mirror of
https://github.com/p2p-ld/nwb-linkml.git
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sneakers-the-rat
be21325123
- split off generated subclasses into "include" files, not sure if that's good, but in any case we have them separable now. - more work on cleanly un-nesting scalar and 1D-vector data into attributes and lists, respectively - brought the pydantic generator in-repo to do a bunch of overrides
695 lines
29 KiB
YAML
695 lines
29 KiB
YAML
name: core.nwb.file.include
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id: core.nwb.file.include
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imports:
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- core.nwb.base
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- hdmf-common.table
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- core.nwb.device
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- core.nwb.ecephys
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- core.nwb.icephys
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- core.nwb.ogen
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- core.nwb.ophys
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- core.nwb.epoch
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- core.nwb.misc
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- nwb.language
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- core.nwb.file.include
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- core.nwb.file
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default_prefix: core.nwb.file.include/
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classes:
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NWBFile__file_create_date:
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name: NWBFile__file_create_date
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description: 'A record of the date the file was created and of subsequent modifications.
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The date is stored in UTC with local timezone offset as ISO 8601 extended formatted
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strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with
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no timezone offset. Date accuracy is up to milliseconds. The file can be created
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after the experiment was run, so this may differ from the experiment start time.
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Each modification to the nwb file adds a new entry to the array.'
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attributes:
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file_create_date:
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name: file_create_date
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description: 'A record of the date the file was created and of subsequent
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modifications. The date is stored in UTC with local timezone offset as ISO
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8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored
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in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds.
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The file can be created after the experiment was run, so this may differ
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from the experiment start time. Each modification to the nwb file adds a
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new entry to the array.'
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multivalued: true
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range: isodatetime
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required: true
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NWBFile__acquisition:
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name: NWBFile__acquisition
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description: Data streams recorded from the system, including ephys, ophys, tracking,
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etc. This group should be read-only after the experiment is completed and timestamps
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are corrected to a common timebase. The data stored here may be links to raw
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data stored in external NWB files. This will allow keeping bulky raw data out
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of the file while preserving the option of keeping some/all in the file. Acquired
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data includes tracking and experimental data streams (i.e., everything measured
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from the system). If bulky data is stored in the /acquisition group, the data
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can exist in a separate NWB file that is linked to by the file being used for
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processing and analysis.
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attributes:
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NWBDataInterface:
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name: NWBDataInterface
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description: Acquired, raw data.
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multivalued: true
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range: NWBDataInterface
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required: false
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DynamicTable:
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name: DynamicTable
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description: Tabular data that is relevant to acquisition
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multivalued: true
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range: DynamicTable
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required: false
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NWBFile__analysis:
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name: NWBFile__analysis
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description: Lab-specific and custom scientific analysis of data. There is no
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defined format for the content of this group - the format is up to the individual
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user/lab. To facilitate sharing analysis data between labs, the contents here
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should be stored in standard types (e.g., neurodata_types) and appropriately
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documented. The file can store lab-specific and custom data analysis without
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restriction on its form or schema, reducing data formatting restrictions on
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end users. Such data should be placed in the analysis group. The analysis data
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should be documented so that it could be shared with other labs.
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attributes:
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NWBContainer:
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name: NWBContainer
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description: Custom analysis results.
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multivalued: true
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range: NWBContainer
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required: false
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DynamicTable:
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name: DynamicTable
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description: Tabular data that is relevant to data stored in analysis
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multivalued: true
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range: DynamicTable
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required: false
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NWBFile__scratch:
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name: NWBFile__scratch
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description: A place to store one-off analysis results. Data placed here is not
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intended for sharing. By placing data here, users acknowledge that there is
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no guarantee that their data meets any standard.
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attributes:
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ScratchData:
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name: ScratchData
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description: Any one-off datasets
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multivalued: true
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range: ScratchData
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required: false
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NWBContainer:
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name: NWBContainer
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description: Any one-off containers
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multivalued: true
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range: NWBContainer
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required: false
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DynamicTable:
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name: DynamicTable
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description: Any one-off tables
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multivalued: true
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range: DynamicTable
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required: false
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NWBFile__processing:
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name: NWBFile__processing
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description: The home for ProcessingModules. These modules perform intermediate
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analysis of data that is necessary to perform before scientific analysis. Examples
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include spike clustering, extracting position from tracking data, stitching
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together image slices. ProcessingModules can be large and express many data
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sets from relatively complex analysis (e.g., spike detection and clustering)
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or small, representing extraction of position information from tracking video,
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or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik,
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MClust) are expected to read/write data here. 'Processing' refers to intermediate
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analysis of the acquired data to make it more amenable to scientific analysis.
