ndx-photometry NWB扩展

介绍

这是一个用于存储光度记录和相关元数据的NWB扩展。此扩展将在NWB文件中的三个文件夹中存储光度信息：获取、处理和通用。获取文件夹包含一个FiberPhotometryResponseSeries，它引用了FibersTable、ExcitationSourcesTable、PhotodetectorsTable和FluorophoresTable的行。此扩展的新类型在元数据和处理中。

元数据

1. FibersTable为每个光纤存储行，包含有关位置、光电探测器和更多信息（与每个光纤相关）。
2. ExcitationSourcesTable为每个激发源存储行，包含有关峰值波长、源类型以及类型为CommandedVoltageSeries的命令电压序列。
3. PhotodectorsTable为每个光电探测器存储行，包含有关峰值波长、类型等信息。
4. FluorophoresTable为每个荧光素存储行，包含有关荧光素本身和注射部位的信息。

处理

1. DeconvoledROIResponseSeries 存储DfOverF和荧光轨迹，并扩展了ROIResponseSeries以包含关于所执行的解卷积和下采样过程的信息。

此扩展由Akshay Jaggi、Ben Dichter和Ryan Ly开发。

安装

pip install ndx-photometry

用法

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)

此扩展使用 ndx-template 创建。