MatNWB

https://matnwb.readthedocs.io/en/latest/
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MatNWB is a MATLAB package for reading and writing Neurodata Without Borders (NWB) files, providing...
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### Read NWB File Examples

Source: https://matnwb.readthedocs.io/en/latest/pages/developer/documentation/formatting_docstrings.html

Examples demonstrating how to read an NWB file using nwbRead with various flags and options.

```matlab
nwb = nwbRead('data.nwb');
```

```matlab
nwb = nwbRead('data.nwb', 'ignorecache');
```

```matlab
nwb = nwbRead('data.nwb', 'savedir', '.');
```

--------------------------------

### Providing Usage Examples

Source: https://matnwb.readthedocs.io/en/latest/pages/developer/documentation/formatting_docstrings.html

Structure usage examples with a descriptive header followed by indented MATLAB code blocks.

```matlab
% Usage:
%  Example 1 - Read an NWB file::
%
%    nwb = nwbRead('data.nwb');
%
%  Example 2 - Read an NWB file without re-generating classes for NWB types::
%
%    nwb = nwbRead('data.nwb', 'ignorecache');
%
%  Note: This is a good option to use if you are reading several files
%  which are created of the same version of the NWB schemas.
%
%  Example 3 - Read an NWB file and generate classes for NWB types in the current working directory::
%
%    nwb = nwbRead('data.nwb', 'savedir', '.');
```

--------------------------------

### Create Imaging Plane and Devices

Source: https://matnwb.readthedocs.io/en/latest/pages/tutorials/ophys.html

Initialize a Device, OpticalChannel, and ImagingPlane to define the optical imaging setup.

```matlab
device = types.core.Device( ...
'description', 'My two-photon microscope', ...
'manufacturer', 'Loki Labs', ...
'model_number', 'ABC-123', ...
'model_name', 'Loki 1.0', ...
'serial_number', '1234567890');
% Add device to nwb object
nwb.general_devices.set('Device', device);
optical_channel = types.core.OpticalChannel( ...
'description', 'description', ...
'emission_lambda', 500.);
imaging_plane_name = 'imaging_plane';
imaging_plane = types.core.ImagingPlane( ...
'optical_channel', optical_channel, ...
'description', 'a very interesting part of the brain', ...
'device', types.untyped.SoftLink(device), ...
'excitation_lambda', 600., ...
'imaging_rate', 5., ...
'indicator', 'GFP', ...
'location', 'Primary visual area');
nwb.general_optophysiology.set(imaging_plane_name, imaging_plane);
```

--------------------------------

### Install a Neurodata Extension

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/using_extensions/installing_extensions.html

Use this function to download and generate classes for a specific published extension by name.

```matlab
nwbInstallExtension("ndx-extension")
```

--------------------------------

### Manage container entries with Set methods

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/working_with_containers.html

Use set and get methods to interact with container entries directly.

```matlab
dataObject = types.core.TimeSeries();

% Add to Set using set() method
processingModule.nwbdatainterface.set('MyData', dataObject);

% Get from Set using get() method
dataObject = processingModule.nwbdatainterface.get('MyData');
```

--------------------------------

### Best Practices for Naming

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/working_with_containers.html

Use valid MATLAB identifiers from the start to ensure consistent naming conventions.

```matlab
processingModule.add('MyTimeSeries', timeSeries);
processingModule.add('myTimeSeries', timeSeries);
processingModule.add('my_time_series', timeSeries);
```

--------------------------------

### Constructing TimestampVectorData

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/TimestampVectorData.html

Examples of initializing a TimestampVectorData object using the constructor with or without name-value pairs.

```matlab
timestampVectorData = types.core.TIMESTAMPVECTORDATA()
```

```matlab
timestampVectorData = types.core.TIMESTAMPVECTORDATA(Name, Value)
```

--------------------------------

### Constructing TimeSeriesReferenceVectorData

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/TimeSeriesReferenceVectorData.html

Examples of initializing the TimeSeriesReferenceVectorData object with or without name-value pairs.

```matlab
timeSeriesReferenceVectorData = types.core.TIMESERIESREFERENCEVECTORDATA()
```

```matlab
timeSeriesReferenceVectorData = types.core.TIMESERIESREFERENCEVECTORDATA(Name, Value)
```

--------------------------------

### Create Isolated Test Environments for Schemas

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/schemas_and_generation.html

