README.md

ndx-photometry Extension for NWB

This extension is deprecated. Please use the more updated https://github.com/catalystneuro/ndx-fiber-photometry extension instead.

Introduction

This is an NWB extension for storing photometry recordings and associated metadata. This extension stores photometry information across three folders in the NWB file: acquisition, processing, and general. The acquisition folder contains a FiberPhotometryResponseSeries which references rows of FibersTable, ExcitationSourcesTable, PhotodetectorsTable and FluorophoresTable. The new types for this extension are in metadata and processing.

Metadata

1. FibersTable stores rows for each fiber with information about the location, photodetector, and more (associated with each fiber).
2. ExcitationSourcesTable stores rows for each excitation source with information about the peak wavelength, source type, and the commanded voltage series of type CommandedVoltageSeries
3. PhotodectorsTable stores rows for each photodetector with information about the peak wavelength, type, etc.
4. FluorophoresTable stores rows for each fluorophore with information about the fluorophore itself and the injeciton site.

Processing

1. DeconvoledROIResponseSeries stores DfOverF and Fluorescence traces and extends ROIResponseSeries to contain information about the deconvolutional and downsampling procedures performed.

This extension was developed by Akshay Jaggi, Ben Dichter, and Ryan Ly.

Installation

pip install ndx-photometry

Usage

import datetime
import numpy as np

from pynwb import NWBHDF5IO, NWBFile
from pynwb.ophys import RoiResponseSeries
from ndx_photometry import (
    FibersTable,
    PhotodetectorsTable,
    ExcitationSourcesTable,
    FluorophoresTable,
    FiberPhotometryResponseSeries,
    FiberPhotometry
)


nwbfile = NWBFile(
    session_description="session_description",
    identifier="identifier",
    session_start_time=datetime.datetime.now(datetime.timezone.utc),
)

# Create a Fibers table, and add one (or many) fiber
fibers_table = FibersTable(description="fibers table")
fibers_table.add_row(
    location="my location",
    notes="notes"
)

# Create an Excitation Sources table, and a one (or many) excitation source
excitationsources_table = ExcitationSourcesTable(description="excitation sources table")
excitationsources_table.add_row(
    peak_wavelength=700.0,
    source_type="laser",
)

# Create a Photodetectors table, and add one (or many) photodetector
photodetectors_table = PhotodetectorsTable(description="photodetectors table")
photodetectors_table.add_row(
    peak_wavelength=500.0,
    type="PMT",
    gain=100.0
)

# Create a Fluorophores table, and add one (or many) fluorophore
fluorophores_table = FluorophoresTable(description="fluorophores")
fluorophores_table.add_row(
    label="dlight",
    location="VTA",
    coordinates=(3.0,2.0,1.0),
    excitation_peak_wavelength=700.0,
    emission_peak_wavelength=500.0
)

# Here we add the metadata tables to the metadata section
nwbfile.add_lab_meta_data(
    FiberPhotometry(
        fibers=fibers_table,
        excitation_sources=excitationsources_table,
        photodetectors=photodetectors_table,
        fluorophores=fluorophores_table
    )
)

# Create a raw FiberPhotometryResponseSeries, this is your main acquisition
# We should create DynamicTableRegion referencing the correct rows for each table
fiber_ref = fibers_table.create_fiber_region(region=[0], description='source fiber')
excitation_ref = excitationsources_table.create_excitation_source_region(region=[0], description='excitation sources')
photodetector_ref = photodetectors_table.create_photodetector_region(region=[0], description='photodetector')
fluorophore_ref = fluorophores_table.create_fluorophore_region(region=[0], description='fluorophore')

fp_response_series = FiberPhotometryResponseSeries(
    name="MyFPRecording",
    data=np.random.randn(100, 1),
    unit='F',
    rate=30.0,
    fibers=fiber_ref,
    excitation_sources=excitation_ref,
    photodetectors=photodetector_ref,
    fluorophores=fluorophore_ref,
)

nwbfile.add_acquisition(fp_response_series)

# write nwb file
filename = 'test.nwb'
with NWBHDF5IO(filename, 'w') as io:
    io.write(nwbfile)

# read nwb file and check its contents
with NWBHDF5IO(filename, 'r', load_namespaces=True) as io:
    nwbfile = io.read()
    # Access and print information about the acquisition
    print(nwbfile.acquisition["MyFPRecording"])
    # Access and print all of the metadata
    print(nwbfile.lab_meta_data)

This extension was created using ndx-template.