p2p-ld/nwb-linkml
1
0
Fork 0
mirror of https://github.com/p2p-ld/nwb-linkml.git synced 2024-11-14 02:34:28 +00:00
Code Issues Projects Releases Packages Wiki Activity Actions
nwb-linkml/nwb_linkml/schema/core.nwb.file.yaml
sneakers-the-rat 4faaa8efe8 I believe that's a full translation 
or at least all the semantics are present. it's not pretty by any stretch of the imagination
2023-08-25 00:22:47 -07:00

1099 lines
48 KiB
YAML
Raw Blame History

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:
notes:
name: notes
description: Any notes the user has about the dataset being stored
range: text
NWBFile:
name: NWBFile
description: An NWB file storing cellular-based neurophysiology data from a single
experimental session.
is_a: NWBContainer
attributes:
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: false
range: NWBFile_file_create_date
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: NWBFile_identifier
required: true
session_description:
name: session_description
description: A description of the experimental session and data in the file.
multivalued: false
range: NWBFile_session_description
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: NWBFile_session_start_time
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: NWBFile_timestamps_reference_time
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: false
range: NWBFile_acquisition
required: true
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: false
range: NWBFile_analysis
required: true
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: false
range: NWBFile_scratch
required: false
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: false
range: NWBFile_processing
required: true
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: NWBFile_units
required: false
NWBFile_file_create_date:
name: NWBFile_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.'
attributes:
array:
name: array
range: NWBFile_file_create_date_Array
NWBFile_file_create_date_Array:
name: NWBFile_file_create_date_Array
is_a: Arraylike
attributes:
num_modifications:
name: num_modifications
range: isodatetime
required: true
NWBFile_identifier:
name: NWBFile_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.
NWBFile_session_description:
name: NWBFile_session_description
description: A description of the experimental session and data in the file.
NWBFile_session_start_time:
name: NWBFile_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.'
NWBFile_timestamps_reference_time:
name: NWBFile_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).'
NWBFile_acquisition:
name: NWBFile_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.
attributes:
NWBDataInterface:
name: NWBDataInterface
description: Acquired, raw data.
multivalued: true
range: NWBDataInterface
required: false
DynamicTable:
name: DynamicTable
description: Tabular data that is relevant to acquisition
multivalued: true
range: DynamicTable
required: false
NWBFile_analysis:
name: NWBFile_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.
attributes:
NWBContainer:
name: NWBContainer
description: Custom analysis results.
multivalued: true
range: NWBContainer
required: false
DynamicTable:
name: DynamicTable
description: Tabular data that is relevant to data stored in analysis
multivalued: true
range: DynamicTable
required: false
NWBFile_scratch:
name: NWBFile_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.
attributes:
ScratchData:
name: ScratchData
description: Any one-off datasets
multivalued: true
range: ScratchData
required: false
NWBContainer:
name: NWBContainer
description: Any one-off containers
multivalued: true
range: NWBContainer
required: false
DynamicTable:
name: DynamicTable
description: Any one-off tables
multivalued: true
range: DynamicTable
required: false
NWBFile_processing:
name: NWBFile_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.
attributes:
ProcessingModule:
name: ProcessingModule
description: Intermediate analysis of acquired data.
multivalued: true
range: ProcessingModule
required: false
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:
presentation:
name: presentation
description: Stimuli presented during the experiment.
multivalued: false
range: NWBFile_stimulus_presentation
required: true
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: false
range: NWBFile_stimulus_templates
required: true
NWBFile_stimulus_presentation:
name: NWBFile_stimulus_presentation
description: Stimuli presented during the experiment.
attributes:
TimeSeries:
name: TimeSeries
description: TimeSeries objects containing data of presented stimuli.
multivalued: true
range: TimeSeries
required: false
NWBFile_stimulus_templates:
name: NWBFile_stimulus_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.