Generate classes in a dedicated directory to test new schema versions without modifying the main installation.

```matlab
% Create isolated test environment
test_dir = '/path/to/test_environment';
generateCore('2.8.0-dev', 'savedir', test_dir);

% Test with experimental schema
addpath(test_dir);
nwb = nwbRead('experimental_file.nwb', 'ignorecache');
```

--------------------------------

### Create a Device object

Source: https://matnwb.readthedocs.io/en/latest/pages/tutorials/ogen.html

Initialize a device and link it to the NWBFile.

```matlab
device = types.core.Device();
nwb.general_devices.set('Device', device);
```

--------------------------------

### Initialize NWBFile and Simulate Data

Source: https://matnwb.readthedocs.io/en/latest/_static/html/tutorials/scratch.html

Sets up a basic NWBFile with required metadata and generates a simulated TimeSeries for analysis.

```matlab
ContextFile = NwbFile(... 
'session_description', 'demonstrate NWBFile scratch', ... % required 
'identifier', 'SCRATCH-0', ... % required 
'session_start_time', datetime(2019, 4, 3, 11, 0, 0, 'TimeZone', 'local'), ... % required 
'file_create_date', datetime(2019, 4, 15, 12, 0, 0, 'TimeZone', 'local'), ... % optional 
'general_experimenter', 'Niu, Lawrence', ... 
'general_institution', 'NWB' ... 
); 
% Simulate some data 
timestamps = 0:100:1024; 
data = sin(0.333 .* timestamps) ... 
+ cos(0.1 .* timestamps) ... 
+ randn(1, length(timestamps)); 
RawTs = types.core.TimeSeries(... 
'data', data, ... 
'data_unit', 'm', ... 
'starting_time', 0., ... 
'starting_time_rate', 100, ... 
'description', 'simulated acquired data' ... 
); 
ContextFile.acquisition.set('raw_timeseries', RawTs);
```

--------------------------------

### Initialize NWBFile object

Source: https://matnwb.readthedocs.io/en/latest/pages/tutorials/ogen.html

Create the primary NWBFile object with required session metadata.

```matlab
nwb = NwbFile( ...
'session_description', 'mouse in open exploration',...
'identifier', char(java.util.UUID.randomUUID), ...
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'), ...
'general_experimenter', 'Last, First M.', ... % optional
'general_session_id', 'session_1234', ... % optional
'general_institution', 'University of My Institution', ... % optional
'general_related_publications', 'DOI:10.1016/j.neuron.2016.12.011'); % optional
nwb
```

--------------------------------

### Access Specific Dataset

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/nwbfile.html

Retrieves a specific dataset from the acquisition set using the get method.

```matlab
>> disp(nwb.acquisition.get('ElectricalSeries'));
```

--------------------------------

### Inspect configuration before export

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/compression/compression_profiles.html

Configure an NWB file and apply a compression profile to inspect the DataPipe properties prior to saving.

```matlab
% 1. Create an NWB file
nwb = NwbFile( ...
    'identifier', 'compression-howto-20250411T153000Z', ...
    'session_description', 'Compression profile how-to guide', ...
    'session_start_time', datetime(2025,4,11,15,30,0,'TimeZone','UTC'));

% 2. Add a large TimeSeries
data = rand(32, 1e6, 'single');  % Example large matrix
es = types.core.TimeSeries(...
    'data', data, ...
    'data_unit', 'volts', ...
    'starting_time', 0, ...
    'starting_time_rate', 30000);
nwb.acquisition.set('ExampleSeries', es);

% 3. Apply the cloud profile (convenience method accepts profile name)
nwb.applyDatasetSettingsProfile('cloud');

% 4. Inspect resulting DataPipe
dataPipe = nwb.acquisition.get('ExampleSeries').data
```

--------------------------------

### inspectNwbFile(nwbFilepath, options)

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/inspectNwbFile.html

Runs nwbinspector on the specified NWB file and returns a tabular report of potential issues.

```APIDOC
## inspectNwbFile(nwbFilepath, options)

### Description
Runs the nwbinspector tool on a specified NWB file to identify potential issues. Returns a table containing the inspection report.

### Syntax
`report = inspectNwbFile(nwbFilepath)`
`report = inspectNwbFile(nwbFilepath, Name, Value)`

### Parameters
- **nwbFilepath** (string) - Required - Filepath pointing to an NWB file.
- **options** (name-value pairs) - Optional - Name-value pairs for customizing the report.
  - **VariableOrder** (string) - Specifies the order to arrange variables in the tabular report.

### Returns
- **report** (table) - A tabular report listing nwbinspector issues.

### Usage Example
```matlab
% Basic inspection
report = inspectNwbFile('my_nwb_file.nwb');

