### MATLAB Usage Examples

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

Provide practical examples of function usage, each starting with 'Example X - Description::'. Include indented MATLAB code blocks with explanatory comments.

```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', '.');

```

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

### Install MatNWB from Source

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

Use these commands to clone the MatNWB repository and add it to your MATLAB path. This is the recommended method for installation.

```matlab
!git clone https://github.com/NeurodataWithoutBorders/matnwb.git
addpath(genpath(pwd));
```

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

### Retrieve All ElectricalSeries Objects

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

This example shows how to get all objects of the 'ElectricalSeries' type from an NwbFile object. It requires running an initialization script 'ecephys.mlx' beforehand.

```matlab
evalc('run("ecephys.mlx")');
nwb.getTypeObjects('ElectricalSeries')
```

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

### Install MatNWB from Source

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

Installs the MatNWB library from GitHub if it's not already on the MATLAB search path. Ensure Git is installed and accessible.

```matlab
if ~exist('nwbRead', 'file') % Skip if MatNWB is on MATLAB's search path
!git clone https://github.com/NeurodataWithoutBorders/matnwb.git
% add the path to matnwb and generate the core classes
addpath('matnwb');
end
```

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

### Install MatNWB from Source

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

Use these commands to clone the MatNWB repository and add it to your MATLAB path. This is the recommended way to install MatNWB.

```matlab
!git clone https://github.com/NeurodataWithoutBorders/matnwb.git
addpath(genpath(pwd));

```

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

### Install hdf5plugin and Get Plugin Path (Windows)

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

Install the hdf5plugin Python package and retrieve the plugin path. This path will be used to set the HDF5_PLUGIN_PATH environment variable.

```bash
pip install hdf5plugin
```

```bash
python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)"
```

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

### Quick Install MatNWB from GitHub

Source: https://matnwb.readthedocs.io/en/latest/pages/getting_started/installation.html

Clones MatNWB into the current directory, adds it to the MATLAB path, and optionally persists the change. Requires git.

```matlab
!git clone https://github.com/NeurodataWithoutBorders/matnwb.git
addpath("matnwb")
% Optional: persist for future MATLAB sessions
savepath()

```

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

### Setup Environment with Acquired Data

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

Initializes an NWBFile with required metadata and simulates acquired data as a TimeSeries object. This sets up the context for demonstrating scratch space usage.

```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);
% "Analyze" the simulated data
% We provide a re-implementation of scipy.signal.correlate(..., mode='same')
% Ideally, you should use MATLAB-native code though using its equivalent 
% function (xcorr) requires the Signal Processing Toolbox
correlatedData = sameCorr(RawTs.data, ones(128, 1)) ./ 128;
% If you are unsure of how HDF5 paths map to MatNWB property structures, we 
% suggest using HDFView to verify. In most cases, MatNWB properties map 
% directly to HDF5 paths.
FilteredTs = types.core.TimeSeries( ...
'data', correlatedData, ...
'data_unit', 'm',
'starting_time', 0,
'starting_time_rate', 100,
'description', 'cross-correlated data' ...
)
FilteredTs = 
TimeSeries with properties: starting_time_unit: 'seconds' timestamps_interval: 1 timestamps_unit: 'seconds' data: [-0.0062 -0.0062 -0.0062 -0.0062 -0.0062 -0.0062 -0.0062 -0.0062 -0.0062 -0.0062 -0.0062] data_unit: 'm' comments: 'no comments' control: [] control_description: '' data_continuity: '' data_conversion: 1 data_offset: 0 data_resolution: -1 description: 'cross-correlated data' starting_time: 0 starting_time_rate: 100 timestamps: [] 
ProcModule = types.core.ProcessingModule( ...
'description', 'a module to store filtering results',
'filtered_timeseries', FilteredTs ...
);
ContextFile.processing.set('core', ProcModule);
nwbExport(ContextFile, 'context_file.nwb');
```

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

### Retrieve ElectricalSeries and Subtype Objects

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

This example retrieves all 'ElectricalSeries' objects and any objects of its subtypes from an NwbFile. Ensure 'ecephys.mlx' is run prior to execution.

```matlab
evalc('run("ecephys.mlx")')
nwb.getTypeObjects('ElectricalSeries', 'IncludeSubTypes', true)
```

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

### Create a New NWB File

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

Initialize a new NWBFile object with required metadata such as session description, identifier, and start time. Optional fields can also be included.

```matlab
nwb = NwbFile(
'session_description', 'mouse in open exploration',
'identifier', 'Mouse5_Day3',
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'),
'general_experimenter', 'Last, First', ... % 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
```