attributes:
TimeSeries:
name: TimeSeries
description: TimeSeries objects containing template data of presented stimuli.
multivalued: true
range: TimeSeries
required: false
Images:
name: Images
description: Images objects containing images of presented stimuli.
multivalued: true
range: Images
required: false
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:
data_collection:
name: data_collection
description: Notes about data collection and analysis.
multivalued: false
range: NWBFile_general_data_collection
required: false
experiment_description:
name: experiment_description
description: General description of the experiment.
multivalued: false
range: NWBFile_general_experiment_description
required: false
experimenter:
name: experimenter
description: Name of person(s) who performed the experiment. Can also specify
roles of different people involved.
multivalued: false
range: NWBFile_general_experimenter
required: false
institution:
name: institution
description: Institution(s) where experiment was performed.
multivalued: false
range: NWBFile_general_institution
required: false
keywords:
name: keywords
description: Terms to search over.
multivalued: false
range: NWBFile_general_keywords
required: false
lab:
name: lab
description: Laboratory where experiment was performed.
multivalued: false
range: NWBFile_general_lab
required: false
notes:
name: notes
description: Notes about the experiment.
multivalued: false
range: NWBFile_general_notes
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: NWBFile_general_pharmacology
required: false
protocol:
name: protocol
description: Experimental protocol, if applicable. e.g., include IACUC protocol
number.
multivalued: false
range: NWBFile_general_protocol
required: false
related_publications:
name: related_publications
description: Publication information. PMID, DOI, URL, etc.
multivalued: false
range: NWBFile_general_related_publications
required: false
session_id:
name: session_id
description: Lab-specific ID for the session.
multivalued: false
range: NWBFile_general_session_id
required: false
slices:
name: slices
description: Description of slices, including information about preparation
thickness, orientation, temperature, and bath solution.
multivalued: false
range: NWBFile_general_slices
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: NWBFile_general_stimulus
required: false
surgery:
name: surgery
description: Narrative description about surgery/surgeries, including date(s)
and who performed surgery.
multivalued: false
range: NWBFile_general_surgery
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: NWBFile_general_virus
required: false
LabMetaData:
name: LabMetaData
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: false
range: NWBFile_general_devices
required: false
subject:
name: subject
description: Information about the animal or person from which the data was
measured.
multivalued: false
range: NWBFile_general_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: false
range: NWBFile_general_optogenetics
required: false
optophysiology:
name: optophysiology
description: Metadata related to optophysiology.
multivalued: false
range: NWBFile_general_optophysiology
required: false
NWBFile_general_data_collection:
name: NWBFile_general_data_collection
description: Notes about data collection and analysis.
NWBFile_general_experiment_description:
name: NWBFile_general_experiment_description
description: General description of the experiment.
NWBFile_general_experimenter:
name: NWBFile_general_experimenter
description: Name of person(s) who performed the experiment. Can also specify
roles of different people involved.
attributes:
array:
name: array
range: NWBFile_general_experimenter_Array
NWBFile_general_experimenter_Array:
name: NWBFile_general_experimenter_Array
is_a: Arraylike
attributes:
num_experimenters:
name: num_experimenters
range: text
required: true
NWBFile_general_institution:
name: NWBFile_general_institution
description: Institution(s) where experiment was performed.
NWBFile_general_keywords:
name: NWBFile_general_keywords
description: Terms to search over.
attributes:
array:
name: array
range: NWBFile_general_keywords_Array
NWBFile_general_keywords_Array:
name: NWBFile_general_keywords_Array
is_a: Arraylike
attributes:
num_keywords:
name: num_keywords
range: text
required: true
NWBFile_general_lab:
name: NWBFile_general_lab
description: Laboratory where experiment was performed.
NWBFile_general_notes:
name: NWBFile_general_notes
description: Notes about the experiment.
NWBFile_general_pharmacology:
name: NWBFile_general_pharmacology
description: Description of drugs used, including how and when they were administered.
