracy of discriminating
 between 2 pulses vs. 1 pulse of optogenetic stimulation where the onset of
 the first pulse occurred at variable latencies relative to the inhalation
 onset (20, 50, 80 ms). * “Fig4F_2vs1_Latencies”: Latencies in ms relative
 to the inhalation onset for the above data. *
 “Fig4F_3vs1_Accuracy_VariableLatencies”: Accuracy of discriminating
 between 3 pulses vs. 1 pulse of optogenetic stimulation where the onset of
 the first pulse occurred at variable latencies relative to the inhalation
 onset (20, 50, 80 ms). * “Fig4F_3vs1_Latencies”: Latencies in ms relative
 to the inhalation onset for the above data. *
 “Fig4F_4vs1_Accuracy_VariableLatencies”: Accuracy of discriminating
 between 4 pulses vs. 1 pulse of optogenetic stimulation where the onset of
 the first pulse occurred at variable latencies relative to the inhalation
 onset (20, 50, 80 ms). * “Fig4F_4vs1_Latencies”: Latencies in ms relative
 to the inhalation onset for the above data. *
 “Fig4F_5vs1_Accuracy_VariableLatencies”: Accuracy of discriminating
 between 5 pulses vs. 1 pulse of optogenetic stimulation where the onset of
 the first pulse occurred at variable latencies relative to the inhalation
 onset (20, 50, 80 ms). * “Fig4F_5vs1_Latencies”: Latencies in ms relative
 to the inhalation onset for the above data. #### File: Figure5.zip *
 “Fig5D_Accuracy_20Vs120ms”: Accuracy of discriminating optogenetic
 stimulations with latencies of 20 ms vs. 120 ms relative to the inhalation
 onset. The accuracies are expressed in auROC. * “Fig5D_Trials_20Vs120ms”:
 time axis for the above data, in trials. * “Fig5D_Accuracy_odour”:
 Accuracy of discriminating between two odours. The accuracies are
 expressed in auROC. * “Fig5E_LastSessionAccuracy_20msVs80ms”: Accuracy of
 discriminating optogenetic stimulations with latencies of 20 ms vs. 80 ms
 relative to the inhalation onset for the last session of training. *
 “Fig5E_LastSessionAccuracy_20msVs120ms”: Accuracy of discriminating
 optogenetic stimulations with latencies of 20 ms vs. 120 ms relative to
 the inhalation onset for the last session of training. *
 “Fig5E_LastSessionAccuracy_80msVs130ms”: Accuracy of discriminating
 optogenetic stimulations with latencies of 80 ms vs. 20 ms relative to the
 inhalation onset for the last session of training. *
 “Fig5E_LastSessionAccuracy_Odour”: Accuracy of discriminating between two
 simple odours for the last session of training. #### File: Figure6.zip *
 “Fig6C_ThresholdTime_Ramp”: The time when the PSTH crossed a threshold
 height for varying threshold levels, in response to a ramp profile light
 stimulus. * “Fig6C_ThresholdTime_Rectangular”: The time when the PSTH
 crossed a threshold height for varying threshold levels, in response to a
 rectangular profile light stimulus. * “Fig6C_ThresholdValues”: Threshold
 values for the PSTH height used in the above plots. *
 “Fig6E_DetectionAccuracy_ramp”: Accuracy of detecting the ramp light
 stimulus over trials, expressed as auROC. * “Fig6E_trials_ramp”: time axis
 for the above plot, in trials. * “Fig6E_DetectionAccuracy_rectangular”:
 Accuracy of detecting the ramp light stimulus over trials, expressed as
 auROC. * “Fig6E_trials_rectangular”: time axis for the above plot, in
 trials. * “Fig 6F_DetectionAccuracy_mouse1”: psychometric curve for
 detecting ramp light stimulus at different amplitude for mouse1. *
 “Fig6F_LightIntensities_mouse1”: Light levels, in mW, for the above plot.
 * “Fig 6F_DetectionAccuracy_mouse2”: psychometric curve for detecting ramp
 light stimulus at different amplitude for mouse2. *
 “Fig6F_LightIntensities_mouse2”: Light levels, in mW, for the above plot.
 * “Fig 6F_DetectionAccuracy_mouse3”: psychometric curve for detecting ramp
 light stimulus at different amplitude for mouse3. *
 “Fig6F_LightIntensities_mouse3”: Light levels, in mW, for the above plot.
 * “Fig6H_DiscriminationAccuracy”: Accuracy of discriminating ramp light
 stimuli delivered at 20 ms relative to the inhalation onset vs. 80 ms. *
 “Fig6H_trials”: time axis for the above data, in trials. #### File:
 Figure7.zip * “Fig7D_DiscriminationAccuracy_250ms”: Accuracy in
 discriminating synchronous vs. asynchronous activations task, expressed as
 auROC, where the interval between the staggered pulses was 250 ms. *
 “Fig7D_trials_250ms”: time axis for the above data, in trials. *
 “Fig7D_DiscriminationAccuracy_500ms”: Accuracy in discriminating
 synchronous vs. asynchronous activations task, expressed as auROC, where
 the interval between the staggered pulses was 500 ms. *
 “Fig7D_trials_500ms”: time axis for the above data, in trials. *
 “Fig7F_DiscriminationAccuracy_FixedLatency1”: Accuracy in discriminating
 synchronous vs. asynchronous activations task for different intervals
 (delta_t), where the onset of stimulus delivery was fixed relative to the
 inhalation onset. * “Fig7F_DiscriminationAccuracy_RandomLatency”: Accuracy
 in discriminating synchronous vs. asynchronous activations task for
 different intervals (delta_t), where the onset of stimulus delivery was
 random. * “Fig7F_DiscriminationAccuracy_FixedLatency2”: Accuracy in
 discriminating synchronous vs. asynchronous activations task for different
 intervals (delta_t), where the onset of stimulus delivery was returned to
 the fixed condition relative to the inhalation onset. * “Fig7F_delta_t”:
 Intervals (delta_t) for the above data. *
 “Fig7G_OverallAccuracy_FixedLatency1”: Accuracy in discriminating
 synchronous vs. asynchronous activations task for all intervals combined,
 where the onset of stimulus delivery was fixed relative to the inhalation
 onset. * “Fig7G_OverallAccuracy_RandomLatency”: Accuracy in discriminating
 synchronous vs. asynchronous activations task for all intervals combined,
 where the onset of stimulus delivery was random. *
 “Fig7G_OverallAccuracy_FixedLatency2”: Accuracy in discriminating
 synchronous vs. asynchronous activations task for all intervals combined,
 where the onset of stimulus delivery was returned to the fixed condition
 relative to the inhalation onset.