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

### Create Minimal NWB File Object

Source: https://matnwb.readthedocs.io/en/latest/pages/getting_started/quickstart.html

Initializes an NwbFile object with required metadata: identifier, session description, and session start time.

```matlab
nwb = NwbFile(
    'identifier', 'quickstart-demo-20250411T153000Z',
    'session_description', 'Quickstart demo session',
    'session_start_time', datetime(2025,4,11,15,30,0,'TimeZone','UTC'));

```

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

### Create NWB File with Metadata

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

Initializes a new NWBFile object with essential metadata like session description, identifier, and start time. Uses keyword argument pairs for configuration.

```matlab
nwb = NwbFile( ...
'session_description', 'mouse in open exploration',
'identifier', 'Mouse5_Day3', ...
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'), ...
'timestamps_reference_time', datetime(2018, 4, 25, 3, 0, 45, 'TimeZone', 'local'), ...
'general_experimenter', 'LastName, FirstName', ... % 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
```

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

### Determine Plugin Path (Windows)

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

Determine the installation path of the hdf5plugin by running a Python command in the Command Prompt. This path is needed to set the environment variable.

```bash
python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)"
```

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

### Initialize Scratch NWBFile and Read Context File

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

Creates a new NWBFile for scratch data and reads an existing NWB file containing processed data. Essential metadata is copied from the context file to the scratch 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;
```

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

### Verify MatNWB Installation

Source: https://matnwb.readthedocs.io/en/latest/pages/getting_started/installation.html

Checks if MatNWB is installed by retrieving its version information. If the folder name differs, update 'matnwb' accordingly.

```matlab
versionInfo = ver("matnwb")

```

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

### Install NWB Extension

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

Installs a specified NWB extension by its name. The extension name must be a valid name from the Neurodata Extensions Catalog.

```APIDOC
## nwbInstallExtension

### Description
Installs a specified NWB extension to extend the functionality of the core NWB schemas. Accepts a scalar string or a string array of extension names.

### Syntax
nwbInstallExtension(_extensionNames_ , _options_)

### Parameters
#### Path Parameters
- **extensionNames** (string or string array) - Required - The name(s) of the NWB extension(s) to install from the Neurodata Extensions Catalog.

#### Query Parameters
- **options** (object) - Optional - Additional options for installation (details not provided in source).

### Usage
**Example 1 - Install “ndx-miniscope” extension** :
```matlab
nwbInstallExtension("ndx-miniscope")
```

### See also
`matnwb.extension.listExtensions()`, `matnwb.extension.installExtension()`
```

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

### Initialize NWBFile with Required Metadata

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

Initializes an NWBFile object with essential session information. Ensure 'session_description', 'identifier', and 'session_start_time' are provided.

```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' ...
);
```

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

### Install hdf5plugin (Linux/Mac)

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

Install the hdf5plugin Python package using pip. This package helps manage dynamically loaded filters for HDF5.

```bash
pip install hdf5plugin
```

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

### Install a Published 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 Neurodata Extension. Replace 'ndx-extension' with the actual name of the extension you want to install.

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

```

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

### Install hdf5plugin and Set Environment Variable (Linux/Mac)

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

Install the hdf5plugin Python package and set the HDF5_PLUGIN_PATH environment variable in your terminal. This is necessary to enable dynamically loaded filters in MATLAB.

```bash
pip install hdf5plugin
```

```bash
export HDF5_PLUGIN_PATH=$(python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)")
```

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

### Create NWB File with Session Metadata

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

Initialize an NWBFile object with essential session details and optional metadata. Ensure 'session_description', 'identifier', and 'session_start_time' are provided.

```matlab
nwb = NwbFile( ...
'session_description', 'mouse in open exploration',
'identifier', 'Mouse5_Day3',
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'),
'general_experimenter', 'My Name', ... % 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

```

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

### Create and Add OptogeneticStimulusSite

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

Create a Device object, link it to the NWBFile, and then create and add an OptogeneticStimulusSite. This site contains metadata about the stimulus location and properties.

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

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)
```

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

### Install a Single NWB Extension

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

Use this function to install a single NWB extension by providing its name as a string. Ensure the extension name is valid and available in the Neurodata Extensions Catalog.

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

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

### Store Running Intervals

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

Use IntervalSeries within BehavioralEpochs to store time intervals, marking the start and end of an activity. Data values of 1 and -1 indicate interval start and end, respectively.