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attributes:
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ProcessingModule:
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name: ProcessingModule
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description: Intermediate analysis of acquired data.
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multivalued: true
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range: ProcessingModule
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required: false
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NWBFile__stimulus:
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name: NWBFile__stimulus
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description: Data pushed into the system (eg, video stimulus, sound, voltage,
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etc) and secondary representations of that data (eg, measurements of something
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used as a stimulus). This group should be made read-only after experiment complete
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and timestamps are corrected to common timebase. Stores both presented stimuli
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and stimulus templates, the latter in case the same stimulus is presented multiple
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times, or is pulled from an external stimulus library. Stimuli are here defined
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as any signal that is pushed into the system as part of the experiment (eg,
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sound, video, voltage, etc). Many different experiments can use the same stimuli,
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and stimuli can be re-used during an experiment. The stimulus group is organized
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so that one version of template stimuli can be stored and these be used multiple
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times. These templates can exist in the present file or can be linked to a remote
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library file.
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attributes:
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presentation:
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name: presentation
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description: Stimuli presented during the experiment.
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multivalued: false
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range: NWBFile__stimulus__presentation
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required: true
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templates:
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name: templates
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description: Template stimuli. Timestamps in templates are based on stimulus
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design and are relative to the beginning of the stimulus. When templates
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are used, the stimulus instances must convert presentation times to the
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experiment`s time reference frame.
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multivalued: false
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range: NWBFile__stimulus__templates
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required: true
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NWBFile__stimulus__presentation:
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name: NWBFile__stimulus__presentation
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description: Stimuli presented during the experiment.
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attributes:
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TimeSeries:
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name: TimeSeries
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description: TimeSeries objects containing data of presented stimuli.
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multivalued: true
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range: TimeSeries
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required: false
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NWBFile__stimulus__templates:
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name: NWBFile__stimulus__templates
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description: Template stimuli. Timestamps in templates are based on stimulus design
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and are relative to the beginning of the stimulus. When templates are used,
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the stimulus instances must convert presentation times to the experiment`s time
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reference frame.
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attributes:
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TimeSeries:
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name: TimeSeries
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description: TimeSeries objects containing template data of presented stimuli.
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multivalued: true
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range: TimeSeries
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required: false
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Images:
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name: Images
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description: Images objects containing images of presented stimuli.
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multivalued: true
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range: Images
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required: false
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NWBFile__general:
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name: NWBFile__general
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description: Experimental metadata, including protocol, notes and description
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of hardware device(s). The metadata stored in this section should be used to
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describe the experiment. Metadata necessary for interpreting the data is stored
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with the data. General experimental metadata, including animal strain, experimental
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protocols, experimenter, devices, etc, are stored under 'general'. Core metadata
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(e.g., that required to interpret data fields) is stored with the data itself,
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and implicitly defined by the file specification (e.g., time is in seconds).
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The strategy used here for storing non-core metadata is to use free-form text
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fields, such as would appear in sentences or paragraphs from a Methods section.
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Metadata fields are text to enable them to be more general, for example to represent
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ranges instead of numerical values. Machine-readable metadata is stored as attributes
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to these free-form datasets. All entries in the below table are to be included
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when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology
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experiment) should not be created unless there is data to store within them.
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attributes:
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data_collection:
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name: data_collection
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description: Notes about data collection and analysis.
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multivalued: false
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range: text
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required: false
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experiment_description:
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name: experiment_description
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description: General description of the experiment.
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multivalued: false
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range: text
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required: false
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experimenter:
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name: experimenter
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description: Name of person(s) who performed the experiment. Can also specify
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roles of different people involved.
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multivalued: false
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range: NWBFile__general__experimenter
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required: false
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institution:
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name: institution
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description: Institution(s) where experiment was performed.
