NwbFile Root object representing data read from an NWB file.
Requires that core and extension NWB types have been generated
and reside in a 'types' package on the matlab path.
Example. Construct an object from scratch for export:
nwb = NwbFile;
nwb.epochs = types.core.Epochs;
nwbExport(nwb, 'epoch.nwb');
| acquisition |
Any objects representing acquired data |
| analysis |
Custom analysis results |
| file_create_date |
A record of the date the file was created and of subsequent modifications. COMMENT: - 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.
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| general |
place-holder than can be extended so that lab-specific meta-data can be placed in /general |
| general_data_collection |
Notes about data collection and analysis.COMMENT: Can be from Methods |
| general_devices |
One of possibly many. Information about device and device description. |
| general_experiment_description |
General description of the experiment.COMMENT: Can be from Methods |
| general_experimenter |
Name of person who performed the experiment.COMMENT: More than one person OK. Can specify roles of different people involved. |
| general_extracellular_ephys |
One of possibly many groups, one for each electrode group. |
| general_extracellular_ephys_electrodes |
A table of all electrodes (i.e. channels) used for recording. |
| general_institution |
Institution(s) where experiment was performed |
| general_intracellular_ephys |
One of possibly many. COMMENT: Name should be informative. |
| general_intracellular_ephys_filtering |
Description of filtering used. COMMENT: 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.
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| general_intracellular_ephys_sweep_table |
The table which groups different PatchClampSeries together. |
| general_keywords |
Terms to search over |
| general_lab |
Lab where experiment was performed |
| general_notes |
Notes about the experiment. COMMENT: Things particular to this experiment |
| general_optogenetics |
One of possibly many groups describing an optogenetic stimulation site. COMMENT: Name is arbitrary but should be meaningful.
Name is referenced by OptogeneticSeries.
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| general_optophysiology |
One of possibly many groups describing an imaging plane. COMMENT: Name is arbitrary but should be meaningful. It is referenced
by TwoPhotonSeries and also ImageSegmentation and DfOverF interfaces.
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| general_pharmacology |
Description of drugs used, including how and when they were administered. COMMENT: Anesthesia(s), painkiller(s), etc., plus
dosage, concentration, etc.
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| general_protocol |
Experimental protocol, if applicable. COMMENT: E.g., include IACUC protocol. |
| general_related_publications |
Publication information. COMMENT: PMID, DOI, URL, etc. If multiple, concatenate together and describe which is which. such
as PMID, DOI, URL, etc
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| general_session_id |
Lab-specific ID for the session.COMMENT: Only 1 session_id per file, with all time aligned to experiment start time. |
| general_slices |
Description of slices, including information about preparation thickness, orientation, temperature and bath solution |
| general_source_script |
Script file used to create this NWB file. |
| general_source_script_file_name |
Name of script file |
| general_specifications |
Dataset for storing contents of a specification file for either the core format or an extension. Name should match name of
file.`
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| general_stimulus |
Notes about stimuli, such as how and where presented. COMMENT: Can be from Methods. |
| general_subject |
Information about the animal or person from which the data was measured. |
| general_surgery |
Narrative description about surgery/surgeries, including date(s) and who performed surgery. COMMENT: Much can be copied from
Methods.
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| general_virus |
Information about virus(es) used in experiments, including virus ID, source, date made, injection location, volume, etc. |
| help |
Short description of what this type of NWBContainer contains. |
| identifier |
A unique text identifier for the file. COMMENT: Eg, 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.
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| intervals |
an optional additional table for describing other experimental time intervals |
| intervals_epochs |
divisions in time marking experimental stages or sub-divisions of a single recording session |
| intervals_invalid_times |
time intervals that should be removed from analysis |
| intervals_trials |
repeated experimental events that have a logical grouping |
| nwb_version |
File version string. COMMENT: Eg, NWB-1.0.0. This will be the name of the format with trailing major, minor and patch numbers. |
| processing |
Intermediate analysis of acquired data |
| session_description |
One or two sentences describing the experiment and data in the file. |
| session_start_time |
Date and time of the experiment/session start. COMMENT: - 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.
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| stimulus_presentation |
TimeSeries objects containing data of presented stimuli |
| stimulus_templates |
TimeSeries objects containing template data of presented stimuli |
| timestamps_reference_time |
Date and time corresponding to time zero of all timestamps. COMMENT: - 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 (ie, time zero).
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| units |
Data about units |
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addlistener |
Add listener for event. |
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delete |
Delete a handle object. |
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eq |
== (EQ) Test handle equality. |
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export |
find reference properties |
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findobj |
Find objects matching specified conditions. |
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findprop |
Find property of MATLAB handle object. |
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ge |
>= (GE) Greater than or equal relation for handles. |
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gt |
> (GT) Greater than relation for handles. |
| Sealed
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isvalid |
Test handle validity. |
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le |
<= (LE) Less than or equal relation for handles. |
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listener |
Add listener for event without binding the listener to the source object. |
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loadAll |
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lt |
< (LT) Less than relation for handles. |
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ne |
~= (NE) Not equal relation for handles. |
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notify |
Notify listeners of event. |
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resolve |
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validate_acquisition |
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validate_analysis |
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validate_file_create_date |
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validate_general |
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validate_general_data_collection |
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validate_general_devices |
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validate_general_experiment_description |
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validate_general_experimenter |
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validate_general_extracellular_ephys |
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validate_general_extracellular_ephys_electrodes |
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validate_general_institution |
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validate_general_intracellular_ephys |
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validate_general_intracellular_ephys_filtering |
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validate_general_intracellular_ephys_sweep_table |
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validate_general_keywords |
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validate_general_lab |
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validate_general_notes |
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validate_general_optogenetics |
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validate_general_optophysiology |
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validate_general_pharmacology |
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validate_general_protocol |
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validate_general_related_publications |
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validate_general_session_id |
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validate_general_slices |
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validate_general_source_script |
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validate_general_source_script_file_name |
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validate_general_specifications |
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validate_general_stimulus |
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validate_general_subject |
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validate_general_surgery |
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validate_general_virus |
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validate_help |
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validate_identifier |
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validate_intervals |
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validate_intervals_epochs |
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validate_intervals_invalid_times |
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validate_intervals_trials |
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validate_processing |
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validate_session_description |
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validate_session_start_time |
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validate_stimulus_presentation |
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validate_stimulus_templates |
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validate_timestamps_reference_time |
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validate_units |
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