```matlab
run_intervals = types.core.IntervalSeries( ...
'description', 'Intervals when the animal was running.', ...
'data', [1, -1, 1, -1, 1, -1], ...
'timestamps', [0.5, 1.5, 3.5, 4.0, 7.0, 7.3] ...
);
behavioral_epochs = types.core.BehavioralEpochs();
behavioral_epochs.intervalseries.set('running', run_intervals);
```

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

### IZeroClampSeries Data

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

Example of creating an IZeroClampSeries object for recordings where current is clamped to 0. Ensure 'electrode' is a valid object.

```matlab
% Create an IZeroClampSeries object
izcs = types.core.IZeroClampSeries(... 
'data', [0.1, 0.2, 0.3, 0.4, 0.5], ...
'electrode', types.untyped.SoftLink(electrode), ...
'gain', 0.02, ...
'data_conversion', 1e-12, ...
'data_resolution', NaN, ...
'starting_time', 345.6, ...
'starting_time_rate', 20e3, ...
'sweep_number', uint64(17) ...
);
nwbfile.acquisition.set('IZeroClampSeries', izcs);
```

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

### Create NWBFile Object

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

Initialize an NWBFile object with required fields and optional metadata. Ensure session_start_time is a datetime object with timezone information.

```matlab
nwb = NwbFile( ...
'session_description', 'mouse in open exploration',
'identifier', 'Mouse5_Day3',
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'), ...
'general_experimenter', 'My Name', ... % 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
```

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

### Create and Add ProcessingModule

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

Organize processed data into ProcessingModules. This example creates a 'behavior' module and adds a 'Position' object to it.

```matlab
% create processing module
behavior_module = types.core.ProcessingModule('description', 'contains behavioral data');
% add the Position object (that holds the SpatialSeries object) to the module 
% and name the Position object "Position"
behavior_module.nwbdatainterface.set('Position', position);
% add the processing module to the NWBFile object, and name the processing module "behavior"
nwb.processing.set('behavior', behavior_module);
```

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

### Create NWB with Default Chunking

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

Demonstrates creating an NWB file with a DataPipe using default chunking. This is useful for understanding the baseline performance before manual optimization.

```matlab
fData = randi(250, 100, 1000); % Create fake data

% create an nwb structure with required fields
nwb = NwbFile( ...
    'session_start_time', datetime('2020-01-01 00:00:00', 'TimeZone', 'local'), ...
    'identifier', 'ident1',
    'session_description', 'DataPipeTutorial');

fData_compressed = types.untyped.DataPipe('data', fData);

fdataNWB=types.core.TimeSeries( ...
    'data', fData_compressed,
    'data_unit', 'mV',
    'starting_time', 0.0,
    'starting_time_rate', 30.0);

nwb.acquisition.set('data', fdataNWB);

nwbExport(nwb, 'DefaultChunks.nwb');


```

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

### Get Spike Times for a Unit

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

Retrieve the spike times for a specific unit from the NWB file using the getRow method.

```matlab
% You can use the getRow method of the table to load spike times of a specific unit.
% To get the values, unpack from the returned table.
nwb.units.getRow(1).spike_times{1}
```

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

### Inspect an NWB file

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

Use this snippet to run nwbinspector on an NWB file and get a basic report of potential issues.

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

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

### Create and Link Device for Optogenetics

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

Create a Device object and link it to the NWBFile. This is a prerequisite for adding optogenetic stimulus sites.

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

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

### Add IntracellularResponsesTable

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

Define the IntracellularResponsesTable to store recorded response data, linking to TimeSeries objects with their respective start indices and counts.

```matlab
ic_rec_table.responses = types.core.IntracellularResponsesTable( ...
'description', 'Table for storing intracellular response related metadata.', ...
'colnames', {'response'}, ...
'id', types.hdmf_common.ElementIdentifiers( ...
'data', int64([0; 1; 2]) ...
),
'response', types.core.TimeSeriesReferenceVectorData( ...
'description', ['Column storing the reference to the recorded response ',
'for the recording (rows)'], ...
'data', struct( ...
'idx_start', [0, 2, 0],
'count', [5, 3, 5],
'timeseries', [ ...
types.untyped.ObjectView(vcs), ... % Voltage clamp response
types.untyped.ObjectView(ccs), ... % Current clamp response
types.untyped.ObjectView(izcs) ... % Current clamp response when current is off
]
)
)
);
```

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

### Read and Display NWB File Contents

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

This snippet demonstrates how to run a tutorial script to generate an NWB file and then read it using `nwbRead`. The `disp(nwb)` command shows the structure and properties of the loaded NwbFile object.