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multivalued: false
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range: text
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required: false
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keywords:
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name: keywords
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description: Terms to search over.
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multivalued: false
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range: NWBFile__general__keywords
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required: false
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lab:
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name: lab
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description: Laboratory where experiment was performed.
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multivalued: false
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range: text
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required: false
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notes:
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name: notes
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description: Notes about the experiment.
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multivalued: false
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range: text
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required: false
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pharmacology:
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name: pharmacology
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description: Description of drugs used, including how and when they were administered.
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Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.
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multivalued: false
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range: text
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required: false
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protocol:
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name: protocol
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description: Experimental protocol, if applicable. e.g., include IACUC protocol
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number.
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multivalued: false
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range: text
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required: false
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related_publications:
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name: related_publications
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description: Publication information. PMID, DOI, URL, etc.
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multivalued: false
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range: NWBFile__general__related_publications
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required: false
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session_id:
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name: session_id
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description: Lab-specific ID for the session.
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multivalued: false
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range: text
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required: false
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slices:
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name: slices
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description: Description of slices, including information about preparation
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thickness, orientation, temperature, and bath solution.
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multivalued: false
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range: text
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required: false
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source_script:
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name: source_script
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description: Script file or link to public source code used to create this
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NWB file.
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multivalued: false
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range: NWBFile__general__source_script
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required: false
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stimulus:
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name: stimulus
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description: Notes about stimuli, such as how and where they were presented.
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multivalued: false
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range: text
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required: false
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surgery:
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name: surgery
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description: Narrative description about surgery/surgeries, including date(s)
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and who performed surgery.
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multivalued: false
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range: text
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required: false
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virus:
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name: virus
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description: Information about virus(es) used in experiments, including virus
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ID, source, date made, injection location, volume, etc.
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multivalued: false
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range: text
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required: false
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LabMetaData:
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name: LabMetaData
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description: Place-holder than can be extended so that lab-specific meta-data
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can be placed in /general.
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multivalued: true
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range: LabMetaData
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required: false
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devices:
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name: devices
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description: Description of hardware devices used during experiment, e.g.,
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monitors, ADC boards, microscopes, etc.
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multivalued: false
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range: NWBFile__general__devices
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required: false
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subject:
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name: subject
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description: Information about the animal or person from which the data was
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measured.
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multivalued: false
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range: NWBFile__general__subject
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required: false
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extracellular_ephys:
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name: extracellular_ephys
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description: Metadata related to extracellular electrophysiology.
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multivalued: false
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range: NWBFile__general__extracellular_ephys
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required: false
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intracellular_ephys:
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name: intracellular_ephys
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description: Metadata related to intracellular electrophysiology.
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multivalued: false
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range: NWBFile__general__intracellular_ephys
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required: false
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optogenetics:
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name: optogenetics
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description: Metadata describing optogenetic stimuluation.
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multivalued: false
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range: NWBFile__general__optogenetics
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required: false
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optophysiology:
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name: optophysiology
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description: Metadata related to optophysiology.
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multivalued: false
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range: NWBFile__general__optophysiology
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required: false
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NWBFile__general__experimenter:
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name: NWBFile__general__experimenter
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description: Name of person(s) who performed the experiment. Can also specify
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roles of different people involved.
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attributes:
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experimenter:
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name: experimenter
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description: Name of person(s) who performed the experiment. Can also specify
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roles of different people involved.
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multivalued: true
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range: text
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required: false
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NWBFile__general__keywords:
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name: NWBFile__general__keywords
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description: Terms to search over.
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attributes:
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keywords:
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name: keywords
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description: Terms to search over.
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multivalued: true
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range: text
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required: false
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NWBFile__general__related_publications:
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name: NWBFile__general__related_publications
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description: Publication information. PMID, DOI, URL, etc.
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attributes:
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related_publications:
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name: related_publications
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description: Publication information. PMID, DOI, URL, etc.
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multivalued: true
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range: text
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required: false
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NWBFile__general__source_script:
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name: NWBFile__general__source_script
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description: Script file or link to public source code used to create this NWB
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file.
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attributes:
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file_name:
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name: file_name
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description: Name of script file.
