name: core.nwb.file id: core.nwb.file imports: - core.nwb.base - hdmf-common.table - core.nwb.device - core.nwb.ecephys - core.nwb.icephys - core.nwb.ogen - core.nwb.ophys - core.nwb.epoch - core.nwb.misc - nwb.language default_prefix: core.nwb.file/ classes: ScratchData: name: ScratchData description: Any one-off datasets is_a: NWBData attributes: name: name: name range: string required: true notes: name: notes description: Any notes the user has about the dataset being stored range: text tree_root: true NWBFile: name: NWBFile description: An NWB file storing cellular-based neurophysiology data from a single experimental session. is_a: NWBContainer attributes: name: name: name ifabsent: string(root) range: string required: true equals_string: root nwb_version: name: nwb_version description: File version string. Use semantic versioning, e.g. 1.2.1. This will be the name of the format with trailing major, minor and patch numbers. range: text file_create_date: name: file_create_date description: 'A record of the date the file was created and of subsequent modifications. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted strings: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds. The file can be created after the experiment was run, so this may differ from the experiment start time. Each modification to the nwb file adds a new entry to the array.' multivalued: true range: isodatetime required: true identifier: name: identifier description: A unique text identifier for the file. For example, concatenated lab name, file creation date/time and experimentalist, or a hash of these and/or other values. The goal is that the string should be unique to all other files. multivalued: false range: text required: true session_description: name: session_description description: A description of the experimental session and data in the file. multivalued: false range: text required: true session_start_time: name: session_start_time description: 'Date and time of the experiment/session start. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds.' multivalued: false range: isodatetime required: true timestamps_reference_time: name: timestamps_reference_time description: 'Date and time corresponding to time zero of all timestamps. The date is stored in UTC with local timezone offset as ISO 8601 extended formatted string: 2018-09-28T14:43:54.123+02:00. Dates stored in UTC end in "Z" with no timezone offset. Date accuracy is up to milliseconds. All times stored in the file use this time as reference (i.e., time zero).' multivalued: false range: isodatetime required: true acquisition: name: acquisition description: Data streams recorded from the system, including ephys, ophys, tracking, etc. This group should be read-only after the experiment is completed and timestamps are corrected to a common timebase. The data stored here may be links to raw data stored in external NWB files. This will allow keeping bulky raw data out of the file while preserving the option of keeping some/all in the file. Acquired data includes tracking and experimental data streams (i.e., everything measured from the system). If bulky data is stored in the /acquisition group, the data can exist in a separate NWB file that is linked to by the file being used for processing and analysis. multivalued: true any_of: - range: NWBDataInterface - range: DynamicTable analysis: name: analysis description: Lab-specific and custom scientific analysis of data. There is no defined format for the content of this group - the format is up to the individual user/lab. To facilitate sharing analysis data between labs, the contents here should be stored in standard types (e.g., neurodata_types) and appropriately documented. The file can store lab-specific and custom data analysis without restriction on its form or schema, reducing data formatting restrictions on end users. Such data should be placed in the analysis group. The analysis data should be documented so that it could be shared with other labs. multivalued: true any_of: - range: NWBContainer - range: DynamicTable scratch: name: scratch description: A place to store one-off analysis results. Data placed here is not intended for sharing. By placing data here, users acknowledge that there is no guarantee that their data meets any standard. multivalued: true any_of: - range: NWBContainer - range: DynamicTable processing: name: processing description: The home for ProcessingModules. These modules perform intermediate analysis of data that is necessary to perform before scientific analysis. Examples include spike clustering, extracting position from tracking data, stitching together image slices. ProcessingModules can be large and express many data sets from relatively complex analysis (e.g., spike detection and clustering) or small, representing extraction of position information from tracking video, or even binary lick/no-lick decisions. Common software tools (e.g., klustakwik, MClust) are expected to read/write data here. 