```matlab
evalc("run('tutorials/ecephys.mlx')"); % Run tutorial with suppressed output
nwb = nwbRead('tutorials/ecephys_tutorial.nwb');
disp(nwb)
```

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

### Access Specific Dataset from Acquisition Set

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

Retrieve a specific dataset, such as 'ElectricalSeries', from the acquisition Set object using the `get()` method.

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

```

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

### Get NWB Schema Version

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

Retrieves the schema version used to create an NWB file. Ensure the file path is correct.

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

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

### Create NWBFile Object

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

Initializes an NWBFile object with essential session metadata. Ensure the session_start_time is timezone-aware.

```python
session_start_time = datetime(2018, 3, 1, 12, 0, 0, 'TimeZone', 'local');
nwbfile = NwbFile(
'session_description', 'my first synthetic recording',
'identifier', 'EXAMPLE_ID',
'session_start_time', session_start_time,
'general_experimenter', 'Dr. Bilbo Baggins',
'general_lab', 'Bag End Laboratory',
'general_institution', 'University of Middle Earth at the Shire',
'general_experiment_description', ['I went on an adventure with thirteen dwarves ',
'to reclaim vast treasures.'],
'general_session_id', 'LONELYMTN'
);
```

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

### Create NWBFile Object with Metadata

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

Initialize an NWBFile object with essential session metadata. Arguments are passed as name-value pairs.

```matlab
nwb = NwbFile(
'session_description', 'mouse in open exploration',
'identifier', 'Mouse5_Day3',
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'),
'timestamps_reference_time', datetime(2018, 4, 25, 3, 0, 45, 'TimeZone', 'local'),
'general_experimenter', 'LastName, FirstName', ... % 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
```

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

### Get Keys from Analysis Set

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

Retrieves all property keys from the 'analysis' property of an NWB file, similar to MATLAB's containers.Map.

```matlab
unit_names = keys(nwb.analysis);
```

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

### Construct and Export a Simple NwbFile Object

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

Demonstrates how to create a basic NwbFile object, assign an Epochs object to it, and then export it to an NWB file. Ensure the 'types.core.Epochs' is available in your MATLAB path.

```matlab
nwb = NwbFile;
nwb.epochs = types.core.Epochs;
nwbExport(nwb, 'epoch.nwb');
```

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

### Accessing Stimulus Image Data

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

Get the data attribute from the StimulusPresentation OpticalSeries. This returns a DataStub, which is a lazy representation of the image data.

```matlab
StimulusImageData = nwb.stimulus_presentation.get('StimulusPresentation').data
```

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

### Update MatNWB via Git

Source: https://matnwb.readthedocs.io/en/latest/pages/getting_started/installation.html

Updates the MatNWB installation by pulling the latest changes from the Git repository. Navigate to the MatNWB directory first.

```bash
cd path/to/matnwb
!git pull

```

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

### NWBREAD Function Documentation

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

This section details the NWBREAD function, explaining its syntax, input arguments (filename, flags, name-value pairs), and output arguments. It also provides usage examples for reading NWB files with different options.

```matlab
% NWBREAD - Read an NWB file.
% 
% 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.
% 
% 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.
% 
% Output Arguments:
%  - nwb (NwbFile) - Nwb file object
% 
% 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', '.');
% 
% See also:
%   generateCore, generateExtension, NwbFile, nwbExport

```

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

### Compress and Add Timeseries Data to NWB

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

This example demonstrates how to create fake data, compress it using DataPipe with specified compression level and chunk size, and then assign it to a TimeSeries object within an NWB file. It also shows how to export the NWB file.

```matlab
fData=randi(250, 1, 10000);

%assign data without compression
nwb=NwbFile(
    'session_start_time', datetime(2020, 1, 1, 0, 0, 0, 'TimeZone', 'local'), 
    'identifier','ident1',
    'session_description', 'DataPipeTutorial');

ephys_module = types.core.ProcessingModule(
    'description', 'holds processed ephys data');

nwb.processing.set('ephys', ephys_module);

% compress the data
fData_compressed=types.untyped.DataPipe(
    'data', fData,
    'compressionLevel', 3,
    'chunkSize', [100 1],
    'axis', 1);

% Assign the data to appropriate module and write the NWB file
fdataNWB=types.core.TimeSeries(
    'data', fData_compressed,
    'data_unit', 'mV',
    'starting_time', 0.0,
    'starting_time_rate', 30.0);

ephys_module.nwbdatainterface.set('data', fdataNWB);
nwb.processing.set('ephys', ephys_module);

% write the file
nwbExport(nwb, 'Compressed.nwb');

