Nincs leírás

Richárd Fiáth e6292c0501 Frissítés "README.md" 3 éve
Rat01 c7ca7c33b8 gin commit from DESKTOP-TEC1O0O 3 éve
Rat02 4333d38a83 gin commit from DESKTOP-TEC1O0O 3 éve
Rat03 4333d38a83 gin commit from DESKTOP-TEC1O0O 3 éve
Rat04 4aa64611bd gin commit from DESKTOP-TEC1O0O 3 éve
Rat05 4aa64611bd gin commit from DESKTOP-TEC1O0O 3 éve
Rat06 4aa64611bd gin commit from DESKTOP-TEC1O0O 3 éve
Rat07 57951f2f2f gin commit from DESKTOP-TEC1O0O 3 éve
Rat08 57951f2f2f gin commit from DESKTOP-TEC1O0O 3 éve
Rat09 57951f2f2f gin commit from DESKTOP-TEC1O0O 3 éve
Rat10 57951f2f2f gin commit from DESKTOP-TEC1O0O 3 éve
Rat11 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat12 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat13 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat14 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat15 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat16 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat17 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat18 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat19 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
Rat20 4e76d0f64b gin commit from DESKTOP-TEC1O0O 3 éve
LICENSE 8de34f0903 Frissítés "LICENSE" 3 éve
README.md e6292c0501 Frissítés "README.md" 3 éve
allSingleUnits.nwb c055803927 gin commit from DESKTOP-TEC1O0O 3 éve
datacite.yml dc7343e0ec Frissítés "datacite.yml" 3 éve

README.md

Dataset of cortical activity recorded with high spatial resolution from anesthetized rats

Summary

Here, we present an electrophysiological dataset recorded from the neocortex of twenty rats anesthetized with ketamine/xylazine. The wideband, spontaneous recordings (n = 109) were acquired with a single-shank silicon-based probe having 128 densely packed recording sites arranged in a 32x4 array. Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the cortex. Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several properties of units packaged in a standardized electrophysiological data format. For technical validation of our dataset, we provide the distributions of derived single unit properties along with various spike sorting quality metrics.

Repository structure

Each recording and corresponding metadata, single unit properties and quality metrics were packaged in the Neurodata Without Borders: Neurophysiology version 2.0 (NWB:N 2.0) data format using the MatNWB API. A single NWB file was created from each recording. NWB files were placed in folders based on the identifier of the animal (from Rat01 to Rat20), probe insertion sequence (Insertion1 or Insertion2) and cortical depth (from Depth1 to Depth3). The filename of the NWB file (identifier) was constructed by concatenating the above information (e.g., Rat01_Insertion2_Depth3).

NWB file structure

Each NWB file contains several main groups which are similar to directories. The acquisition group contains the continuous wideband 128-channel data (‘wideband_multichannel_recording’) in a compressed form, as well as several parameters related to the raw data such as the measurement unit or the data conversion number. The general group contains metadata about the experiments and consists of several subgroups, related to the recording probe (‘general/devices’; ‘general/extracellular_ephys’) or the subjects of the experiments (‘general/subject’). Former subgroups carry information about the probe location (brain area and stereotaxic coordinates) and the relative positions and laminar location of recordings sites, while the latter contains metadata about the animal (e.g., sex, species, subject ID, or weight). Information about spike sorting and single units and corresponding data are available in the units group. For each unit, we included here the mean and standard deviation of their spike waveform on all channels, calculated both from the filtered (‘mean_waveform_all_channels_filt’; ’waveform_sd_all_channels_filt’) and the wideband data (‘mean_waveform_all_channels_raw’; ’ waveform_sd_all_channels_raw’). For an easier visualization of the multichannel spike waveform in two dimensions, we have also added an array which contains the mean spike waveform in the 32 x 4 shape of the electrode array (‘mean_waveform_all_channels_filt_32x4’; ’mean_waveform_all_channels_raw_32x4’). Furthermore, the spike waveform recorded on the channel with the largest spike (i.e., peak waveform channel) was saved separately (‘mean_waveform_peak_channel_filt’, ‘mean_waveform_peak_channel_raw’). Several single unit properties and cluster quality metrics, as well as the spike times and spike count of each unit were saved in the units group. Furthermore, to aid users in selecting and analyzing a subset of this dataset appropriate for the research goals, we also created an NWB file (‘allSingleUnits.nwb’) which contains all single unit with all the properties listed above, along with the identifier of the recording they originate from (located in ‘units/session_id’). The NWB file structure can be explored using the HDFView software.

Downloading the dataset

Recordings can be downloaded individually through the web interface or using the GIN Client.

Using the GIN Client, the dataset can be downloaded the following way:

  1. A local repository needs to be initialized in the current directory using the following command:

    gin init
    
  2. Then, the remote repository located on GIN needs to be added:

    gin add-remote RemoteRepo gin:UlbertLab/High_Resolution_Cortical_Spikes
    
  3. After that, the user needs to download the contents of the repository:

    gin dowload
    
  4. The previous command will download the small files and the file structure of the repository. Large files (i.e., all files of the dataset) will be included as pointer files but the data will not be included. To get the content of the big files you need to download them individually the following way:

    gin get-content filePath/fileName
    
  5. Examples

  • Downloading a single file:

    gin get-content allSingleUnits.nwb
    gin get-content Rat01/Insertion1/Depth1/Rat01_Insertion1_Depth1.nwb
    
  • Downloading all files located in a particular directory:

    gin get-content Rat01
    
  • Or you may download the contents of all files by using the command with no arguments:

    gin get-content
    

More information and guides for the GIN Client are available here. For more ways of accessing the data, please refer to GIN's FAQ.

