groups: - neurodata_type_def: NWBFile neurodata_type_inc: NWBContainer name: root doc: An NWB file storing cellular-based neurophysiology data from a single experimental session. attributes: - name: nwb_version dtype: text value: "2.6.0" doc: 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. datasets: - name: file_create_date dtype: isodatetime dims: - num_modifications shape: - null doc: '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.' - name: identifier dtype: text doc: 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. - name: session_description dtype: text doc: A description of the experimental session and data in the file. - name: session_start_time dtype: isodatetime doc: '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.' - name: timestamps_reference_time dtype: isodatetime doc: '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).' groups: - name: acquisition doc: 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. groups: - neurodata_type_inc: NWBDataInterface doc: Acquired, raw data. quantity: '*' - neurodata_type_inc: DynamicTable doc: Tabular data that is relevant to acquisition quantity: '*' - name: analysis doc: 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. groups: - neurodata_type_inc: NWBContainer doc: Custom analysis results. quantity: '*' - neurodata_type_inc: DynamicTable doc: Tabular data that is relevant to data stored in analysis quantity: '*' - name: scratch doc: '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.' quantity: '?' groups: - neurodata_type_inc: NWBContainer doc: Any one-off containers quantity: '*' - neurodata_type_inc: DynamicTable doc: Any one-off tables quantity: '*' datasets: - neurodata_type_inc: ScratchData doc: Any one-off datasets quantity: '*' - name: processing doc: "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." groups: - neurodata_type_inc: ProcessingModule doc: Intermediate analysis of acquired data. quantity: '*' - name: stimulus doc: '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.' groups: - name: presentation doc: Stimuli presented during the experiment. groups: - neurodata_type_inc: TimeSeries doc: TimeSeries objects containing data of presented stimuli. quantity: '*' - name: templates doc: '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.' groups: - neurodata_type_inc: TimeSeries doc: TimeSeries objects containing template data of presented stimuli. quantity: '*' - neurodata_type_inc: Images doc: Images objects containing images of presented stimuli. quantity: '*' - name: general doc: "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." datasets: - name: data_collection dtype: text doc: Notes about data collection and analysis. quantity: '?' - name: experiment_description dtype: text doc: General description of the experiment. quantity: '?' - name: experimenter dtype: text doc: Name of person(s) who performed the experiment. Can also specify roles of different people involved. quantity: '?' dims: - num_experimenters shape: - null - name: institution dtype: text doc: Institution(s) where experiment was performed. quantity: '?' - name: keywords dtype: text dims: - num_keywords shape: - null doc: Terms to search over. quantity: '?' - name: lab dtype: text doc: Laboratory where experiment was performed. quantity: '?' - name: notes dtype: text doc: Notes about the experiment. quantity: '?' - name: pharmacology dtype: text doc: Description of drugs used, including how and when they were administered. Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc. quantity: '?' - name: protocol dtype: text doc: Experimental protocol, if applicable. e.g., include IACUC protocol number. quantity: '?' - name: related_publications dtype: text doc: Publication information. PMID, DOI, URL, etc. dims: - num_publications shape: - null quantity: '?' - name: session_id dtype: text doc: Lab-specific ID for the session. quantity: '?' - name: slices dtype: text doc: Description of slices, including information about preparation thickness, orientation, temperature, and bath solution. quantity: '?' - name: source_script dtype: text doc: Script file or link to public source code used to create this NWB file. quantity: '?' attributes: - name: file_name dtype: text doc: Name of script file. - name: stimulus dtype: text doc: Notes about stimuli, such as how and where they were presented. quantity: '?' - name: surgery dtype: text doc: Narrative description about surgery/surgeries, including date(s) and who performed surgery. quantity: '?' - name: virus dtype: text doc: Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. quantity: '?' groups: - neurodata_type_inc: LabMetaData doc: Place-holder than can be extended so that