% Inspection with custom variable order
variableOrder = ["importance", "message", "check_function_name", "object_name"];
report = inspectNwbFile('my_nwb_file.nwb', 'VariableOrder', variableOrder);
```
```

--------------------------------

### Constructing an Image object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/Image.html

Demonstrates the syntax for initializing an Image object with or without name-value pair arguments.

```matlab
image = types.core.IMAGE()
```

```matlab
image = types.core.IMAGE(Name, Value)
```

--------------------------------

### Documenting Output Arguments

Source: https://matnwb.readthedocs.io/en/latest/pages/developer/documentation/formatting_docstrings.html

Format output arguments by listing the name, type in parentheses, and a brief description.

```matlab
% Output Arguments:
%  - nwb (NwbFile) - Nwb file object
```

--------------------------------

### List and display extensions

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/matnwb/extension/matnwb.extension.listExtensions.html

Retrieves the table of available extensions and displays it in the command window.

```matlab
T = matnwb.extension.listExtensions();
disp(T)
```

--------------------------------

### Specify Class Generation Directory

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/troubleshooting.html

Use the savedir argument to direct MatNWB to generate class files in a specific local directory instead of the default installation path.

```matlab
nwb = nwbRead('/path/to/matnwb/file.nwb', 'savedir', '.'); % write class files to current working directory.
```

--------------------------------

### Exporting an NWB file with a built-in compression profile

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/compression/compression_profiles.html

Demonstrates creating an NWB file and applying the 'cloud' compression profile during the export process.

```matlab
% 1. Create an NWB file
nwb = NwbFile( ...
    'identifier', 'compression-howto-20250411T153000Z', ...
    'session_description', 'Compression profile how-to guide', ...
    'session_start_time', datetime(2025,4,11,15,30,0,'TimeZone','UTC'));

% 2. Add a large TimeSeries
data = rand(32, 1e6, 'single');  % Example large matrix
es = types.core.TimeSeries(...
    'data', data, ...
    'data_unit', 'volts', ...
    'starting_time', 0, ...
    'starting_time_rate', 30000);
nwb.acquisition.set('ExampleSeries', es);

% 3. Use a built-in profile on export
nwbExport(nwb, 'example_cloud_profile.nwb', ...
    'DatasetSettingsProfile', 'cloud');
```

--------------------------------

### Constructing a ScratchData object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/ScratchData.html

Demonstrates the syntax for initializing a ScratchData object with or without name-value pairs.

```matlab
scratchData = types.core.SCRATCHDATA()
```

```matlab
scratchData = types.core.SCRATCHDATA(Name, Value)
```

--------------------------------

### Initialize SimpleMultiContainer

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/hdmf_common/SimpleMultiContainer.html

Demonstrates the syntax for creating a SimpleMultiContainer object, either empty or with specified name-value pairs.

```matlab
simpleMultiContainer = types.hdmf_common.SIMPLEMULTICONTAINER()
```

```matlab
simpleMultiContainer = types.hdmf_common.SIMPLEMULTICONTAINER(Name, Value)
```

--------------------------------

### Apply Dataset Settings

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/compression/compression_profiles.html

Applies the custom configuration file to an existing NwbFile object.

```matlab
% Apply configuration from file to the NwbFile object
nwb.applyDatasetSettings('configuration/myprofile_dataset_configuration.json');
```

--------------------------------

### NWBFile Constructor

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/NWBFile.html

The NWBFile constructor initializes a new NWB file object. It can be instantiated empty or with name-value pairs to set properties such as acquisition, analysis, and various general metadata fields.

```APIDOC
## types.core.NWBFile

### Description
Constructor for the NWBFile class, which serves as the root container for NWB data files.

### Syntax
- `nwbFile = types.core.NWBFile()`
- `nwbFile = types.core.NWBFile(Name, Value)`

### Parameters
#### Name-Value Arguments
- **acquisition** (DynamicTable|NWBDataInterface) - Optional - Tabular data relevant to acquisition.
- **analysis** (DynamicTable|NWBContainer) - Optional - Tabular data relevant to analysis.
- **events** (EventsTable) - Optional - Collection of event times and metadata.
- **file_create_date** (datetime) - Required - Date of file creation or modification in ISO 8601 format.
- **general_experimenter** (char) - Optional - Name of person(s) who performed the experiment.
- **general_institution** (char) - Optional - Institution where the experiment was performed.
```

