Igor Pro module for reading and writing NeurodataWithoutBorder files

This modules allows to easily write and read valid NeurodataWithoutBorder style HDF5 files. It encapsulates the most commonly used parts of the specification in easy to use functions.

Main features

• Read and write NWB compliant files
  • specification version 1.0.5, Aug 8 2016
  • specification version 2.9.0, June 2025
• Compatible with Igor Pro 7 or later on Windows/MacOSX
• Requires the stock HDF5 XOP only

Installation

• Quit Igor Pro
• Install the HDF5 XOP and the HDF5 Browser as described in DisplayHelpTopic "Installing The HDF5 Package"
• Create the following shortcut in C:\Users\$username\Documents\WaveMetrics\Igor Pro XXX User Files where XXX is your major Igor Pro version
  • In "Igor Procedures" a shortcut pointing to the basefolder of the IPNWB package
• Restart Igor Pro

Examples

The following examples show how to read and write into NWB version 1.0.5

writing into NWB

.. literalinclude:: examples/IPNWB_Examples_Writer.ipf
   :language: igorpro

reading from NWB

.. literalinclude:: examples/IPNWB_Examples_Reader.ipf
   :language: igorpro

NWB file format description

• Datasets which originate from Igor Pro waves have the special attributes IGORWaveScaling, IGORWaveType, IGORWaveUnits, IGORWaveNote. These attributes allow easy and convenient loading of the data into Igor Pro back.
• For AD/DA/TTL groups the naming scheme is data_XXXXX_[AD/DA/TTL] suffix where XXXXX is a running number and suffix the channel number. For some hardware types the suffix includes the TTL line as well. It is important to note that the number of digits in XXXXX is variable und subject to change, and that XXXXX is not the sweep number.
• In NWB v1, the sweep number is accessible from the source attribute only. Example source contents: Device=ITC18USB_Dev_0;Sweep=0;AD=0;ElectrodeNumber=0;ElectrodeName=0
• For I=0 clamp mode neither the DA data nor the stimset is saved.
• Some entries in the following tree are specific to MIES, these are marked as custom entries. Users running MIES are encouraged to use the same NWB layout and extensions.

NWB File Organization

The current major version of the file format is 2. Version 1 is considered supported but deprecated.

.. toctree::

   doc/nwb1.rst
   doc/nwb2.rst

NWB schema upgrade

• python -m venv ~/.venvs/ipnwb
• pip install -r requirements.txt
• ./update_specifications.sh
• # The last command should not change anything in the repo, if yes investigate why and commit the changes
• Choose a new nwb-schema version
• Update the specifcations submodule to that version
• ./update_specifications.sh
• Commit the changes, update versions in README.rst and check if MIES works with this new IPNWB version

Online Resources

• https://neurodatawithoutborders.github.io
• https://crcns.org/NWB