lab-specific meta-data can be placed in /general. quantity: '*' - name: devices doc: Description of hardware devices used during experiment, e.g., monitors, ADC boards, microscopes, etc. quantity: '?' groups: - neurodata_type_inc: Device doc: Data acquisition devices. quantity: '*' - name: subject neurodata_type_inc: Subject doc: Information about the animal or person from which the data was measured. quantity: '?' - name: extracellular_ephys doc: Metadata related to extracellular electrophysiology. quantity: '?' groups: - neurodata_type_inc: ElectrodeGroup doc: Physical group of electrodes. quantity: '*' - name: electrodes neurodata_type_inc: DynamicTable doc: A table of all electrodes (i.e. channels) used for recording. 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: '?' datasets: - name: filtering dtype: text doc: '[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.' quantity: '?' groups: - neurodata_type_inc: IntracellularElectrode doc: An intracellular electrode. quantity: '*' - name: sweep_table neurodata_type_inc: SweepTable doc: '[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.' quantity: '?' - name: intracellular_recordings neurodata_type_inc: IntracellularRecordingsTable doc: 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. quantity: '?' - name: simultaneous_recordings neurodata_type_inc: SimultaneousRecordingsTable doc: A table for grouping different intracellular recordings from the IntracellularRecordingsTable table together that were recorded simultaneously from different electrodes quantity: '?' - name: sequential_recordings neurodata_type_inc: SequentialRecordingsTable doc: 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. quantity: '?' - name: repetitions neurodata_type_inc: RepetitionsTable doc: 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. quantity: '?' - name: experimental_conditions neurodata_type_inc: ExperimentalConditionsTable doc: A table for grouping different intracellular recording repetitions together that belong to the same experimental experimental_conditions. quantity: '?' - name: optogenetics doc: Metadata describing optogenetic stimuluation. quantity: '?' groups: - neurodata_type_inc: OptogeneticStimulusSite doc: An optogenetic stimulation site. quantity: '*' - name: optophysiology doc: Metadata related to optophysiology. quantity: '?' groups: - neurodata_type_inc: ImagingPlane doc: An imaging plane. quantity: '*' - name: intervals doc: 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. quantity: '?' groups: - name: epochs neurodata_type_inc: TimeIntervals doc: Divisions in time marking experimental stages or sub-divisions of a single recording session. quantity: '?' - name: trials neurodata_type_inc: TimeIntervals doc: Repeated experimental events that have a logical grouping. quantity: '?' - name: invalid_times neurodata_type_inc: TimeIntervals doc: Time intervals that should be removed from analysis. quantity: '?' - neurodata_type_inc: TimeIntervals doc: Optional additional table(s) for describing other experimental time intervals. quantity: '*' - name: units neurodata_type_inc: Units doc: Data about sorted spike units. quantity: '?' - neurodata_type_def: LabMetaData neurodata_type_inc: NWBContainer doc: Lab-specific meta-data. - neurodata_type_def: Subject neurodata_type_inc: NWBContainer doc: Information about the animal or person from which the data was measured. datasets: - name: age dtype: text doc: Age of subject. Can be supplied instead of 'date_of_birth'. quantity: '?' attributes: - name: reference doc: "Age is with reference to this event. Can be 'birth' or 'gestational'. If reference is omitted, 'birth' is implied." dtype: text required: false default_value: birth - name: date_of_birth dtype: isodatetime doc: Date of birth of subject. Can be supplied instead of 'age'. quantity: '?' - name: description dtype: text doc: Description of subject and where subject came from (e.g., breeder, if animal). quantity: '?' - name: genotype dtype: text doc: Genetic strain. If absent, assume Wild Type (WT). quantity: '?' - name: sex dtype: text doc: Gender of subject. quantity: '?' - name: species dtype: text doc: Species of subject. quantity: '?' - name: strain dtype: text doc: Strain of subject. quantity: '?' - name: subject_id dtype: text doc: ID of animal/person used/participating in experiment (lab convention). quantity: '?' - name: weight dtype: text doc: Weight at time of experiment, at time of surgery and at other important times. quantity: '?' datasets: - neurodata_type_def: ScratchData neurodata_type_inc: NWBData doc: Any one-off datasets attributes: - name: notes doc: 'Any notes the user has about the dataset being stored' dtype: text