--------------------------------

### Constructing an IntervalSeries

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/IntervalSeries.html

Demonstrates the syntax for initializing an IntervalSeries object with or without name-value pair arguments.

```matlab
intervalSeries = types.core.INTERVALSERIES()
```

```matlab
intervalSeries = types.core.INTERVALSERIES(Name, Value)
```

--------------------------------

### Using legacy Set syntax

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/untyped.html

Legacy methods for retrieving and setting items in a Set, similar to containers.Map.

```matlab
value = someSet.get('key name');
```

```matlab
someSet.set('key name', value);
```

--------------------------------

### Construct an OpticalSeries object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/OpticalSeries.html

Create an instance of the OpticalSeries class using either default values or specified name-value pairs.

```matlab
opticalSeries = types.core.OPTICALSERIES()
```

```matlab
opticalSeries = types.core.OPTICALSERIES(Name, Value)
```

--------------------------------

### Copy and Edit Configuration File

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/compression/compression_profiles.html

Copies the default dataset configuration to a new file path and opens it for editing.

```matlab
sourceFile = fullfile(misc.getMatnwbDir, 'configuration', 'default_dataset_configuration.json');
targetFile = fullfile(misc.getMatnwbDir, 'configuration', 'myprofile_dataset_configuration.json');
copyfile(sourceFile, targetFile)
edit(targetFile)
```

--------------------------------

### Constructing an EnumData object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/hdmf_experimental/EnumData.html

Demonstrates the syntax for initializing an EnumData object using name-value pairs or default constructors.

```matlab
enumData = types.hdmf_experimental.ENUMDATA()
```

```matlab
enumData = types.hdmf_experimental.ENUMDATA(Name, Value)
```

--------------------------------

### listExtensions

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/matnwb/extension/index.html

Lists the available NWB extensions.

```APIDOC
## listExtensions

### Description
Retrieves a list of available NWB extensions.
```

--------------------------------

### Construct a Subject object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/Subject.html

Demonstrates how to instantiate a Subject object using either default values or specific name-value pairs.

```matlab
subject = types.core.SUBJECT()
```

```matlab
subject = types.core.SUBJECT(Name, Value)
```

--------------------------------

### Constructing a DecompositionSeries object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/DecompositionSeries.html

Demonstrates the syntax for initializing a DecompositionSeries object with or without name-value property pairs.

```matlab
decompositionSeries = types.core.DECOMPOSITIONSERIES()
```

```matlab
decompositionSeries = types.core.DECOMPOSITIONSERIES(Name, Value)
```

--------------------------------

### Inspect an NWB file

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/inspectNwbFile.html

Basic usage to run nwbinspector on a specified NWB file.

```matlab
report = inspectNwbFile('my_nwb_file.nwb');
```

--------------------------------

### Construct a DeviceModel object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/DeviceModel.html

Create an instance of the DeviceModel class using either default values or name-value pairs.

```matlab
deviceModel = types.core.DEVICEMODEL()
```

```matlab
deviceModel = types.core.DEVICEMODEL(Name, Value)
```

--------------------------------

### Add and Retrieve Container Entries

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/working_with_containers.html

Basic syntax for adding entries using the add() method and retrieving them via dot-indexing.

```matlab
% Use the add() method
container.add('MyTimeSeries', timeSeriesObject);
```

```matlab
% Use dot-indexing like any MATLAB property
timeSeries = container.MyTimeSeries;
```

--------------------------------

### Construct a OnePhotonSeries object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/OnePhotonSeries.html

Create an instance of the OnePhotonSeries class using either default values or specified name-value pairs.

```matlab
onePhotonSeries = types.core.ONEPHOTONSERIES()
```

```matlab
onePhotonSeries = types.core.ONEPHOTONSERIES(Name, Value)
```

--------------------------------

### Construct a Device object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/Device.html

Instantiate a Device object using either default values or name-value pairs.

```matlab
device = types.core.DEVICE()
```

```matlab
device = types.core.DEVICE(Name, Value)
```

--------------------------------

### Verify compression with h5info

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/compression/compression_profiles.html

Use h5info to inspect chunking and filter settings on an exported NWB file.

```matlab
info = h5info('example_cloud_profile.nwb', '/acquisition/ExampleSeries/data');
info.ChunkSize   % should reflect computed chunkSize
info.Filters     % lists compression + shuffle if present
```

--------------------------------

### Write Data to Scratch Space

Source: https://matnwb.readthedocs.io/en/latest/_static/html/tutorials/scratch.html

