Each recording and corresponding metadata were packaged in the\nNeurodata Without Borders: Neurophysiology version 2.0 (NWB:N 2.0) data format using the NeuroConv Python package. A single NWB file was created from each thalamic recording. NWB files were placed in folders based on the identifier of the animal (e.g., Rat1 or Mouse2), probe insertion sequence (e.g., Insertion1 or Insertion2) and thalamic depth (e.g., from Depth1 to Depth4). The filename of the NWB file (identifier) was constructed by concatenating the above information (e.g., Rat01_Insertion2_Depth3). For chronic recordings, each file identifier contains the day on which the data file was recorded.
\n\nThe CSV/tab file named \"Animal_characteristics_...\" contains information about the weight, sex, species and strain of the animals used in the study. The \"Recording_characteristics_...\" CSV/tab file lists several useful properties for each NWB file including the file size, the duration of the recording, the thalamic location,the stereotaxic coordinates corresponding to each probe insertion, and whether population activity propagation in the thalamus was observed.
\nDirectory structure of the dataset:
Rat/64_channel_multishank_recordings/Coronal_insertions (55 NWB files)
\nRat/64_channel_multishank_recordings/Sagittal_insertions (27 NWB files)
\nRat/Acute_Neuropixels_recordings (41 NWB files)
\nRat/Chronic_Neuropixels_recordings (24 NWB files)
\nRat/Simultaneous_thalamic_and_cortical_recordings (10 NWB files)
\nMouse/128_channel_multishank_recordings (18 NWB files)
\nMouse/Acute_Neuropixels_recordings (11 NWB files)
\nEach NWB file contains several main groups (similar to directories). The acquisition group contains the continuous wideband data in a compressed form (in Neuropixels recordings, field potential and action potential recordings are separate), 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’). The former subgroup carries information about the probe location (thalamic area and stereotaxic coordinates) and the relative positions of recordings sites, while the latter contains metadata about the animal (e.g., sex, species, subject ID, or weight).
\n After downloading, the structure of NWB files can be explored using the freely available HDFView software. Neurosift can be used to open NWB files in a browser and explore their contents using the download URL of the selected data file (e.g. https://science-data.hu/api/access/datafile/12193):\n
\n
\n https://flatironinstitute.github.io/neurosift/?p=/nwb&url=FILE_URL
\nhttps://flatironinstitute.github.io/neurosift/?p=/nwb&url=https://science-data.hu/api/access/datafile/12193 \n
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\nUsers can import data from NWB files offline using the PyNWB and MatNWB APIs, or using SpikeInterface. \nLoaded samples of the raw data have to be multiplied by a conversion number (e.g., 0.195 for 64-channel recordings) 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.
\n1.\tnwb = nwbRead('Rat01_Insertion1_Depth1.nwb');\n\n\n2.\tdataChunk=nwb.acquisition.get('ElectricalSeries').data.load([1, 1], [128, 20000]);\n\nWe also provide a Matlab script (\"NWB_tutorial_script.m\") which can be used to load, visualize and preprocess (e.g., filter) files in the dataset using MatNWB.
\nFor Neuropixels recordings, channels 1, 2, 3, ... correspond to the most ventral thalamic positions, located closest to the probe tip, whereas channels ...383, 384 correspond to dorsal locations (located further away from the probe tip). For multishank recodings, the first 8 channels (or 16 channels for mouse recordings) correspond to the recording sites of the first shank, with channel 1 corresponding to the most dorsal site and channel 8 located at the most ventral position (site located closest to the shank tip). Similarly, the second 8 channels (or 16 channels for mice) correspond to the sites of the second shank, and so on. For the eight-shank, 64-channel Buzsaki probe recordings from the neocortex, the mapping is the same as described above (shank1: channels 1-8, shank2: channels 9-16, etc.)
","relatedMaterial":"NeuroConv software to generate NWB files: https://neuroconv.readthedocs.io/en/main/\n