'Processing' refers to intermediate analysis of the acquired data to make it more amenable to scientific analysis. multivalued: true any_of: - range: ProcessingModule stimulus: name: stimulus description: Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. multivalued: false range: NWBFile__stimulus required: true general: name: general description: Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. multivalued: false range: NWBFile__general required: true intervals: name: 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. multivalued: false range: NWBFile__intervals required: false units: name: units description: Data about sorted spike units. multivalued: false range: Units required: false tree_root: true NWBFile__stimulus: name: NWBFile__stimulus description: Data pushed into the system (eg, video stimulus, sound, voltage, etc) and secondary representations of that data (eg, measurements of something used as a stimulus). This group should be made read-only after experiment complete and timestamps are corrected to common timebase. Stores both presented stimuli and stimulus templates, the latter in case the same stimulus is presented multiple times, or is pulled from an external stimulus library. Stimuli are here defined as any signal that is pushed into the system as part of the experiment (eg, sound, video, voltage, etc). Many different experiments can use the same stimuli, and stimuli can be re-used during an experiment. The stimulus group is organized so that one version of template stimuli can be stored and these be used multiple times. These templates can exist in the present file or can be linked to a remote library file. attributes: name: name: name ifabsent: string(stimulus) range: string required: true equals_string: stimulus presentation: name: presentation description: Stimuli presented during the experiment. multivalued: true any_of: - range: TimeSeries templates: name: templates description: Template stimuli. Timestamps in templates are based on stimulus design and are relative to the beginning of the stimulus. When templates are used, the stimulus instances must convert presentation times to the experiment`s time reference frame. multivalued: true any_of: - range: TimeSeries - range: Images NWBFile__general: name: NWBFile__general description: Experimental metadata, including protocol, notes and description of hardware device(s). The metadata stored in this section should be used to describe the experiment. Metadata necessary for interpreting the data is stored with the data. General experimental metadata, including animal strain, experimental protocols, experimenter, devices, etc, are stored under 'general'. Core metadata (e.g., that required to interpret data fields) is stored with the data itself, and implicitly defined by the file specification (e.g., time is in seconds). The strategy used here for storing non-core metadata is to use free-form text fields, such as would appear in sentences or paragraphs from a Methods section. Metadata fields are text to enable them to be more general, for example to represent ranges instead of numerical values. Machine-readable metadata is stored as attributes to these free-form datasets. All entries in the below table are to be included when data is present. Unused groups (e.g., intracellular_ephys in an optophysiology experiment) should not be created unless there is data to store within them. attributes: name: name: name ifabsent: string(general) range: string required: true equals_string: general data_collection: name: data_collection description: Notes about data collection and analysis. multivalued: false range: text required: false experiment_description: name: experiment_description description: General description of the experiment. multivalued: false range: text required: false experimenter: name: experimenter description: Name of person(s) who performed the experiment. Can also specify roles of different people involved. multivalued: true range: text required: false institution: name: institution description: Institution(s) where experiment was performed. multivalued: false range: text required: false keywords: name: keywords description: Terms to search over. multivalued: true range: text required: false lab: name: lab description: Laboratory where experiment was performed. multivalued: false range: text required: false notes: name: notes description: Notes about the experiment. multivalued: false range: text required: false pharmacology: name: pharmacology description: Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. multivalued: false range: text required: false protocol: name: protocol description: Experimental protocol, if applicable. e.g., include IACUC protocol number. multivalued: false range: text required: false related_publications: name: related_publications description: Publication information. PMID, DOI, URL, etc. multivalued: true range: text required: false session_id: name: session_id description: Lab-specific ID for the session. multivalued: false range: text required: false slices: name: slices description: Description of slices, including information about preparation thickness, orientation, temperature, and bath solution. multivalued: false range: text required: false source_script: name: source_script description: Script file or link to public source code used to create this NWB file. multivalued: false range: NWBFile__general__source_script required: false stimulus: name: stimulus description: Notes about stimuli, such as how and where they were presented. multivalued: false range: text required: false surgery: name: surgery description: Narrative description about surgery/surgeries, including date(s) and who performed surgery. multivalued: false range: text required: false virus: name: virus description: Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. multivalued: false range: text required: false lab_meta_data: name: lab_meta_data description: Place-holder than can be extended so that lab-specific meta-data can be placed in /general. multivalued: true range: LabMetaData required: false devices: name: devices description: Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc. multivalued: true any_of: - range: Device subject: name: subject description: Information about the animal or person from which the data was measured. multivalued: false range: