Tags: dataformat spike nwb

Getting started with Neurodata Without Borders (NWB) data

Neurodata Without Borders (NWB) is a consortium founded to promote data sharing in neuroscience. Among their efforts, NWB created a data standard called NWB: Neurophysiology (NWB:N). Many datasets in this format are already freely available (e.g. here).

Introduction

Fieldtrip allows reading in spike and LFP data from .nwb files. Importantly, the user has to install the NWB Matlab interface MatNWB (instructions on how to install MatNWB) and run the MatNWB function generateCore successfully before attempting to read files with FieldTrip.

Example script

% Data taken from https://osf.io/hv7ja/
% About the data: https://github.com/rutishauserlab/recogmem-release-NWB

% Optional: Make sure no duplicate versions of +types are in the search path
% restoredefaultpath()

% Navigate to an appropriate working directory (necessary because a few folders and files will be created by MatNWB here)
cd('X:/examplefolder') % change as needed

% Add fieldtrip to search path and initialize
addpath('../fieldtrip') % change as needed
ft_defaults

% Add matnwb to search path
addpath(genpath('../matnwb'))

% (re-)generate core classes for matNWB from it's schema (lands in +types)
generateCore()

% Filename and path
nwbFile = 'X:/examplefolder/sub-YutaMouse41_ses-YutaMouse41-150831_behavior+ecephys.nwb';

% Show schema version of the file. If this does not match your installed version, see 'Change NWB schema version' below
disp(util.getSchemaVersion(nwbFile))

% Load data in nwb format
nwb = nwbRead(nwbFile);
disp(nwb)

% Try to obtain hdr, lfp data and spike data in FieldTrip format
try
	hdr = ft_read_header(nwbFile); % contains no lfp data: throws error
catch ME
	disp('Could not load in hdr information')
	rethrow(ME)
end
try
	dat = ft_read_data(nwbFile); % contains no lfp data: throws error
catch ME
	disp('Could not load in NWB data')
	rethrow(ME)
end
try
	spike = ft_read_spike(nwbFile); % contains spike data: Converts
catch ME
	disp('Could not read in spike data from NWB file.')
	rethrow(ME)
end

Change NWB schema version

In case you are trying to load a file using a different schema version than the one installed on your system this may cause an error (often something like ‘Unable to resolve the name types.core.DynamicTableRegion’). If so:

  • go to the NWB release site,
  • choose the schema closest to your file’s schema,
  • download the zip file associated with that schema,
  • copy the files in the zip’s \nwb-schema-2.2.1\core into the \nwb-schema\core subfolder of your MatNWB directory (you probably want to make a backup of the original files first).

Missing functionality

At its current stage, the NWB integration into Fieldtrip is not feature-complete. For example:

  • Reading events (ft_read_event). NWB:N is a pretty generic dataformat and can contain very diverse types of data. Therefore, it is not trivial to programmatically and reliably create an event output that could be used in a trial function.

  • Reading waveforms (voltage time series around identified spikes) by ft_read_spike.