Demonstrates how to extract processed data and store it as ScratchData in a new NWB file.

```matlab
ScratchFile = NwbFile('identifier', 'SCRATCH-1'); 
ContextFile = nwbRead('./context_file.nwb', 'ignorecache'); 
% again, copy the required metadata from the processed file. 
ScratchFile.session_description = ContextFile.session_description; 
ScratchFile.session_start_time = ContextFile.session_start_time; 
% ProcessingModule stores its timeseries inside of the "nwbdatainterface" property which is a 
% Set of NWBDataInterface objects. This is not directly mapped to the NWB file but is used to 
% distinguish it and DynamicTable objects which it stores under the "dynamictable" property. 
FilteredTs = ContextFile.processing.get('core').nwbdatainterface.get('filtered_timeseries'); 
% note: MatNWB does not currently support complex numbers. If you wish to store the data, consider 
% storing each number as a struct which will write the data to HDF5 using compound types. 
dataFft = real(fft(FilteredTs.data.load())); 
ScratchData = types.core.ScratchData( ... 
'data', dataFft, ... 
'notes', 'discrete Fourier transform from filtered data' ... 
) 
ScratchData = 
ScratchData with properties: notes: 'discrete Fourier transform from filtered data' data: [11×1 double] 
ScratchFile.scratch.set('dft_filtered', ScratchData); 
nwbExport(ScratchFile, 'scratch_analysis.nwb');
```

--------------------------------

### Document Input Arguments

Source: https://matnwb.readthedocs.io/en/latest/pages/developer/documentation/formatting_docstrings.html

Detail each input argument including its type and description, using indented lists for optional parameters.

```matlab
% Input Arguments:
%  - filename (string) -
%    Filepath pointing to an NWB file.
%
%  - flags (string) -
%    Flag for setting the mode for the NWBREAD operation. Available options are:
%    'ignorecache'. If the 'ignorecache' flag is used, classes for NWB data types
%    are not re-generated based on the embedded schemas in the file.
%
%  - options (name-value pairs) -
%    Optional name-value pairs. Available options:
%
%    - savedir (string) -
%      A folder to save generated classes for NWB types.
```

--------------------------------

### nwbRead(filename, ...)

Source: https://matnwb.readthedocs.io/en/latest/pages/developer/documentation/formatting_docstrings.html

Reads an NWB file and returns an NWBFile object. Supports optional flags and name-value pairs for configuration.

```APIDOC
## nwbRead(filename, [flags], [Name, Value])

### Description
Reads the NWB file at the specified filename and returns an NWBFile object representing its contents.

### Parameters
- **filename** (string) - Required - Filepath pointing to an NWB file.
- **flags** (string) - Optional - Mode for the operation. Available option: 'ignorecache' (classes for NWB data types are not re-generated).
- **options** (name-value pairs) - Optional - Available options: 'savedir' (string) to specify a folder to save generated classes for NWB types.

### Usage Examples
- Read an NWB file: `nwb = nwbRead('data.nwb');`
- Read without re-generating classes: `nwb = nwbRead('data.nwb', 'ignorecache');`
- Read and generate classes in a specific directory: `nwb = nwbRead('data.nwb', 'savedir', '.');`

### Returns
- **nwb** (NwbFile) - Nwb file object
```

--------------------------------

### Construct an OpticalChannel object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/OpticalChannel.html

Create an instance of the OpticalChannel class using either default values or name-value pairs.

```matlab
opticalChannel = types.core.OPTICALCHANNEL()
```

```matlab
opticalChannel = types.core.OPTICALCHANNEL(Name, Value)
```

--------------------------------

### Inspect an NWB file with custom variable order

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/inspectNwbFile.html

Run nwbinspector while specifying the order of columns in the resulting report table.

```matlab
variableOrder = ["importance", "message", "check_function_name", "object_name"];
nwb = inspectNwbFile('my_nwb_file.nwb', ...
    'VariableOrder', variableOrder);
```

--------------------------------

### Download NWB Dataset via Dandi Python Package

Source: https://matnwb.readthedocs.io/en/latest/_static/html/tutorials/read_demo_dandihub.html

Configures the target directory based on the environment and executes the download command using the Python dandi interface.

```matlab
environment = "DandiHub";
switch environment
case "DandiHub"
targetFolder = "/home/jovyan/dandisets/000004";
case "Local"
targetFolder = fullfile(userpath(), "dandisets", "000004");
end
py.dandi.download.download("dandi://dandi/000004/sub-P11HMH/", targetFolder, existing='overwrite')
```