```

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

### Set HDF5_PLUGIN_PATH (Linux/Mac)

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

Set the HDF5_PLUGIN_PATH environment variable to the location of the installed hdf5plugin filters. This allows MATLAB to find and use the filters.

```bash
export HDF5_PLUGIN_PATH=$(python -c "import hdf5plugin; print(hdf5plugin.PLUGINS_PATH)")
```

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

### Create NWBFile Object

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

Initialize an NWBFile object with essential session metadata. This is the first step when creating a new NWB file.

```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
```

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

### Create NWB with Default Chunking

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

Demonstrates creating an NWB file with a TimeSeries using DataPipe's default chunking. This is useful for understanding the baseline performance before manual optimization.

```matlab
fData = randi(250, 100, 1000);

% create an nwb structure with required fields
nwb = NwbFile(
    'session_start_time', datetime('2020-01-01 00:00:00', 'TimeZone', 'local'),
    'identifier', 'ident1',
    'session_description', 'DataPipeTutorial');

fData_compressed = types.untyped.DataPipe('data', fData);

fdataNWB=types.core.TimeSeries(
    'data', fData_compressed,
    'data_unit', 'mV',
    'starting_time', 0.0,
    'starting_time_rate', 30.0);

nwb.acquisition.set('data', fdataNWB);

nwbExport(nwb, 'DefaultChunks.nwb');

```

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

### Create Regularly Sampled TimeSeries

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

Use TimeSeries for data sampled at regular intervals. Specify the starting time and sampling rate for efficiency.

```matlab
time_series_with_rate = types.core.TimeSeries( ...
'description', 'an example time series', ...
'data', linspace(0, 100, 10), ...
'data_unit', 'm', ...
'starting_time', 0.0, ...
'starting_time_rate', 1.0);
```

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

### Current Clamp Stimulus and Response Data

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

Example of creating and setting CurrentClampStimulusSeries and CurrentClampSeries for a current clamp recording. Ensure 'electrode' is a valid object.

```matlab
% Create a CurrentClampStimulusSeries object
ccss = types.core.CurrentClampStimulusSeries(... 
'data', [1, 2, 3, 4, 5], ...
'starting_time', 123.6, ...
'starting_time_rate', 10e3, ...
'electrode', types.untyped.SoftLink(electrode), ...
'gain', 0.02, ...
'sweep_number', uint64(16), ...
'stimulus_description', 'N/A' ...
);
nwbfile.stimulus_presentation.set('CurrentClampStimulusSeries', ccss);
% Create a CurrentClampSeries object
ccs = types.core.CurrentClampSeries(... 
'data', [0.1, 0.2, 0.3, 0.4, 0.5], ...
'data_conversion', 1e-12, ...
'data_resolution', NaN, ...
'starting_time', 123.6, ...
'starting_time_rate', 20e3, ...
'electrode', types.untyped.SoftLink(electrode), ...
'gain', 0.02, ...
'bias_current', 1e-12, ...
'bridge_balance', 70e6, ...
'capacitance_compensation', 1e-12, ...
'stimulus_description', 'N/A', ...
'sweep_number', uint64(16) ...
);
nwbfile.acquisition.set('CurrentClampSeries', ccs);
```

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

### Create NWB File

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

Initializes a new NWB file with essential session metadata. Ensure timestamps are correctly set with timezone information.

```matlab
nwb = NwbFile( ...
'session_description', 'mouse in open exploration',
'identifier', 'Mouse5_Day3',
'session_start_time', datetime(2018, 4, 25, 2, 30, 3, 'TimeZone', 'local'), ...
'timestamps_reference_time', datetime(2018, 4, 25, 3, 0, 45, 'TimeZone', 'local'), ...
'general_experimenter', 'LastName, FirstName', ... % 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
);
```

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

### Create and Export NWB File

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

Instantiate an NwbFile object with essential session information and assign the created TimeIntervals table to the 'intervals_trials' property. Finally, export the NWB file.

```matlab
% Create NwbFile object with required arguments
file = NwbFile( ...
'session_start_time', datetime('2022-01-01 00:00:00', 'TimeZone', 'local'), ...
'identifier', 'ident1',
'session_description', 'test file' ...
);
% Assign to intervals_trials
file.intervals_trials = trials_table;
% Export
nwbExport(file, 'testFileNoDataPipes.nwb');

```