Merge remote-tracking branch 'refs/remotes/test/master'

LICENSE

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README.md

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+# 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 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.
+
+## Downloading the data
+## 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 the appropriate folder based on the identifier of the animal (from Rat01 to Rat20), 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
+The 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 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 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’). All single unit properties and cluster quality metrics described in the Methods section, as well as the spike times and spike count of each unit were saved in the units group. However, if needed, potential future users can use the provided wideband recordings to redo the spike sorting either by applying different parameters in Kilosort2 or using other spike sorting algorithms. 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 (‘units/session_id’).
+
+## 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
+
+
+

Rat1/Insertion1/Depth1/128ch_probe_um.prb

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+channel_groups = {
+    # Tetrode index
+    0:
+        {
+          'channels': [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 57, 58, 59, 60, 61, 62, 63, 64, 65, 66, 67, 68, 69, 70, 71, 72, 73, 74, 75, 76, 77, 78, 79, 80, 81, 82, 83, 84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95, 96, 97, 98, 99, 100, 101, 102, 103, 104, 105, 106, 107, 108, 109, 110, 111, 112, 113, 114, 115, 116, 117, 118, 119, 120, 121, 122, 123, 124, 125, 126, 127],
+          'geometry': [[16, 707.5], [38.5, 707.5], [61, 707.5], [83.5, 707.5], [16, 685], [38.5, 685], [61, 685], [83.5, 685], [16, 662.5], [38.5, 662.5], [61, 662.5], [83.5, 662.5], [16, 640], [38.5, 640], [61, 640], [83.5, 640], [16, 617.5], [38.5, 617.5], [61, 617.5], [83.5, 617.5], [16, 595], [38.5, 595], [61, 595], [83.5, 595], [16, 572.5], [38.5, 572.5], [61, 572.5], [83.5, 572.5], [16, 550], [38.5, 550], [61, 550], [83.5, 550], [16, 527.5], [38.5, 527.5], [61, 527.5], [83.5, 527.5], [16, 505], [38.5, 505], [61, 505], [83.5, 505], [16, 482.5], [38.5, 482.5], [61, 482.5], [83.5, 482.5], [16, 460], [38.5, 460], [61, 460], [83.5, 460], [16, 437.5], [38.5, 437.5], [61, 437.5], [83.5, 437.5], [16, 415], [38.5, 415], [61, 415], [83.5, 415], [16, 392.5], [38.5, 392.5], [61, 392.5], [83.5, 392.5], [16, 370], [38.5, 370], [61, 370], [83.5, 370], [16, 347.5], [38.5, 347.5], [61, 347.5], [83.5, 347.5], [16, 325], [38.5, 325], [61, 325], [83.5, 325], [16, 302.5], [38.5, 302.5], [61, 302.5], [83.5, 302.5], [16, 280], [38.5, 280], [61, 280], [83.5, 280], [16, 257.5], [38.5, 257.5], [61, 257.5], [83.5, 257.5], [16, 235], [38.5, 235], [61, 235], [83.5, 235], [16, 212.5], [38.5, 212.5], [61, 212.5], [83.5, 212.5], [16, 190], [38.5, 190], [61, 190], [83.5, 190], [16, 167.5], [38.5, 167.5], [61, 167.5], [83.5, 167.5], [16, 145], [38.5, 145], [61, 145], [83.5, 145], [16, 122.5], [38.5, 122.5], [61, 122.5], [83.5, 122.5], [16, 100], [38.5, 100], [61, 100], [83.5, 100], [16, 77.5], [38.5, 77.5], [61, 77.5], [83.5, 77.5], [16, 55], [38.5, 55], [61, 55], [83.5, 55], [16, 32.5], [38.5, 32.5], [61, 32.5], [83.5, 32.5], [16, 10], [38.5, 10], [61, 10], [83.5, 10]],
+        }
+}

datacite.yml

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+# Metadata for DOI registration according to DataCite Metadata Schema 4.1.
+# For detailed schema description see https://doi.org/10.5438/0014
+
+## Required fields
+
+# The main researchers involved. Include digital identifier (e.g., ORCID)
+# if possible, including the prefix to indicate its type.
+authors:
+  -
+    firstname: "Csaba"
+    lastname: "Horváth"
+    affiliation: "Institute of Cognitive Neuroscience and Psychology, Research Centre for Natural Sciences, Eötvös Loránd Research Network, Budapest, Hungary"
+  -
+    firstname: "Lili Fanni"
+    lastname: "Tóth"
+    affiliation: "Faculty of Information Technology and Bionics, Pázmány Péter Catholic University, Budapest, Hungary"
+  -
+    firstname: "István"
+    lastname: "Ulbert"
+    id: "ORCID:0000-0001-9941-9159"
+  -
+    firstname: "Richárd"
+    lastname: "Fiáth"
+    id: "ORCID:0000-0001-8732-2691"
+
+# A title to describe the published resource.
+title: "Dataset of cortical activity recorded with high spatial resolution from anesthetized rats"
+
+# Additional information about the resource, e.g., a brief abstract.
+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. This large collection of in vivo data 
+  enables the investigation of the high-resolution electrical footprint of cortical neurons which in
+  turn may aid their electrophysiology-based classification. Furthermore, the dataset might be used 
+  to study the laminar-specific neuronal activity during slow oscillation, a brain rhythm strongly 
+  involved in neural mechanisms underlying memory consolidation and sleep.  
+
+# Lit of keywords the resource should be associated with.
+# Give as many keywords as possible, to make the resource findable.
+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
+
+# License information for this resource. Please provide the license name and/or a link to the license.
+# Please add also a corresponding LICENSE file to the repository.
+license:
+  name: "Creative Commons CC0 1.0 Public Domain Dedication"
+  url: "https://creativecommons.org/publicdomain/zero/1.0/"
+
+
+
+## Optional Fields
+
+# Funding information for this resource.
+# Separate funder name and grant number by comma.
+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"
+
+
+# Related publications. reftype might be: IsSupplementTo, IsDescribedBy, IsReferencedBy.
+# Please provide digital identifier (e.g., DOI) if possible.
+# Add a prefix to the ID, separated by a colon, to indicate the source.
+# Supported sources are: DOI, arXiv, PMID
+# In the citation field, please provide the full reference, including title, authors, journal etc.
+references:
+  -
+    id: "doi:10.xxx/zzzz"
+    reftype: "IsSupplementTo"
+    citation: "Citation1"
+  -
+    id: "arxiv:mmmm.nnnn"
+    reftype: "IsSupplementTo"
+    citation: "Citation2"
+  -
+    id: "pmid:nnnnnnnn"
+    reftype: "IsReferencedBy"
+    citation: "Citation3"
+
+
+# Resource type. Default is Dataset, other possible values are Software, DataPaper, Image, Text.
+resourcetype: Dataset
+
+# Do not edit or remove the following line
+templateversion: 1.2