Data from: Beyond rhythm - a framework for understanding the frequency spectrum of neural activity
Data files
Aug 25, 2023 version files 715.59 MB
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2019-09-20_10-32-27_1.zip
715.59 MB
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README.md
6.41 KB
Abstract
Cognitive and behavioral processes are often accompanied by changes within well-defined frequency bands of the local field potential (LFP i.e., the voltage induced by neuronal activity). These changes are detectable in the frequency domain using the Fourier transform and are often interpreted as neuronal oscillations. However, aside some well-known exceptions, the processes underlying such changes are difficult to track in time, making their oscillatory nature hard to verify. In addition, many non-periodic neural processes can also have spectra that emphasize specific frequencies. Thus, the notion that spectral changes reflect oscillations is likely too restrictive. In this study, we use a simple yet versatile framework to understand the frequency spectra of neural recordings. Using simulations, we derive the Fourier spectra of periodic, quasi-periodic and non-periodic neural processes having diverse waveforms, illustrating how these attributes shape their spectral signatures. We then show how neural processes sum their energy in the local field potential in simulated and real-world recording scenarios. We find that the spectral power of neural processes is essentially determined by two aspects: 1) the distribution of neural events in time and 2) the waveform of the voltage induced by single neural events. Taken together, this work guides the interpretation of the Fourier spectrum of neural recordings and indicates that power increases in specific frequency bands do not necessarily reflect periodic neural activity.
# Beyond Rhythm - A framework for understanding the frequency spectrum of neural activity
The present data set comprises an example neural recording and 8 matlab scripts that were used to generate the figures of a manuscript entitled *Beyond rhythm – A framework for understanding the frequency spectrum of neural activity* by Quentin Perrenoud and Jessica A. Cardin. This manuscript was accepted for publication in the journal *Frontiers in Systems Neuroscience* on August 14th 2023. The scripts can be used to reproduce the figures of the article and perform simulations illustrating how the temporal distribution and waveform of neural processes influence their Fourier Spectrum.
## Description of the data and file structure
The data set comprises a recording of the activity of the mouse visual cortex performed with a 16 contact multi-electrode array (Neuronexus A16 probe) spaced 50um apart and implanted vertically through cortical layers. This recording was part of larger study which is detailed in the following preprint (https://doi.org/10.1101/2022.05.13.491832). This recording is stored in the zip file: **2019-09-20_10-32-27_1**.This file contains two .mat files:
-*PCP_L4_MakeMetaDataStructure.mat*:
This file a structure **sCFG** containing curated recording data with the following fields:
-**sPARAM**: a structure containing the parameters that were used to generated the currated data (CAN BE IGNORED)
-**sREC**: a structure containing general information about the recording (CAN BE IGNORED)
-**sINPUT**: a structure containing information about the input file used to generate the currated data (CAN BE IGNORED)
-**sL4MMDS**: a structure containing the curated data with the following fields:
-**inWorkSampleRate**: the sample rate of the recording
-**db1TStamps**: time stamps for the all the samples in the recording
-**db2LFP**: the Local Field Potential recording (a 16 channels x 5249484 samples matrix)
-**in2MUATrace**: the Multi Unit Activity recording (a 16 channels x 5249484 samples matrix). Counts the number of extracellular spikes at the time of each sample
-**db1LChan**: Boundaries between cortical layer 1, 2-3, 4, 5 and 6 relative to channel order
-**db1ChannelDepth**: Approximate depth of each channel in db2LFP or in2MUATrace
-**db1ChanLayer**: The cortical layer in which each channel in db2LFP or in2MUATrace is situated
-**bl1WheelOn**: a 5249484 samples boolean vector indexing the epochs of the recording where the mouse was running
-**db1PupilArea**: a 5249484 samples vector of the pupil area
-**db1FacePC1**: a 5249484 samples vector of the first principal component of facial motion energy
-**bl1Whisk**: a 5249484 samples vector indexing epochs when the mouse was whisking
-**chScriptName**: the file name for the script used to compile the data (CAN BE IGNORED)
-**chTimeComputed**: the time the data was compiled (CAN BE IGNORED)
-*PCP_L5_GetPulse.mat*:
This file a structure **sCFG** containing the output of the CBASS method for the data in *PCP_L4_MakeMetaDataStructure.mat*. CBASS ties power in a given frequency band to discrete events in time. Here the method has been applied to detect events having energy in the beta range [15-30Hz] occurring more often during visual stimulation or events having energy in the gamma range [30-80Hz] occurring more often during locomotion. A full description of the method can be found in (https://github.com/cardin-higley-lab/CBASS) and in the following preprint (https://doi.org/10.1101/2022.05.13.491832). The structure has the following fields:
-**sPARAM**: a structure containing the parameters that were used to generated the currated data (CAN BE IGNORED)
-**sINPUT**: a structure containing information about the input file used to generate the currated data (CAN BE IGNORED)
-**sL5**: a structure containing CBASS related data with the following fields:
-**sBAND**: a structure array of the output of the CBASS methods for visual evokded beta [15-30Hz] (1) and locomotion modulated gamma [30-80Hz] (2) with the following fields:
-**db1Band**: a 2 element vector describing the frequency band of interest
-**chBandLabel** : a character array describing the frequency band of interest
-**chStateLabel**: a character array describing the state of interest
-**in1Index**: the indices of candidate events
-**db1Power**: the power of the band filtered signal at the time of each events
-**db1Score**: the enrichment score describing how much each candidate events is associated with the state of interest
-**dbThreshold**: a threshold for the enrichment score, everything above is retained
-**db1Score_Rnd**: an enrichment score calculated on random surrogate data with matching power spectra and correlation between channels for comparison
-**bl1WheelOn**: a 5249484 samples boolean vector indexing the epochs of the recording where the mouse was running
-**bl1Stim**: a 5249484 samples boolean vector indexing the epochs of the recording where a visual stimulation of any contrast was displayed
-**bl1StimFull**: a 5249484 samples boolean vector indexing the epochs of the recording where a full contrast visual stimulation was displayed
-**inSampleRate**: the sample rate of the recording
-**inRefChan**: the reference channel used to compute the CBASS method
-**chScriptName**: the file name for the script used to compile the data (CAN BE IGNORED)
-**chTimeComputed**: the time the data was compiled (CAN BE IGNORED)
## Code/Software
The main component of the data set is a set of 8 matlab scripts that can be used to reproduce the figures of the manuscript:
-*Script1_Fig_1.m*
-*Script2_Fig_S1.m*
-*Script3_Fig_S2.m*
-*Script4_Fig_2_S3.m*
-*Script5_Fig_S4.m*
-*Script6_Fig_3.m*
-*Script5_Fig_S5.m*
-*Script8_Fig_4.m*
The scripts were written using version 2018b of Matlab. They make use of the following utilities, also included in the data set:
-*NS_ETA.m*
-*NS_FourierPowerHann.m*
-*NS_MeanErrPlot.m
-*NS_PlotLFP.m*
-*NS_SaveFig.m*
-*PCP_U_NormalizeLFP.m*
-*PPS_MakePulse.m*
-*PPS_PointProcess1.m*
Script 1 to 7 should run without modification provided that the utilities are on the path. Script 8 will need to be modified so that the data in **2019-09-20_10-32-27_1** is loaded from the local address on the computer.
The script included here can be openned with Matlab (Mathwork) and have been developped with version 2018b. An open-source alternative is GNU octave (https://octave.org/.) but full compatibility was not tested.