Reading NWB Files

This section provides an introduction on how to read NWB files in Python using PyNWB and Matlab using MatNWB. If you are interested in converting your data to NWB, then please see the User Guide as well as for more in-depth tutorials visit the PyNWB and MatNWB tutorials and documentation.

Reading With PyNWB

• See the PyNWB tutorial on Reading and Exploring an NWB File for an introduction to how to read, explore, and do basic visualizations with an NWB file in Python.

• The Query Intracellular Electrophysiology Metadata PyNWB tutorial then focuses specifically on how to read and query metadata related to intracellular electrophysiology data.

Reading with MatNWB

For most files, MatNWB only requires the nwbRead call:

nwb = nwbRead('path/to/filename.nwb');

This call will read the file, create the necessary NWB schema class files, as well as any extension schemata that is needed for the file itself. This is because both PyNWB and MatNWB embed a copy of the schema environment into the NWB file when it is written.

The returned object above is an NwbFile which serves as the root object with which you can use to browse the contents of the file. More detail about the NwbFile class can be found here: Using the NwbFile Class.

• Using the NwbFile Class
  • Searching by Type
• The Dynamic Table Type
  • Row-by-row viewing
• Utility Types in MatNWB
  • Sets and Anons
  • DataStubs and DataPipes
  • Links and Views
• Troubleshooting File Reads in MatNWB
  • Schema Version Conflicts
  • Multiple Schema Environments
  • Missing Embedded Schemata
  • Avoiding Class Regeneration
  • Bottom of the Barrel