Anesthesia(s), painkiller(s), etc., plus dosage, concentration, etc.
NWBFile_general_protocol:
name: NWBFile_general_protocol
description: Experimental protocol, if applicable. e.g., include IACUC protocol
number.
NWBFile_general_related_publications:
name: NWBFile_general_related_publications
description: Publication information. PMID, DOI, URL, etc.
attributes:
array:
name: array
range: NWBFile_general_related_publications_Array
NWBFile_general_related_publications_Array:
name: NWBFile_general_related_publications_Array
is_a: Arraylike
attributes:
num_publications:
name: num_publications
range: text
required: true
NWBFile_general_session_id:
name: NWBFile_general_session_id
description: Lab-specific ID for the session.
NWBFile_general_slices:
name: NWBFile_general_slices
description: Description of slices, including information about preparation thickness,
orientation, temperature, and bath solution.
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:
file_name:
name: file_name
description: Name of script file.
range: text
NWBFile_general_stimulus:
name: NWBFile_general_stimulus
description: Notes about stimuli, such as how and where they were presented.
NWBFile_general_surgery:
name: NWBFile_general_surgery
description: Narrative description about surgery/surgeries, including date(s)
and who performed surgery.
NWBFile_general_virus:
name: NWBFile_general_virus
description: Information about virus(es) used in experiments, including virus
ID, source, date made, injection location, volume, etc.
NWBFile_general_devices:
name: NWBFile_general_devices
description: Description of hardware devices used during experiment, e.g., monitors,
ADC boards, microscopes, etc.
attributes:
Device:
name: Device
description: Data acquisition devices.
multivalued: true
range: Device
required: false
NWBFile_general_subject:
name: NWBFile_general_subject
description: Information about the animal or person from which the data was measured.
is_a: Subject
NWBFile_general_extracellular_ephys:
name: NWBFile_general_extracellular_ephys
description: Metadata related to extracellular electrophysiology.
attributes:
ElectrodeGroup:
name: ElectrodeGroup
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: NWBFile_general_extracellular_ephys_electrodes
required: false
NWBFile_general_extracellular_ephys_electrodes:
name: NWBFile_general_extracellular_ephys_electrodes
description: A table of all electrodes (i.e. channels) used for recording.
is_a: DynamicTable
attributes:
x:
name: x
description: x coordinate of the channel location in the brain (+x is posterior).
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_x
required: false
y:
name: y
description: y coordinate of the channel location in the brain (+y is inferior).
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_y
required: false
z:
name: z
description: z coordinate of the channel location in the brain (+z is right).
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_z
required: false
imp:
name: imp
description: Impedance of the channel, in ohms.
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_imp
required: false
location:
name: location
description: 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.
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_location
required: true
filtering:
name: filtering
description: Description of hardware filtering, including the filter name
and frequency cutoffs.
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_filtering
required: false
group:
name: group
description: Reference to the ElectrodeGroup this electrode is a part of.
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_group
required: true
group_name:
name: group_name
description: Name of the ElectrodeGroup this electrode is a part of.
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_group_name
required: true
rel_x:
name: rel_x
description: x coordinate in electrode group
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_rel_x
required: false
rel_y:
name: rel_y
description: y coordinate in electrode group
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_rel_y
required: false
rel_z:
name: rel_z
description: z coordinate in electrode group
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_rel_z
required: false
reference:
name: reference
description: Description of the reference electrode and/or reference scheme
used for this electrode, e.g., "stainless steel skull screw" or "online
common average referencing".
multivalued: false
range: NWBFile_general_extracellular_ephys_electrodes_reference
required: false
NWBFile_general_extracellular_ephys_electrodes_x:
name: NWBFile_general_extracellular_ephys_electrodes_x
description: x coordinate of the channel location in the brain (+x is posterior).