Interacting with NWB files

Users can import data from NWB files using the PyNWB and MatNWB APIs, or using SpikeInterface. Loaded samples of the raw data have to be multiplied by a conversion number (0.195) to get the amplitudes in microvolts. Here we provide some examples how users can import data from NWB files using the MATLAB-based MatNWB API.

Loading a short segment (20.000 samples corresponding to 1 second of data) of the raw wideband recording on all (128) channels:

1.	nwb = nwbRead('Rat01_Insertion1_Depth1.nwb');
2.	dataChunk=nwb.acquisition.get('wideband_multichannel_recording').data.load([1, 1], [128, 20000]);

It is important to note that TimeSeries data types in NWB files are stored with time in the first dimension and channels in the second, but dimensions are reversed in MatNWB.

Loading and plotting the mean spike waveform of a specific single unit on the peak waveform channel:

3.	peakChannels = nwb.units.vectordata.get('peak_waveform_channel').data.load();
4.	meanWaveforms = nwb.units.vectordata.get('mean_waveform_all_channels_filt').data.load();
5.	mySingleUnit = 11;
6.	singleUnitWaveform = meanWaveforms(peakChannels(mySingleUnit), :, mySingleUnit);
7.	plot(singleUnitWaveform);

Loading the isolation distance quality metric of all units found in a single NWB file:

8.	IDvalues = nwb.units.vectordata.get('isolation_distance').data.load();

Spike times are stored in a special structure called ragged arrays15. We can load the spikes times of a specific single unit (in seconds) the following way:

9.	allSpikeTimes = nwb.units.spike_times.data.load();
10.	spikeTimesIndex = nwb.units.spike_times_index.data.load();
11.	spikesOfSingleUnit2 = allSpikeTimes(spikeTimesIndex(1)+1 : spikeTimesIndex(2));

SpikeInterface can also be used to load the wideband data and single unit properties (in Python):

1.	import spikeextractors as se
2.	nwbPath = 'Rat01_Insertion1_Depth1.nwb'
3.	recording = se.NwbRecordingExtractor(nwbPath)
4.	sorting = se.NwbSortingExtractor(nwbPath)
5.	mySingleUnit = 2
6.	sorting.get_unit_property(mySingleUnit,'isolation_distance')

Related Publications

  • Fiáth, R., Raducanu, B. C., Musa, S., Andrei, A., Lopez, C. M., van Hoof, C., Ruther, P., Aarts, A., Horváth, D., Ulbert, I. (2018) A silicon-based neural probe with densely-packed low-impedance titanium nitride microelectrodes for ultrahigh-resolution in vivo recordings. Biosensors and Bioelectronics 106: 86-92. https://doi.org/10.1016/j.bios.2018.01.060

Licensing

LicenseImg

The dataset is licensed under a Creative Commons Attribution 4.0 International License.

See the LICENSE file for the full license.

datacite.yml
Title Dataset of cortical activity recorded with high spatial resolution from anesthetized rats
Authors Horváth,Csaba;Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary;ORCID:0000-0001-8176-8975
Tóth,Lili Fanni;Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary
Ulbert,István;Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary and Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary;ORCID:0000-0001-9941-9159
Fiáth,Richárd;Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary and Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary;ORCID:0000-0001-8732-2691
Description Publicly available neural recordings obtained with high spatial resolution are scarce. Here, we present an electrophysiological dataset recorded from the neocortex of twenty rats anesthetized with ketamine/xylazine. The wideband, spontaneous recordings were acquired with a single-shank silicon-based probe having 128 densely packed recording sites arranged in a 32x4 array. Using spike sorting, the activity of a total of 7126 single units was extracted from all layers of the cortex. Here, we share raw neural recordings, as well as spike times, extracellular spike waveforms and several properties of units packaged in a standardized electrophysiological data format. For technical validation of our dataset, we provide the distributions of derived single unit properties along with various spike sorting quality metrics.
License CC-BY (http://creativecommons.org/licenses/by/4.0/)
References Fiáth, R., Raducanu, B. C., Musa, S., Andrei, A., Lopez, C. M., van Hoof, C., Ruther, P., Aarts, A., Horváth, D., Ulbert, I. (2018) A silicon-based neural probe with densely-packed low-impedance titanium nitride microelectrodes for ultrahigh-resolution in vivo recordings. Biosensors and Bioelectronics 106: 86-92. [doi:10.1016/j.bios.2018.01.060] (IsDescribedBy)
Funding Hungarian Brain Research Program; 2017-1.2.1-NKP-2017-00002
Hungarian National Research, Development and Innovation Office; PD124175
Hungarian National Research, Development and Innovation Office; PD134196
Hungarian National Research, Development and Innovation Office; TUDFO/51757-1/2019-ITM
Keywords Neuroscience
Silicon probe
High density recording
High spatial resolution
Electrophysiology
Neurophysiology
Neural recording
Extracellular action potential
Single unit activity
Spike sorting
Slow oscillation
Slow wave activity
Rat
Ketamine/xylazine anesthesia
Neocortex
Resource Type Dataset