NWB Extension for documenting odor stimulus metadata
Project description
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 = "od
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)
Demonstration
For more detailed demonstration, please visit the demo
folder.
TODOs
- Create test
- Publish on
conda
- Publish on
pypi
- Fetch pubchem data using
pubchempy
- Use
pyproject.toml
instead ofsetup.py
This extension was created using ndx-template.
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