bids-specification/src/schema/rules/tabular_data/microephys.yaml at 866aced16dabc624431566cbf3ad72fcb017d132 · bids-standard/bids-specification · GitHub

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---
microephysProbes:
  selectors:
    - intersects([datatype], ["ecephys", "icephys"])
    - suffix == "probes"
    - extension == ".tsv"
  initial_columns:
    - probe_name
    - type__probes
    - AP__probes
    - ML__probes
    - DV__probes
    - AP_angle
    - ML_angle
  columns:
    probe_name: required
    type__probes: required
    AP__probes: recommended
    ML__probes: recommended
    DV__probes: recommended
    AP_angle: recommended
    ML_angle: recommended
    manufacturer__probes: recommended
    model__probes: recommended
    device_serial_number: recommended
    electrode_count: optional
    width__probes: optional
    height__probes: optional
    depth__probes: optional
    rotation_angle: recommended
    coordinate_reference_point: recommended
    anatomical_reference_point: optional
    hemisphere__probes: recommended
    associated_brain_region: recommended
    associated_brain_region_id: recommended
    associated_brain_region_quality_type: recommended
    reference_atlas: recommended
    material__probes: optional
  index_columns: [probe_name]
  additional_columns: allowed_if_defined

microephysElectrodes:
  selectors:
    - intersects([datatype], ["ecephys", "icephys"])
    - suffix == "electrodes"
    - extension == ".tsv"
  initial_columns:
    - name__electrodes
    - probe_name
    - x
    - y
    - z
  columns:
    name__electrodes: required
    probe_name: required
    x:
      level: required
      description_addendum: |
        When no [`space-<label>`](SPEC_ROOT/appendices/entities.md#space) entity is used in the filename,
        the position along the local width-axis relative to the probe origin
        (see `coordinate_reference_point` in `*_probes.tsv`) in micrometers (um).
        When a `space-<label>` entity is used in the filename,
        the position relative to the origin of the coordinate system along the first axis.
        Units are specified by `MicroephysCoordinateUnits` in the corresponding `*_coordsystem.json` file.
    y:
      level: required
      description_addendum: |
        When no [`space-<label>`](SPEC_ROOT/appendices/entities.md#space) entity is used in the filename,
        the position along the local height-axis relative to the probe origin
        (see `coordinate_reference_point` in `*_probes.tsv`) in micrometers (um).
        When a `space-<label>` entity is used in the filename,
        the position relative to the origin of the coordinate system along the second axis.
        Units are specified by `MicroephysCoordinateUnits` in the corresponding `*_coordsystem.json` file.
    z:
      level: required
      description_addendum: |
        When no [`space-<label>`](SPEC_ROOT/appendices/entities.md#space) entity is used in the filename,
        the position along the local depth-axis relative to the probe origin
        (see `coordinate_reference_point` in `*_probes.tsv`) in micrometers (um).
        When a `space-<label>` entity is used in the filename,
        the position relative to the origin of the coordinate system along the third axis.
        Units are specified by `MicroephysCoordinateUnits` in the corresponding `*_coordsystem.json` file.
        For 2D electrode localizations (for example, when the coordinate system is
        `Pixels`), this SHOULD be a column of `n/a` values.
    hemisphere: recommended
    impedance: recommended
    shank_id: optional
    size__microephys: optional
    electrode_shape: optional
    material: optional
    location: recommended
    pipette_solution: optional
    internal_pipette_diameter: optional
    external_pipette_diameter: optional
  index_columns: [name__electrodes]
  additional_columns: allowed_if_defined

microephysChannels:
  selectors:
    - intersects([datatype], ["ecephys", "icephys"])
    - suffix == "channels"
    - extension == ".tsv"
  initial_columns:
    - name__channels
    - reference__microephys
    - type__channels
    - units
    - sampling_frequency
  columns:
    name__channels: required
    reference__microephys: required
    type__channels: required
    units: required
    sampling_frequency: optional
    low_cutoff: optional
    high_cutoff: optional
    notch: optional
    channel_label: optional
    stream_id: optional
    description: optional
    software_filter_types: optional
    status: optional
    status_description: optional
    gain: recommended
    time_offset: optional
    time_reference_channel: optional
    ground: optional
    recording_mode: recommended
  index_columns: [name__channels]
  additional_columns: allowed_if_defined