Subject required: false extracellular_ephys: name: extracellular_ephys description: Metadata related to extracellular electrophysiology. multivalued: false range: NWBFile__general__extracellular_ephys required: false intracellular_ephys: name: intracellular_ephys description: Metadata related to intracellular electrophysiology. multivalued: false range: NWBFile__general__intracellular_ephys required: false optogenetics: name: optogenetics description: Metadata describing optogenetic stimuluation. multivalued: true any_of: - range: OptogeneticStimulusSite optophysiology: name: optophysiology description: Metadata related to optophysiology. multivalued: true any_of: - range: ImagingPlane NWBFile__general__source_script: name: NWBFile__general__source_script description: Script file or link to public source code used to create this NWB file. attributes: name: name: name ifabsent: string(source_script) range: string required: true equals_string: source_script file_name: name: file_name description: Name of script file. range: text value: name: value range: text required: true NWBFile__general__extracellular_ephys: name: NWBFile__general__extracellular_ephys description: Metadata related to extracellular electrophysiology. attributes: name: name: name ifabsent: string(extracellular_ephys) range: string required: true equals_string: extracellular_ephys electrode_group: name: electrode_group description: Physical group of electrodes. multivalued: true range: ElectrodeGroup required: false electrodes: name: electrodes description: A table of all electrodes (i.e. channels) used for recording. multivalued: false range: DynamicTable required: false NWBFile__general__intracellular_ephys: name: NWBFile__general__intracellular_ephys description: Metadata related to intracellular electrophysiology. attributes: name: name: name ifabsent: string(intracellular_ephys) range: string required: true equals_string: intracellular_ephys filtering: name: filtering description: '[DEPRECATED] Use IntracellularElectrode.filtering instead. Description of filtering used. Includes filtering type and parameters, frequency fall-off, etc. If this changes between TimeSeries, filter description should be stored as a text attribute for each TimeSeries.' multivalued: false range: text required: false intracellular_electrode: name: intracellular_electrode description: An intracellular electrode. multivalued: true range: IntracellularElectrode required: false sweep_table: name: 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.' multivalued: false range: SweepTable 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: IntracellularRecordingsTable 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: SimultaneousRecordingsTable 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: SequentialRecordingsTable 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: RepetitionsTable 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: ExperimentalConditionsTable 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: name: name: name ifabsent: string(intervals) range: string required: true equals_string: intervals epochs: name: epochs description: Divisions in time marking experimental stages or sub-divisions of a single recording session. multivalued: false range: TimeIntervals required: false trials: name: trials description: Repeated experimental events that have a logical grouping. multivalued: false range: TimeIntervals required: false invalid_times: name: invalid_times description: Time intervals that should be removed from analysis. multivalued: false range: TimeIntervals required: false time_intervals: name: time_intervals description: Optional additional table(s) for describing other experimental time intervals. multivalued: true range: TimeIntervals required: false LabMetaData: name: LabMetaData description: Lab-specific meta-data. is_a: NWBContainer attributes: name: name: name range: string required: true tree_root: true Subject: name: Subject description: Information about the animal or person from which the data was measured. is_a: NWBContainer attributes: name: name: name range: string required: true age: name: age description: Age of subject. Can be supplied instead of 'date_of_birth'. multivalued: false range: Subject__age required: false date_of_birth: name: date_of_birth description: Date of birth of subject. Can be supplied instead of 'age'. multivalued: false range: isodatetime required: false description: name: description description: Description of subject and where subject came from (e.g., breeder, if animal). multivalued: false range: text required: false genotype: name: genotype description: Genetic strain. If absent, assume Wild Type (WT). multivalued: false range: text required: false sex: name: sex description: Gender of subject. multivalued: false range: text required: false species: name: species description: Species of subject. multivalued: false range: text required: false strain: name: strain description: Strain of subject. multivalued: false range: text required: false subject_id: name: subject_id description: ID of animal/person used/participating in experiment (lab convention). multivalued: false range: text required: false weight: name: weight description: Weight at time of experiment, at time of surgery and at other important times. multivalued: false range: text required: false tree_root: true Subject__age: name: Subject__age description: Age of subject. Can be supplied instead of 'date_of_birth'. attributes: name: name: name ifabsent: string(age) range: string required: true equals_string: age 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 value: name: value range: text required: true