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range: text
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NWBFile__general__devices:
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name: NWBFile__general__devices
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description: Description of hardware devices used during experiment, e.g., monitors,
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ADC boards, microscopes, etc.
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attributes:
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Device:
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name: Device
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description: Data acquisition devices.
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multivalued: true
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range: Device
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required: false
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NWBFile__general__subject:
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name: NWBFile__general__subject
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description: Information about the animal or person from which the data was measured.
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is_a: Subject
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NWBFile__general__extracellular_ephys:
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name: NWBFile__general__extracellular_ephys
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description: Metadata related to extracellular electrophysiology.
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attributes:
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ElectrodeGroup:
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name: ElectrodeGroup
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description: Physical group of electrodes.
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multivalued: true
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range: ElectrodeGroup
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required: false
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electrodes:
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name: electrodes
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description: A table of all electrodes (i.e. channels) used for recording.
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multivalued: false
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range: NWBFile__general__extracellular_ephys__electrodes
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required: false
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NWBFile__general__extracellular_ephys__electrodes:
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name: NWBFile__general__extracellular_ephys__electrodes
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description: A table of all electrodes (i.e. channels) used for recording.
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is_a: DynamicTable
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attributes:
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x:
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name: x
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description: x coordinate of the channel location in the brain (+x is posterior).
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multivalued: true
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range: float32
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y:
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name: y
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description: y coordinate of the channel location in the brain (+y is inferior).
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multivalued: true
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range: float32
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z:
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name: z
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description: z coordinate of the channel location in the brain (+z is right).
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multivalued: true
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range: float32
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imp:
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name: imp
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description: Impedance of the channel, in ohms.
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multivalued: true
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range: float32
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location:
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name: location
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description: Location of the electrode (channel). Specify the area, layer,
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comments on estimation of area/layer, stereotaxic coordinates if in vivo,
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etc. Use standard atlas names for anatomical regions when possible.
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multivalued: true
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range: text
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filtering:
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name: filtering
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description: Description of hardware filtering, including the filter name
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and frequency cutoffs.
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multivalued: true
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range: text
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group:
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name: group
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description: Reference to the ElectrodeGroup this electrode is a part of.
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multivalued: true
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range: ElectrodeGroup
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group_name:
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name: group_name
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description: Name of the ElectrodeGroup this electrode is a part of.
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multivalued: true
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range: text
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rel_x:
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name: rel_x
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description: x coordinate in electrode group
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multivalued: true
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range: float32
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rel_y:
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name: rel_y
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description: y coordinate in electrode group
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multivalued: true
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range: float32
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rel_z:
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name: rel_z
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description: z coordinate in electrode group
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multivalued: true
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range: float32
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reference:
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name: reference
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description: Description of the reference electrode and/or reference scheme
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used for this electrode, e.g., "stainless steel skull screw" or "online
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common average referencing".
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multivalued: true
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range: text
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NWBFile__general__intracellular_ephys:
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name: NWBFile__general__intracellular_ephys
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description: Metadata related to intracellular electrophysiology.
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attributes:
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filtering:
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name: filtering
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description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description
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of filtering used. Includes filtering type and parameters, frequency fall-off,
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etc. If this changes between TimeSeries, filter description should be stored
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as a text attribute for each TimeSeries.'
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multivalued: false
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range: text
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required: false
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IntracellularElectrode:
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name: IntracellularElectrode
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description: An intracellular electrode.
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multivalued: true
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range: IntracellularElectrode
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required: false
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sweep_table:
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name: sweep_table
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description: '[DEPRECATED] Table used to group different PatchClampSeries.