--------------------------------

### Export an NWB file using an older schema version

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/nwbExport.html

Demonstrates generating specific schema classes before exporting the NWB file.

```matlab
% Generate classes for an older version of NWB schemas:
generateCore('2.5.0')

% Create an NWB object with some properties:
nwb = NwbFile;
nwb.session_start_time = datetime('now');
nwb.identifier = 'EMPTY';
nwb.session_description = 'empty test file';

% Write the nwb object to a file:
nwbExport(nwb, 'empty.nwb');
```

--------------------------------

### Access Session Description

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/nwbfile.html

Displays the session description property of the NwbFile object.

```matlab
disp(nwb.session_description);
```

--------------------------------

### Retrieve and display extension information

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/matnwb/extension/matnwb.extension.getExtensionInfo.html

Fetches metadata for the 'ndx-miniscope' extension and prints its version to the console.

```matlab
info = matnwb.extension.getExtensionInfo('ndx-miniscope');

% Display the version of the extension.
fprintf('Extension version: %s\n', info.version);
```

--------------------------------

### Construct an EventWaveform object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/EventWaveform.html

Create an instance of the EventWaveform class using the constructor, optionally specifying properties via name-value pairs.

```matlab
eventWaveform = types.core.EVENTWAVEFORM()
```

```matlab
eventWaveform = types.core.EVENTWAVEFORM(Name, Value)
```

--------------------------------

### Configure legacy display mode

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/working_with_containers.html

Set the ContainerDisplayMode preference to legacy to mimic older MatNWB versions.

```matlab
% Set legacy display mode
setpref('matnwb', 'ContainerDisplayMode', 'legacy');
disp(processingModule);
```

```matlab
ProcessingModule with properties:

        description: 'My processing module'
    nwbdatainterface: [1×1 types.untyped.Set]
        dynamictable: [1×1 types.untyped.Set]
```

--------------------------------

### LabMetaData()

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/LabMetaData.html

Constructor for creating a new LabMetaData object.

```APIDOC
## LabMetaData()

### Description
Creates a new instance of the LabMetaData class for storing lab-specific metadata.

### Syntax
`labMetaData = types.core.LABMETADATA()`

### Output Arguments
- **labMetaData** (types.core.LabMetaData) - A new LabMetaData object with unset property values.
```

--------------------------------

### Construct an ImagingRetinotopy object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/ImagingRetinotopy.html

Create an instance of the ImagingRetinotopy class using either default values or name-value pairs.

```matlab
imagingRetinotopy = types.core.IMAGINGRETINOTOPY()
```

```matlab
imagingRetinotopy = types.core.IMAGINGRETINOTOPY(Name, Value)
```

--------------------------------

### Construct an OptogeneticSeries object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/OptogeneticSeries.html

Create an instance of OptogeneticSeries with either default values or specified name-value pairs.

```matlab
optogeneticSeries = types.core.OPTOGENETICSERIES()
```

```matlab
optogeneticSeries = types.core.OPTOGENETICSERIES(Name, Value)
```

--------------------------------

### Load Full Dataset

Source: https://matnwb.readthedocs.io/en/latest/_static/html/tutorials/read_demo_dandihub.html

Use the load method on a DataStub to read an entire dataset into memory.

```matlab
stimulus_times = nwb.stimulus_presentation.get('StimulusPresentation').timestamps.load();
```

--------------------------------

### Construct a SimultaneousRecordingsTable

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/SimultaneousRecordingsTable.html

Syntax for initializing a SimultaneousRecordingsTable object with or without name-value pair arguments.

```matlab
simultaneousRecordingsTable = types.core.SIMULTANEOUSRECORDINGSTABLE()
```

```matlab
simultaneousRecordingsTable = types.core.SIMULTANEOUSRECORDINGSTABLE(Name, Value)
```

--------------------------------

### Constructing an ExternalImage object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/ExternalImage.html

Demonstrates the syntax for initializing an ExternalImage object with or without name-value pairs.

```matlab
externalImage = types.core.EXTERNALIMAGE()
externalImage = types.core.EXTERNALIMAGE(Name, Value)
```

--------------------------------

### Define and assign Subject metadata

Source: https://matnwb.readthedocs.io/en/latest/pages/tutorials/ogen.html

Create a Subject object to store experimental subject details and attach it to the NWBFile.

```matlab
subject = types.core.Subject( ...
'subject_id', '001', ...
'age', 'P90D', ...
'description', 'mouse 1', ...
'species', 'Mus musculus', ...
'sex', 'M' ...
);
nwb.general_subject = subject;
```

