matnwb

MatNWB

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

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.

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 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).

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

Setup

Step 1: Download MatNWB

Download the current release of MatNWB from https://github.com/NeurodataWithoutBorders/matnwb/releases or check out the latest development version via git clone https://github.com/NeurodataWithoutBorders/matnwb.git

Step 2: Download the NWB Schema

Download the current release of the NWB format schema from https://github.com/NeurodataWithoutBorders/nwb-schema/releases or check out the latest development via git clone https://github.com/NeurodataWithoutBorders/nwb-schema.git

Step 3: Generate the API

From the Matlab command line, generate code from the copy of the NWB schema. The command also takes variable arguments from any extensions.

generateCore(); % generate core namespace located in the repository.

The 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');

API Documentation

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

Tutorials

Extracellular Electrophysiology

Calcium Imaging

Intracellular Electrophysiology

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!