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_y:
name: NWBFile_general_extracellular_ephys_electrodes_y
description: y coordinate of the channel location in the brain (+y is inferior).
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_z:
name: NWBFile_general_extracellular_ephys_electrodes_z
description: z coordinate of the channel location in the brain (+z is right).
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_imp:
name: NWBFile_general_extracellular_ephys_electrodes_imp
description: Impedance of the channel, in ohms.
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_location:
name: NWBFile_general_extracellular_ephys_electrodes_location
description: 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.
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_filtering:
name: NWBFile_general_extracellular_ephys_electrodes_filtering
description: Description of hardware filtering, including the filter name and
frequency cutoffs.
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_group:
name: NWBFile_general_extracellular_ephys_electrodes_group
description: Reference to the ElectrodeGroup this electrode is a part of.
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_group_name:
name: NWBFile_general_extracellular_ephys_electrodes_group_name
description: Name of the ElectrodeGroup this electrode is a part of.
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_rel_x:
name: NWBFile_general_extracellular_ephys_electrodes_rel_x
description: x coordinate in electrode group
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_rel_y:
name: NWBFile_general_extracellular_ephys_electrodes_rel_y
description: y coordinate in electrode group
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_rel_z:
name: NWBFile_general_extracellular_ephys_electrodes_rel_z
description: z coordinate in electrode group
is_a: VectorData
NWBFile_general_extracellular_ephys_electrodes_reference:
name: NWBFile_general_extracellular_ephys_electrodes_reference
description: Description of the reference electrode and/or reference scheme used
for this electrode, e.g., "stainless steel skull screw" or "online common average
referencing".
is_a: VectorData
NWBFile_general_intracellular_ephys:
name: NWBFile_general_intracellular_ephys
description: Metadata related to intracellular electrophysiology.
attributes:
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: NWBFile_general_intracellular_ephys_filtering
required: false
IntracellularElectrode:
name: IntracellularElectrode
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: 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_filtering:
name: NWBFile_general_intracellular_ephys_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.'
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
LabMetaData:
name: LabMetaData
description: Lab-specific meta-data.
is_a: NWBContainer
Subject:
name: Subject
description: Information about the animal or person from which the data was measured.
is_a: NWBContainer
attributes:
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: Subject_date_of_birth
required: false
description:
name: description
description: Description of subject and where subject came from (e.g., breeder,
if animal).
multivalued: false
range: Subject_description
required: false
genotype:
name: genotype
description: Genetic strain. If absent, assume Wild Type (WT).
multivalued: false
range: Subject_genotype
required: false
sex:
name: sex
description: Gender of subject.
multivalued: false
range: Subject_sex
required: false
species:
name: species
description: Species of subject.
multivalued: false
range: Subject_species
required: false
strain:
name: strain
description: Strain of subject.
multivalued: false
range: Subject_strain
required: false
subject_id:
name: subject_id
description: ID of animal/person used/participating in experiment (lab convention).
multivalued: false
range: Subject_subject_id
required: false
weight:
name: weight
description: Weight at time of experiment, at time of surgery and at other
important times.
multivalued: false
range: Subject_weight
required: false
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
Subject_date_of_birth:
name: Subject_date_of_birth
description: Date of birth of subject. Can be supplied instead of 'age'.
Subject_description:
name: Subject_description
description: Description of subject and where subject came from (e.g., breeder,
if animal).
Subject_genotype:
name: Subject_genotype
description: Genetic strain. If absent, assume Wild Type (WT).
Subject_sex:
name: Subject_sex
description: Gender of subject.
Subject_species:
name: Subject_species
description: Species of subject.
Subject_strain:
name: Subject_strain
description: Strain of subject.
Subject_subject_id:
name: Subject_subject_id
description: ID of animal/person used/participating in experiment (lab convention).
Subject_weight:
name: Subject_weight
description: Weight at time of experiment, at time of surgery and at other important
times.
Reference in a new issue View git blame Copy permalink