Dynamic Table for .nwb

I have a dynamic table. the "location" column should pull data from another file "fields" and return the values. I have attached the code. Please help

'label', sprintf(fields)); --- I have tried this and left it as "fields"

numShanks = 1;
numChannelsPerShank = 8;
 
ElectrodesDynamicTable = types.hdmf_common.DynamicTable(...
    'colnames', {'location', 'label'}, ...
    'description', 'all electrodes');

Device = types.core.Device(...
    'NeuroOmega', 'NeuroOmega', ...
    'Alpha Omega', 'Alpha Omega' ...
);
nwb.general_devices.set('array', Device);
for iShank = 1:numShanks
    shankGroupName = sprintf('shank%d', iShank);
    EGroup = types.core.ElectrodeGroup( ...
        'description', sprintf('electrode group for %s', shankGroupName), ...
        'location', 'GPi', ...
        'device', types.untyped.SoftLink(Device) ...
    );
    
    nwb.general_extracellular_ephys.set(shankGroupName, EGroup);
    for iElectrode = 1:numChannelsPerShank
        ElectrodesDynamicTable.addRow( ...
            'location', 'GPi', ...
            'label', sprintf(fields));
    end
end
ElectrodesDynamicTable.toTable()
nwb.general_extracellular_ephys_electrodes = ElectrodesDynamicTable;

Answer 1

[Zinea]

Hi Siri,

I gather from the code snippet that you are trying to pull the ‘label’ values from ‘fields.mat’ and use it in ‘ElectrodesDynamicTable’.

Here is the code for doing the same:

numShanks = 1; 
numChannelsPerShank = 8; 

% Assuming 'fields' is stored in a file named 'fields.mat' and is a cell array 
% Load 'fields' from the file 
load('fields.mat', 'fields'); % Make sure 'fields' is the correct variable name in your .mat file 

ElectrodesDynamicTable = types.hdmf_common.DynamicTable(... 
    'colnames', {'location', 'label'}, ... 
    'description', 'all electrodes'); 
Device = types.core.Device(... 
    'NeuroOmega', 'NeuroOmega', ... 
    'Alpha Omega', 'Alpha Omega' ... 
    ); 
nwb.general_devices.set('array', Device); 
for iShank = 1:numShanks 
    shankGroupName = sprintf('shank%d', iShank); 
    EGroup = types.core.ElectrodeGroup( ... 
        'description', sprintf('electrode group for %s', shankGroupName), ... 
        'location', 'GPi', ... 
        'device', types.untyped.SoftLink(Device) ... 
        ); 
    
    nwb.general_extracellular_ephys.set(shankGroupName, EGroup); 
    for iElectrode = 1:numChannelsPerShank 
        % Ensure 'fields' has enough entries for each electrode 
        if iElectrode <= length(fields) 
            label = fields{iElectrode}; % Access the corresponding label from 'fields' 
        else 
            label = sprintf('Electrode%d', iElectrode); % Fallback label if 'fields' is shorter than expected 
        end 
        ElectrodesDynamicTable.addRow( ... 
            'location', 'GPi', ... 
            'label', label); 
    end 
end 
ElectrodesDynamicTable.toTable() 
nwb.general_extracellular_ephys_electrodes = ElectrodesDynamicTable; 

Here is the output of executing the above code :

For more information on working with NWB Data, refer to the following link:

https://www.mathworks.com/matlabcentral/fileexchange/67741-neurodatawithoutborders-matnwb

Hope it helps!