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SweepTable is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
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tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions
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|
tables provide enhanced support for experiment metadata.'
|
|
multivalued: false
|
|
range: NWBFile__general__intracellular_ephys__sweep_table
|
|
required: false
|
|
intracellular_recordings:
|
|
name: intracellular_recordings
|
|
description: A table to group together a stimulus and response from a single
|
|
electrode and a single simultaneous recording. Each row in the table represents
|
|
a single recording consisting typically of a stimulus and a corresponding
|
|
response. In some cases, however, only a stimulus or a response are recorded
|
|
as as part of an experiment. In this case both, the stimulus and response
|
|
will point to the same TimeSeries while the idx_start and count of the invalid
|
|
column will be set to -1, thus, indicating that no values have been recorded
|
|
for the stimulus or response, respectively. Note, a recording MUST contain
|
|
at least a stimulus or a response. Typically the stimulus and response are
|
|
PatchClampSeries. However, the use of AD/DA channels that are not associated
|
|
to an electrode is also common in intracellular electrophysiology, in which
|
|
case other TimeSeries may be used.
|
|
multivalued: false
|
|
range: NWBFile__general__intracellular_ephys__intracellular_recordings
|
|
required: false
|
|
simultaneous_recordings:
|
|
name: simultaneous_recordings
|
|
description: A table for grouping different intracellular recordings from
|
|
the IntracellularRecordingsTable table together that were recorded simultaneously
|
|
from different electrodes
|
|
multivalued: false
|
|
range: NWBFile__general__intracellular_ephys__simultaneous_recordings
|
|
required: false
|
|
sequential_recordings:
|
|
name: sequential_recordings
|
|
description: A table for grouping different sequential recordings from the
|
|
SimultaneousRecordingsTable table together. This is typically used to group
|
|
together sequential recordings where the a sequence of stimuli of the same
|
|
type with varying parameters have been presented in a sequence.
|
|
multivalued: false
|
|
range: NWBFile__general__intracellular_ephys__sequential_recordings
|
|
required: false
|
|
repetitions:
|
|
name: repetitions
|
|
description: A table for grouping different sequential intracellular recordings
|
|
together. With each SequentialRecording typically representing a particular
|
|
type of stimulus, the RepetitionsTable table is typically used to group
|
|
sets of stimuli applied in sequence.
|
|
multivalued: false
|
|
range: NWBFile__general__intracellular_ephys__repetitions
|
|
required: false
|
|
experimental_conditions:
|
|
name: experimental_conditions
|
|
description: A table for grouping different intracellular recording repetitions
|
|
together that belong to the same experimental experimental_conditions.
|
|
multivalued: false
|
|
range: NWBFile__general__intracellular_ephys__experimental_conditions
|
|
required: false
|
|
NWBFile__general__intracellular_ephys__sweep_table:
|
|
name: NWBFile__general__intracellular_ephys__sweep_table
|
|
description: '[DEPRECATED] Table used to group different PatchClampSeries. SweepTable
|
|
is being replaced by IntracellularRecordingsTable and SimultaneousRecordingsTable
|
|
tables. Additional SequentialRecordingsTable, RepetitionsTable and ExperimentalConditions
|
|
tables provide enhanced support for experiment metadata.'
|
|
is_a: SweepTable
|
|
NWBFile__general__intracellular_ephys__intracellular_recordings:
|
|
name: NWBFile__general__intracellular_ephys__intracellular_recordings
|
|
description: A table to group together a stimulus and response from a single electrode
|
|
and a single simultaneous recording. Each row in the table represents a single
|
|
recording consisting typically of a stimulus and a corresponding response. In
|
|
some cases, however, only a stimulus or a response are recorded as as part of
|
|
an experiment. In this case both, the stimulus and response will point to the
|
|
same TimeSeries while the idx_start and count of the invalid column will be
|
|
set to -1, thus, indicating that no values have been recorded for the stimulus
|
|
or response, respectively. Note, a recording MUST contain at least a stimulus
|
|
or a response. Typically the stimulus and response are PatchClampSeries. However,
|
|
the use of AD/DA channels that are not associated to an electrode is also common
|
|
in intracellular electrophysiology, in which case other TimeSeries may be used.
|
|
is_a: IntracellularRecordingsTable
|
|
NWBFile__general__intracellular_ephys__simultaneous_recordings:
|
|
name: NWBFile__general__intracellular_ephys__simultaneous_recordings
|
|
description: A table for grouping different intracellular recordings from the
|
|
IntracellularRecordingsTable table together that were recorded simultaneously
|
|
from different electrodes
|
|
is_a: SimultaneousRecordingsTable
|
|
NWBFile__general__intracellular_ephys__sequential_recordings:
|
|
name: NWBFile__general__intracellular_ephys__sequential_recordings
|
|
description: A table for grouping different sequential recordings from the SimultaneousRecordingsTable
|
|
table together. This is typically used to group together sequential recordings
|
|
where the a sequence of stimuli of the same type with varying parameters have
|
|
been presented in a sequence.
