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Create new ElectrodesTable neurodata type #539

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69 changes: 69 additions & 0 deletions core/nwb.ecephys.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -257,6 +257,75 @@ groups:
target_type: Device
doc: Link to the device that was used to record from this electrode group.

- neurodata_type_def: ElectrodesTable
neurodata_type_inc: DynamicTable
doc: A table of all electrodes (i.e. channels) used for recording. Introduced in NWB 3.0.0. Replaces the "electrodes"
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table (neurodata_type_inc DynamicTable, no neurodata_type_def) that is part of NWBFile.
datasets:
- name: location
neurodata_type_inc: VectorData
dtype: text
doc: Location of the electrode (channel). Specify the area, layer, comments
on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
standard atlas names for anatomical regions when possible.
- name: group
neurodata_type_inc: VectorData
dtype:
target_type: ElectrodeGroup
reftype: object
doc: Reference to the ElectrodeGroup this electrode is a part of.
- name: group_name
neurodata_type_inc: VectorData
dtype: text
doc: Name of the ElectrodeGroup this electrode is a part of.
quantity: '?'
- name: x
neurodata_type_inc: VectorData
dtype: float32
doc: x coordinate of the channel location in the brain (+x is posterior).
quantity: '?'
- name: y
neurodata_type_inc: VectorData
dtype: float32
doc: y coordinate of the channel location in the brain (+y is inferior).
quantity: '?'
- name: z
neurodata_type_inc: VectorData
dtype: float32
doc: z coordinate of the channel location in the brain (+z is right).
quantity: '?'
- name: imp
neurodata_type_inc: VectorData
dtype: float32
doc: Impedance of the channel, in ohms.
quantity: '?'
- name: filtering
neurodata_type_inc: VectorData
dtype: text
doc: Description of hardware filtering, including the filter name and frequency cutoffs.
quantity: '?'
- name: rel_x
neurodata_type_inc: VectorData
dtype: float32
doc: x coordinate in electrode group
quantity: '?'
- name: rel_y
neurodata_type_inc: VectorData
dtype: float32
doc: y coordinate in electrode group
quantity: '?'
- name: rel_z
neurodata_type_inc: VectorData
dtype: float32
doc: z coordinate in electrode group
quantity: '?'
- name: reference
neurodata_type_inc: VectorData
dtype: text
doc: Description of the reference electrode and/or reference scheme used for this electrode, e.g.,
"stainless steel skull screw" or "online common average referencing".
quantity: '?'

# The types below have been deprecated
- neurodata_type_def: ClusterWaveforms
neurodata_type_inc: NWBDataInterface
Expand Down
68 changes: 3 additions & 65 deletions core/nwb.file.yaml
Original file line number Diff line number Diff line change
Expand Up @@ -292,72 +292,10 @@ groups:
doc: Physical group of electrodes.
quantity: '*'
- name: electrodes
neurodata_type_inc: DynamicTable
doc: A table of all electrodes (i.e. channels) used for recording.
neurodata_type_inc: ElectrodesTable
doc: A table of all electrodes (i.e. channels) used for recording. Changed in NWB 2.7.0 to use the newly added
ElectrodesTable neurodata type instead of a DynamicTable with added columns.
quantity: '?'
datasets:
- name: x
neurodata_type_inc: VectorData
dtype: float32
doc: x coordinate of the channel location in the brain (+x is posterior).
quantity: '?'
- name: y
neurodata_type_inc: VectorData
dtype: float32
doc: y coordinate of the channel location in the brain (+y is inferior).
quantity: '?'
- name: z
neurodata_type_inc: VectorData
dtype: float32
doc: z coordinate of the channel location in the brain (+z is right).
quantity: '?'
- name: imp
neurodata_type_inc: VectorData
dtype: float32
doc: Impedance of the channel, in ohms.
quantity: '?'
- name: location
neurodata_type_inc: VectorData
dtype: text
doc: Location of the electrode (channel). Specify the area, layer, comments
on estimation of area/layer, stereotaxic coordinates if in vivo, etc. Use
standard atlas names for anatomical regions when possible.
- name: filtering
neurodata_type_inc: VectorData
dtype: text
doc: Description of hardware filtering, including the filter name and frequency cutoffs.
quantity: '?'
- name: group
neurodata_type_inc: VectorData
dtype:
target_type: ElectrodeGroup
reftype: object
doc: Reference to the ElectrodeGroup this electrode is a part of.
- name: group_name
neurodata_type_inc: VectorData
dtype: text
doc: Name of the ElectrodeGroup this electrode is a part of.
- name: rel_x
neurodata_type_inc: VectorData
dtype: float32
doc: x coordinate in electrode group
quantity: '?'
- name: rel_y
neurodata_type_inc: VectorData
dtype: float32
doc: y coordinate in electrode group
quantity: '?'
- name: rel_z
neurodata_type_inc: VectorData
dtype: float32
doc: z coordinate in electrode group
quantity: '?'
- name: reference
neurodata_type_inc: VectorData
dtype: text
doc: Description of the reference electrode and/or reference scheme used for this electrode, e.g.,
"stainless steel skull screw" or "online common average referencing".
quantity: '?'
- name: intracellular_ephys
doc: Metadata related to intracellular electrophysiology.
quantity: '?'
Expand Down
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