Readme for the description of datasets and data analysis for the paper titled "Differential modulation of cortical codes for sounds of varying intensity by distinct inhibitory neurons" by Tobin, Sheth, Wood, and Geffen.

Description of the data and file structure

Data Folders

Data: Folder SST
Experimental data for the mice SST-Cre x Cdh23 injected with GCaMP7f + Flex.ChrimsonR.tdTomato
Each dataset is a recording from a different population of neurons in AC

Data: Folder VIP
Experimental data for the mice VIP-Cre x Cdh23 injected with GCaMP7f + Flex.ChrimsonR.tdTomato
Each dataset is a recording from a different population of neurons in AC

Data: Folder Control_VIP
Control data with the VIP cells in mice VIP-Cre x Cdh23 injected with GCaMP7f + Flex.tdTomato
Each dataset is a recording from a different population of neurons in AC

Data: Folder Control_NonVIP
Control data with the Non-VIP cells in mice VIP-Cre x Cdh23 injected with GCaMP7f + Flex.tdTomato
Each dataset is a recording from a different population of neurons in AC

Dataset Types

SingleCellData

Emplacement: in folders SST ; VIP ; Control_VIP ; Control_NonVIP

There is one dataset per recording.

Each recording contains:

• fr : imaging frame rate in Hz
• raster_ordered : raster of the fluorescence for each trial as a function of frame number (=time) for each neuron in the population, ordered by combination of laser power and sound level (example: trials for combination 1: raster_ordered(1:10,:,:); trials for combination 5: raster_ordered(51:60,:,:) ... ) size is (210 x 181 x Ncells) with 210 the number of different combinations of laser and sound (21 combinations) times the number of trials (=repeats) per combination (10 repeats); 181 the number of frames (~ 30 frames/sec * 5 sec); Ncells the number of neurons in the population
• rasterInfo : structure containing the information about the construction of raster_ordered from the original fluorescence trace
  rasterInfo.preOnsetTime : duration in seconds before stimulus onset (in raster_ordered, mean_Trace, std_mean_Trace)
  rasterInfo.postOnsetTime : duration in seconds after stimulus onset (in raster_ordered, mean_Trace, std_mean_Trace)
  rasterInfo.doDFoverF0 : if equal to 1, do baseline correction. For each trial, the average over the baseline (duration preOnsetTime) is subtracted from the fluorescence trace, and the result is normalized by the standard deviation of the baseline (in raster_ordered, mean_Trace, std_mean_Trace)
• mean_Trace : fluorescence trace averaged over the different repeats of a laser+sound combination as a function of frame number (=time) for each neuron in the population (average of raster_ordered over the trials for each sound+laser combination)
  size is (21 x 181 x Ncells) with 21 the number of different combinations of laser (3 powers) and sound (7 levels); 181 the number of frames (~ 30 frames/sec * 6 sec); Ncells the number of neurons in the population
• std_mean_Trace : standard deviation of the fluorescence trace over the different repeats of a laser+sound combination as a function of frame number (=time) for each neuron in the population (standard deviation of raster_ordered over the trials for each sound+laser combination)
  size is (21 x 181 x Ncells) with 21 the number of different combinations of laser (3 powers) and sound (7 levels); 181 the number of frames (~ 30 frames/sec * 6 sec); Ncells the number of neurons in the population
• exptInfo : structure containing the following experimental information:
  exptInfo.mouse : experimental mouse name
  exptInfo.recDate : recording date
  exptInfo.Filename : original file name
  exptInfo.mouseline : experimental mouse line
• RedCells : structure containing the information about the identification of the "red" neurons (VIP or SST depending on mouseline) from the 2p recording
  RedCells.Threshold : threshold in standard deviations (sigma, see Methods) above which a cell is identified as "red"
  RedCells.AvGrayValue_red : Average value in standard deviations of the fluorescence of each neuron in the red channel
  RedCells.isCell_red : Array with 1 if a neuron is identified as a "red" cell (AvGrayValue_red above Threshold), and 0 otherwise
  RedCells.SourceData : original source data for the fluorescence
  RedCells.AnalysisFile : original analysis file for red cell identification
  RedCells.bleedthrough_fitcoeff : bleedthrough coefficient from the green channel to the red channel