|
|
is_a: SequentialRecordingsTable
|
|
NWBFile__general__intracellular_ephys__repetitions:
|
|
name: NWBFile__general__intracellular_ephys__repetitions
|
|
description: A table for grouping different sequential intracellular recordings
|
|
together. With each SequentialRecording typically representing a particular
|
|
type of stimulus, the RepetitionsTable table is typically used to group sets
|
|
of stimuli applied in sequence.
|
|
is_a: RepetitionsTable
|
|
NWBFile__general__intracellular_ephys__experimental_conditions:
|
|
name: NWBFile__general__intracellular_ephys__experimental_conditions
|
|
description: A table for grouping different intracellular recording repetitions
|
|
together that belong to the same experimental experimental_conditions.
|
|
is_a: ExperimentalConditionsTable
|
|
NWBFile__general__optogenetics:
|
|
name: NWBFile__general__optogenetics
|
|
description: Metadata describing optogenetic stimuluation.
|
|
attributes:
|
|
OptogeneticStimulusSite:
|
|
name: OptogeneticStimulusSite
|
|
description: An optogenetic stimulation site.
|
|
multivalued: true
|
|
range: OptogeneticStimulusSite
|
|
required: false
|
|
NWBFile__general__optophysiology:
|
|
name: NWBFile__general__optophysiology
|
|
description: Metadata related to optophysiology.
|
|
attributes:
|
|
ImagingPlane:
|
|
name: ImagingPlane
|
|
description: An imaging plane.
|
|
multivalued: true
|
|
range: ImagingPlane
|
|
required: false
|
|
NWBFile__intervals:
|
|
name: NWBFile__intervals
|
|
description: Experimental intervals, whether that be logically distinct sub-experiments
|
|
having a particular scientific goal, trials (see trials subgroup) during an
|
|
experiment, or epochs (see epochs subgroup) deriving from analysis of data.
|
|
attributes:
|
|
epochs:
|
|
name: epochs
|
|
description: Divisions in time marking experimental stages or sub-divisions
|
|
of a single recording session.
|
|
multivalued: false
|
|
range: NWBFile__intervals__epochs
|
|
required: false
|
|
trials:
|
|
name: trials
|
|
description: Repeated experimental events that have a logical grouping.
|
|
multivalued: false
|
|
range: NWBFile__intervals__trials
|
|
required: false
|
|
invalid_times:
|
|
name: invalid_times
|
|
description: Time intervals that should be removed from analysis.
|
|
multivalued: false
|
|
range: NWBFile__intervals__invalid_times
|
|
required: false
|
|
TimeIntervals:
|
|
name: TimeIntervals
|
|
description: Optional additional table(s) for describing other experimental
|
|
time intervals.
|
|
multivalued: true
|
|
range: TimeIntervals
|
|
required: false
|
|
NWBFile__intervals__epochs:
|
|
name: NWBFile__intervals__epochs
|
|
description: Divisions in time marking experimental stages or sub-divisions of
|
|
a single recording session.
|
|
is_a: TimeIntervals
|
|
NWBFile__intervals__trials:
|
|
name: NWBFile__intervals__trials
|
|
description: Repeated experimental events that have a logical grouping.
|
|
is_a: TimeIntervals
|
|
NWBFile__intervals__invalid_times:
|
|
name: NWBFile__intervals__invalid_times
|
|
description: Time intervals that should be removed from analysis.
|
|
is_a: TimeIntervals
|
|
NWBFile__units:
|
|
name: NWBFile__units
|
|
description: Data about sorted spike units.
|
|
is_a: Units
|
|
Subject__age:
|
|
name: Subject__age
|
|
description: Age of subject. Can be supplied instead of 'date_of_birth'.
|
|
attributes:
|
|
reference:
|
|
name: reference
|
|
description: Age is with reference to this event. Can be 'birth' or 'gestational'.
|
|
If reference is omitted, 'birth' is implied.
|
|
range: text
|