vatthaphon / matnwb

A Matlab interface for reading and writing NWB files

MatNWB

A Matlab interface for reading and writing Neurodata Without Borders (NWB) 2.0 files.

Setup

Step 1: Download MatNWB

Download the current release of MatNWB from the MatNWB releases page or from the . You can also check out the latest development version via

git clone https://github.com/NeurodataWithoutBorders/matnwb.git

Step 2: Generate the API

From the Matlab command line, add MatNWB to the Matlab path and generate the core classes for the NWB schema.

cd matnwb
addpath(genpath(pwd));
generateCore(); % generate core namespace located in the repository.

Optional: Generate MatNWB code for extensions

The generateCore command also takes variable arguments from any extensions.

generateCore('schema/core/nwb.namespace.yaml', '.../my_extensions1.namespace.yaml',...);

You can also generate extensions without generating the core classes in this way:

generateExtension('my_extension.namespace.yaml');

Generated Matlab code will be put a +types subdirectory. This is a Matlab package. When the +types folder is accessible to the Matlab path, the generated code will be used for reading NWBFiles.

nwb=nwbRead('data.nwb');

Optional: Download the NWB format schema

Download the current release of the NWB format schema from the nwb-schema releases page or check out the latest development via

git clone --recursive https://github.com/NeurodataWithoutBorders/nwb-schema.git

Then re-run generateCore() to update the API from the updated schema.

Tutorials

Extracellular Electrophysiology

Calcium Imaging

Intracellular Electrophysiology

Advanced data write

API Documentation

For more information regarding the MatNWB API or any of the NWB Core types in MatNWB, visit the MatNWB API Documentation pages.

How does it work

NWB files are HDF5 files with data stored according to the Neurodata Without Borders: Neurophysiology (NWB:N) schema. The schema is described in a set of yaml documents. These define the various types and their attributes.

This package provides two functions generateCore and generateExtension that transform the yaml files that describe the schema into Matlab m-files. The generated code defines classes that reflect the types defined in the schema. Object attributes, relationships, and documentation are automatically generated to reflect the schema where possible.

Once the code generation step is done, NWB objects can be read, constructed and written from Matlab.

PyNWB's cached schemas are also supported, bypassing the need to run generateCore or generateExtension if present.

Sources

MatNWB is available online at https://github.com/NeurodataWithoutBorders/matnwb

Caveats

The NWB:N schema is in a state of some evolution. This package assumes a certain set of rules are used to define the schema. As the schema is updated, some of the rules may be changed and these will break this package.

For those planning on using matnwb alongside pynwb, please keep the following in mind:

• The ordering of dimensions in MATLAB are reversed compared to numpy (and pynwb). Thus, a 3-D SpikeEventSeries, which in pynwb would normally be indexed in order (num_samples, num_channels, num_events), would be indexed in form (num_events, num_channels, num_samples) in MatNWB.
• MatNWB is dependent on the schema, which may not necessary correspond with your PyNWB schema version. Please consider overwriting the contents within MatNWB's ~/schema/core directory with the generating PyNWB's src/pynwb/data directory and running generateCore to ensure compatibilty between systems.

The master branch in this repository is considered perpetually unstable. If you desire matnwb's full functionality (full round-trip with nwb data), please consider downloading the more stable releases in the Releases tab. Keep in mind that the Releases are generally only compatible with older versions of pynwb and may not supported newer data types supported by pynwb (such as data references or compound types). Most releases will coincide with nwb-schema releases and contain compatibility with those features.

This package reads and writes NWB:N 2.0 files and does not support older formats.

Examples

Basic Data Retrieval | showcases how one would read and process converted NWB file data to display a raster diagram.

Conversion of Real Electrophysiology/Optophysiology Data | converts Electrophysiology/Optophysiology Data recorded from:

Li, Daie, Svoboda, Druckman (2016); Data and simulations related to: Robust neuronal dynamics in premotor cortex during motor planning. Li, Daie, Svoboda, Druckman, Nature. CRCNS.org http://dx.doi.org/10.6080/K0RB72JW

Third-party Support

The +contrib folder contains tools for converting from other common data formats/specifications to NWB. Currently supported data types are TDT, MWorks, and Blackrock. We are interested in expanding this section to other data specifications and would greatly value your contribution!

Testing

Run the test suite with nwbtest.

FAQ

1. "A class definition must be in an "@" directory."

Make sure that there are no "@" signs anywhere in your full file path. This includes even directories that are not part of the matnwb root path and any "@" signs that are not at the beginning of the directory path.

Alternatively, this issue disappears after MATLAB version 2017b. Installing this version may also resolve these issues. Note that the updates provided with 2017b should also be installed.