StimInfo: structure containing information about the stimulus:

stimInfo.fs : stimulus sampling frequency in Hz
stimInfo.tDur_opto : Duration in sec that laser stimulus is on overall
stimInfo.tOn_opto : Duration in sec of the "on" part of the laser pulse during the laser stimulus
stimInfo.tOff_opto : Duration in sec of the "off" part of the laser pulse during the laser stimulus
stimInfo.ISI_opto : Interstimulus interval in sec between two laser stimuli
stimInfo.amplitude_opto : laser powers as the ratio of maximum power (see Methods for calibration)
stimInfo.nPulses : number of laser pulses during a laser stimulus
stimInfo.delay_OptoTone : delay in seconds between the onset of the laser stimulus and the onset of the sound stimulus
stimInfo.index : combination of sound level (in dB, first column) and laser power (in the ratio of maximum power, second column)
stimInfo.index_names : names of columns for index
stimInfo.order : order of presentation of the different laser+sound combinations (row of index)
stimInfo.noiseDur : duration in milliseconds of a noise burst
stimInfo.nClicks : number of clicks during a noise burst
stimInfo.clickRate : frequency in Hz of the clicks
stimInfo.intensity : sound pressure levels in dB
stimInfo.ISI : the interstimulus interval between two sound stimuli
stimInfo.repeats : number of repeats per sound+laser combination

SingleCellFits

Emplacement: in folders SST; VIP;

This is the output from the fitting of the rate-level curves (code for fitting in singeCellFittingCode).

Sigmoid fits

sigmoidFit* : contains the parameters to the single-cell fits to the rate-level curves from all recordings with:
sigmoidNoLight* : set of parameters of cells fit with a sigmoid function at no laser power
sigmoidMidLight* : set of parameters of cells fit with a sigmoid function at medium laser power
sigmoidHighLight* : set of parameters of cells fit with a sigmoid function at high laser power
The set of parameters are :
sigmoid*(:,1) : recording number - 1 (python indexing)
sigmoid*(:,2) : cell number in recording -1 (python indexing)
sigmoid*(:,3) : y_0
sigmoid*(:,4) : y_0 + y_range
sigmoid*(:,5) : x_0
sigmoid*(:,6) : Delta x (with no constraint on sign)
sigmoid*(:,7) : interpolated error

Gaussian fits

gaussianFit* : contains the parameters to the single-cell fits the rate-level curves from all recordings with:
gaussNoLight* : set of parameters of cells fit with a Gaussian function at no laser power
gaussMidLight* : set of parameters of cells fit with a Gaussian function at medium laser power
gaussHighLight* : set of parameters of cells fit with a Gaussian function at high laser power
The set of parameters are :
gauss*(:,1) : recording number - 1 (python indexing)
gauss*(:,2) : cell number in recording -1 (python indexing)
gauss*(:,3) : y_range
gauss*(:,4) : x_mean
gauss*(:,5) : sigma
gauss*(:,6) : y_0
gauss*(:,7) : interpolated error

Code/Software

Set up

In the code scripts, replace with local folder location for datasets in:

• AnalysisScript_DataLoad
• AnalysisScript_Fig4
• AnalysisScript_Fig5

Code for functions used in AnalysisScript_DataLoad is in Code\functions

Code for fitting the rate-level curves of single cells is in the folder Code\singleCellFittingCode\ (the datasets of the fit parameters are available so no need to re-run this code to plot the figures)

Dataset selection and plotting figures

In AnalysisScript_DataLoad.m, replace line 11 of the code with the chosen dataset: SST, VIP, Control_VIP, or Control_NonVIP.

Start by compiling Analysis_DataLoad.m with a chosen dataset (SST, VIP, Control_VIP, or Control_NonVIP) then compile the code for a chosen figure.

The code for plotting the figures is in AnalysisScript_* from Fig1 to Fig6.