ndx-odor-metadata

NWB extension to store odor stimulus metadata with DynamicTable format. Entries that have a PubChem and stim_types indicate odor/chemical will also be queried with pubchempy for more information.

This is in alpha development stages WITHOUT any appropriate tests yet. Please use with discretion.

Requirement

The requirements and additional development requirements can be seen in pyproject.toml file.

Here are the minimum requirements:

• python >=3.8
• pynwb>=1.5.0,<3
• hdmf>=3.4.7,<4
• pubchempy>=1.0.4
• pyyaml>=5.0

Installation

You can install via pip:

pip install ndx-odor-metadata

Or conda:

conda install -c fleischmannlab ndx-odor-metadata

Or directly from the git repository:

pip install git+https://gitlab.com/fleischmann-lab/ndx/ndx-odor-metadata

Usage

Main usage

from ndx_odor_metadata import OdorMetaData

odor_table = OdorMetaData(name='odor_table', description='an odor table')

odor_table.add_stimulus(
    pubchem_id = 7662.0,
    stim_name = "3-Phenylpropyl isobutyrate",
    raw_id = 3,
    stim_id = 1,
    stim_types = "odor",
    chemical_dilution_type='vaporized',
    chemical_concentration = 0.01,
    chemical_concentration_unit='%',
    chemical_solvent = "Mineral Oil",
    chemical_provider = "Sigma",
    stim_description = "Legit odor stimulus #1",
)

nwbfile.add_acquisition(odor_table)

Details on arguments

Demonstration

For more detailed demonstration, please visit the demo folder.

TODOs

• Create test
• Update documentation for sphinx (also update style)
• Publish on conda
• Publish on pypi
• Fetch pubchem data using pubchempy
• Use pyproject.toml instead of setup.py

This extension was created using ndx-template.