--------------------------------

### Document Function Syntax

Source: https://matnwb.readthedocs.io/en/latest/pages/developer/documentation/formatting_docstrings.html

List all possible function signatures and describe their specific behaviors.

```matlab
% Syntax:
%  nwb = NWBREAD(filename) Reads the nwb file at filename and returns an
%  NWBFile object representing its contents.
%
%  nwb = NWBREAD(filename, flags) Reads the nwb file using optional
%  flags controlling the mode for how to read the file. See input
%  arguments for a list of available flags.
%
%  nwb = NWBREAD(filename, Name, Value) Reads the nwb file using optional
%  name-value pairs controlling options for how to read the file.
```

--------------------------------

### Add an OptogeneticStimulusSite

Source: https://matnwb.readthedocs.io/en/latest/pages/tutorials/ogen.html

Define the stimulus site metadata and add it to the NWB file's general optogenetics section.

```matlab
ogen_stim_site = types.core.OptogeneticStimulusSite( ...
'device', types.untyped.SoftLink(device), ...
'description', 'This is an example optogenetic site.', ...
'excitation_lambda', 600.0, ...
'location', 'VISrl');
nwb.general_optogenetics.set('OptogeneticStimulusSite', ogen_stim_site);
```

--------------------------------

### Manage Parallel MATLAB Sessions with Custom Directories

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/schemas_and_generation.html

Use separate directories for generated classes when running multiple MATLAB sessions to prevent file conflicts.

```matlab
nwbClearGenerated();  % Clear previously generated classes

% Session 1: Generate classes in a temporary directory
session1_dir = '/tmp/matlab_session_1_classes';
generateCore('savedir', session1_dir);

% Session 2: Use different temporary directory in parallel session 2
session2_dir = '/tmp/matlab_session_2_classes';
generateCore('savedir', session2_dir);
```

--------------------------------

### Construct TimeIntervals objects

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/TimeIntervals.html

Demonstrates the syntax for initializing a TimeIntervals object with or without name-value pair arguments.

```matlab
timeIntervals = types.core.TIMEINTERVALS()
```

```matlab
timeIntervals = types.core.TIMEINTERVALS(Name, Value)
```

--------------------------------

### Write Data to Scratch Space

Source: https://matnwb.readthedocs.io/en/latest/pages/tutorials/scratch.html

Demonstrates how to extract processed data, perform additional analysis, and store it using the ScratchData type.

```matlab
ScratchFile = NwbFile('identifier', 'SCRATCH-1'); 
ContextFile = nwbRead('./context_file.nwb', 'ignorecache'); 
% again, copy the required metadata from the processed file. 
ScratchFile.session_description = ContextFile.session_description; 
ScratchFile.session_start_time = ContextFile.session_start_time; 
% ProcessingModule stores its timeseries inside of the "nwbdatainterface" property which is a 
% Set of NWBDataInterface objects. This is not directly mapped to the NWB file but is used to 
% distinguish it and DynamicTable objects which it stores under the "dynamictable" property. 
FilteredTs = ContextFile.processing.get('core').nwbdatainterface.get('filtered_timeseries'); 
% note: MatNWB does not currently support complex numbers. If you wish to store the data, consider 
% storing each number as a struct which will write the data to HDF5 using compound types. 
dataFft = real(fft(FilteredTs.data.load())); 
ScratchData = types.core.ScratchData( ... 
'data', dataFft, ... 
'notes', 'discrete Fourier transform from filtered data' ... 
) 
ScratchFile.scratch.set('dft_filtered', ScratchData); 
nwbExport(ScratchFile, 'scratch_analysis.nwb');
```

--------------------------------

### NwbFile.searchFor(type, options)

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/nwbfile.html

Searches for objects of a specific type within the NWB file. Returns a containers.Map where keys are paths and values are the objects.

```APIDOC
## NwbFile.searchFor

### Description
Searches for specific types of data across the entire NWB file. Returns a MATLAB containers.Map object containing the paths and data objects found.

### Signature
`map = nwb.searchFor(type)`
`map = nwb.searchFor(type, 'includeSubClasses')`

### Parameters
- **type** (string) - Required - The name of the NWB schema-defined type to search for (e.g., 'ElectricalSeries').
- **'includeSubClasses'** (string) - Optional - A flag to include specialized subclasses of the specified type in the search results.

### Returns
- **map** (containers.Map) - A map where keys are the file paths to the objects and values are the actual data objects.

### Example
```matlab
% Basic search
electricalseries_map = nwb.searchFor('ElectricalSeries');

% Search including subclasses
all_timeseries = nwb.searchFor('TimeSeries', 'includeSubClasses');
```
```

