NWB Schema Version For Multimodal Characterization in Mouse Visual Cortex

Technical
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1

I understand from reading the community forum that you do not support MATLAB reading of NWB files, but I am wondering the following, so that I can fix my own problem.

The intracellular ephys data for the Multimodal Characterization in Mouse Visual Cortex (DANDI set 20) is not readable with the current version of the MATLAB matnwb set of functions. I think it has to do with the version of the NWB schema, because I can open files produced for other Allen databases that were produced later in the year. What version of the schema was it encoded with? That way I can set about finding the correct version of the schema. Thanks for your help.

For what it’s worth, the error feedback I get is as follows.

nwb = nwbRead(‘sub-605770584_ses-606098055_icephys.nwb’);
Dot indexing is not supported for variables of this type.

Error in file.fillExport>traverseRaw (line 120)
attrmatch = strcmp({raw.attributes.name}, propname);

Error in file.fillExport>traverseRaw (line 111)
res = traverseRaw(suffix, raw.datasets(i));

Error in file.fillExport (line 23)
pathProps = traverseRaw(pnm, raw);

Error in file.fillClass (line 93)
exporterFcns = file.fillExport(nonInherited, class, depnm);

Error in file.writeNamespace (line 22)
fwrite(fid, file.fillClass(className, Namespace, processed, …

Error in nwbRead>tryWriteSpec (line 103)
file.writeNamespace(namespaceName);

Error in nwbRead>generateSpec (line 91)
if ~tryWriteSpec(name)

Error in nwbRead>checkEmbeddedSpec (line 44)
generateSpec(fid, h5info(filename, specLocation));

Error in nwbRead (line 27)
specLocation = checkEmbeddedSpec(filename);

2

Those files were created with PyNWB 1.3.2 using NWB schema 2.2.5.

3

Thank you!

4

It appears that you’re encountering compatibility issues between the version of the NWB schema used to encode the data in the Multimodal Characterization in Mouse Visual Cortex (DANDI set 20) and the version supported by the current MATLAB matnwb set of functions.

To find out the version of the NWB schema used in the file, you can check the ‘nwb_version’ attribute within the NWB file. You can do this using an HDF5 viewer or by inspecting the file programmatically in MATLAB. Here’s an example of how you might do this in MATLAB:
info = h5info(‘sub-605770584_ses-606098055_icephys.nwb’);
nwb_version = h5readatt(‘sub-605770584_ses-606098055_icephys.nwb’, ‘/’, ‘nwb_version’);
disp(['NWB Version: ', nwb_version]);