Framework for converting data from various formats to NWB 2.0

Features:

• Command line interface
• Python API
• Qt GUI for customized metadata curation
• Leverages SpikeExtractor to support conversion from a number or proprietary formats.

To install nwb-conversion-tools directly in an existing environment:

$ pip install nwb-conversion-tools

Alternatively, to clone the repository and set up a conda environment, do:

$ git clone https://github.com/NeurodataWithoutBorders/nwb-conversion-tools
$ cd nwb-conversion-tools
$ conda env create -f make_env.yml
$ conda activate nwb_conversion_env
$ pip install .

The Graphic User Interface of nwb-conversion-tools provides an user-friendly way of editing metafiles for the conversion tasks and for exploring nwb files with nwb-jupyter-widgets and an embedded IPython console.

After activating the correct environment, nwb_conversion_tools GUI can be called from command line:

nwb-gui

To initiate the GUI with a specific metafile:

nwb-gui metafile.yml

The GUI can also be imported and run from python scripts:

from nwb_conversion_tools.gui.nwb_conversion_gui import nwb_conversion_gui

# YAML metafile
metafile = 'metafile.yml'

# Conversion module
conversion_module = 'conversion_module.py'

# Source files path
source_paths = {}
source_paths['source_file_1'] = {'type': 'file', 'path': ''}
source_paths['source_file_2'] = {'type': 'file', 'path': ''}

# Other options
kwargs = {'option_1': True, 'option_2': False}

nwb_conversion_gui(
    metafile=metafile,
    conversion_class=conversion_class,
    source_paths=source_paths,
    kwargs_fields=kwargs,
)

Here you can find templates for metafile.yml and conversion_module.py.

• CELLMax
• Miniscope

• SpikeGLX
• Intan

• Bpod

• Axel lab: axel-lab-to-nwb
• Buffalo lab: buffalo-lab-data-to-nwb
• Giocomo lab: giocomo-lab-to-nwb
• Jaeger lab: jaeger-lab-to-nwb
• Tolias lab: tolias-lab-to-nwb