--------------------------------

### Construct an ImagingPlane object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/ImagingPlane.html

Create an instance of the ImagingPlane class using either default values or specified name-value pairs.

```matlab
imagingPlane = types.core.IMAGINGPLANE()
```

```matlab
imagingPlane = types.core.IMAGINGPLANE(Name, Value)
```

--------------------------------

### Construct a TwoPhotonSeries object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/TwoPhotonSeries.html

Create a new instance of the TwoPhotonSeries class, either empty or with specified name-value pairs.

```matlab
twoPhotonSeries = types.core.TWOPHOTONSERIES()
```

```matlab
twoPhotonSeries = types.core.TWOPHOTONSERIES(Name, Value)
```

--------------------------------

### Troubleshooting Version Conflicts

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/schemas_and_generation.html

Clear the workspace and generated classes before regenerating core classes for a specific file version to resolve compatibility errors.

```matlab
clear all;  % Clear workspace to avoid conflicts
nwbClearGenerated();  % Clear previously generated classes

% Check the file's schema version
file_version = util.getSchemaVersion('problematic_file.nwb');

% Generate classes for that specific version
generateCore(file_version);

% Try reading again
nwb = nwbRead('problematic_file.nwb');
```

--------------------------------

### Constructing an Images object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/Images.html

Create an instance of the Images class using either default values or name-value pairs.

```matlab
images = types.core.IMAGES()
```

```matlab
images = types.core.IMAGES(Name, Value)
```

--------------------------------

### Export an NWB file using dataset settings tuned for cloud storage

Source: https://matnwb.readthedocs.io/en/latest/pages/functions/nwbExport.html

Applies a predefined 'cloud' configuration profile for dataset chunking and compression during export.

```matlab
nwbExport(nwb, 'empty.nwb', 'DatasetSettingsProfile', 'cloud');
```

--------------------------------

### Check NWB Schema Version

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/schemas_and_generation.html

Retrieves and displays the schema version used to create a specific NWB file.

```matlab
version = util.getSchemaVersion('path/to/file.nwb');
fprintf('File uses NWB schema version: %s\n', version);
```

--------------------------------

### Generate Schemas for Older Files

Source: https://matnwb.readthedocs.io/en/latest/pages/concepts/file_read/troubleshooting.html

Manually generate core and extension schemas for NWB files that lack embedded schema information.

```matlab
schemaVersion = util.getSchemaVersion('/path/to/matnwb/file.nwb');
generateCore(schemaVersion);
generateExtension(path/to/extension/namespace.yaml);
```

--------------------------------

### Construct an IntracellularElectrode object

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/IntracellularElectrode.html

Demonstrates the syntax for creating an IntracellularElectrode object with or without name-value pairs.

```matlab
intracellularElectrode = types.core.INTRACELLULARELECTRODE()
```

```matlab
intracellularElectrode = types.core.INTRACELLULARELECTRODE(Name, Value)
```

--------------------------------

### types.core.GrayscaleImage

Source: https://matnwb.readthedocs.io/en/latest/pages/neurodata_types/core/GrayscaleImage.html

Constructor for creating a GrayscaleImage object. Users can initialize the object with optional name-value pairs for data, description, and resolution.

```APIDOC
## Constructor: types.core.GrayscaleImage

### Description
Creates a new GrayscaleImage object. This can be initialized with empty values or via name-value pairs.

### Syntax
- `grayscaleImage = types.core.GRAYSCALEIMAGE()`
- `grayscaleImage = types.core.GRAYSCALEIMAGE(Name, Value)`

### Input Arguments (Name-Value Pairs)
- **data** (numeric) - Required - The image data.
- **description** (char) - Optional - Description of the image.
- **resolution** (single) - Optional - Pixel resolution of the image, in pixels per centimeter.

### Output Arguments
- **grayscaleImage** (types.core.GrayscaleImage) - The initialized GrayscaleImage object.
```

--------------------------------

### Configure flat display mode

Source: https://matnwb.readthedocs.io/en/latest/pages/how_to/working_with_containers.html

Set the ContainerDisplayMode preference to flat to list all entries without nesting.

```matlab
% Set flat display mode
setpref('matnwb', 'ContainerDisplayMode', 'flat');
disp(processingModule);
```

```matlab
ProcessingModule with properties:

     description: 'My processing module'
       DataTable: [1×1 types.hdmf_common.DynamicTable]
  NeuralActivity: [1×1 types.core.TimeSeries]
```
Tokens:
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