This is an NWB extension for storing fiber photometry recordings and associated metadata. It replaces the deprecated ndx-photometry extension.
This extension consists of 11 new neurodata types:
IndicatorextendsDeviceto hold metadata on the fluorescent indicator (ex. label=GCaMP6).OpticalFiberextendsDeviceto hold metadata on the optical fiber (ex. numerical_aperture=0.39).ExcitationSourceextendsDeviceto hold metadata on the excitation source (ex. excitation_wavelength_in_nm=470.0).PhotodetectorextendsDeviceto hold metadata on the photodetector (ex. detected_wavelength_in_nm=520.0).DichroicMirrorextendsDeviceto hold metadata on the dichroic mirror (ex. cut_on_wavelength_in_nm=470.0).BandOpticalFilterextendsDeviceto hold metadata on any bandpass or bandstop optical filters (ex. center_wavelength_in_nm=505.0).EdgeOpticalFilterextendsDeviceto hold metadata on any edge optical filters (ex. cut_wavelength_in_nm=585.0).FiberPhotometryResponseSeriesextendsTimeSeriesto hold the recorded fiber photometry responses.CommandedVoltageSeriesextendsTimeSeriesto hold the commanded voltage values for a single fiber photometry trace.FiberPhotometryTableextendsDynamicTableto hold information on the fiber photometry setup. Each row of the table reference a combination of the devices and a commanded voltage series that correspond to a single fiber photometry trace.FiberPhotometryextendsLabMetaDatato hold theFiberPhotometryTable.
To install the latest stable release through PyPI,
pip install ndx-fiber-photometryimport datetime
import numpy as np
from pynwb import NWBFile, NWBHDF5IO
from ndx_fiber_photometry import (
Indicator,
OpticalFiber,
ExcitationSource,
Photodetector,
DichroicMirror,
BandOpticalFilter,
EdgeOpticalFilter,
FiberPhotometry,
FiberPhotometryTable,
FiberPhotometryResponseSeries,
CommandedVoltageSeries,
)
nwbfile = NWBFile(
session_description='session_description',
identifier='identifier',
session_start_time=datetime.datetime.now(datetime.timezone.utc)
)
indicator_green = Indicator(
name="indicator_1",
description="Green indicator",
label="GCamp6f",
injection_location="VTA",
injection_coordinates_in_mm=(3.0, 2.0, 1.0),
)
indicator_red = Indicator(
name="indicator_2",
description="Red indicator",
label="Tdtomato",
injection_location="VTA",
injection_coordinates_in_mm=(3.0, 2.0, 1.0),
)
optical_fiber_1 = OpticalFiber(
name="optical_fiber_1",
model="fiber_model",
numerical_aperture=0.2,
core_diameter_in_um=400.0,
)
optical_fiber_2 = OpticalFiber(
name="optical_fiber_2",
model="fiber_model",
numerical_aperture=0.2,
core_diameter_in_um=400.0,
)
excitation_source_1 = ExcitationSource(
name="excitation_source_1",
description="excitation sources for green indicator",
model="laser model",
illumination_type="laser",
excitation_wavelength_in_nm=470.0,
)
excitation_source_2 = ExcitationSource(
name="excitation_source_2",
description="excitation sources for red indicator",
model="laser model",
illumination_type="laser",
excitation_wavelength_in_nm=525.0,
)
photodetector_1 = Photodetector(
name="photodetector_1",
description="photodetector for green emission",
detector_type="PMT",
detected_wavelength_in_nm=520.0,
gain=100.0,
)
photodetector_2 = Photodetector(
name="photodetector_2",
description="photodetector for red emission",
detector_type="PMT",
detected_wavelength_in_nm=585.0,
gain=100.0,
)
dichroic_mirror_1 = DichroicMirror(
name="dichroic_mirror_1",
description="Dichroic mirror for green indicator",
model="dicdichroic mirror model",
cut_on_wavelength_in_nm=470.0,
transmission_band_in_nm=(460.0, 480.0),
cut_off_wavelength_in_nm=500.0,
reflection_band_in_nm=(490.0, 520.0),
angle_of_incidence_in_degrees=45.0,
)
dichroic_mirror_2 = DichroicMirror(
name="dichroic_mirror_2",
description="Dichroic mirror for red indicator",
model="dicdichroic mirror model",
cut_on_wavelength_in_nm=525.0,
transmission_band_in_nm=(515.0, 535.0),
cut_off_wavelength_in_nm=585.0,
reflection_band_in_nm=(575.0, 595.0),
angle_of_incidence_in_degrees=45.0,
)
band_optical_filter = BandOpticalFilter(
name="band_optical_filter",
description="emission filter for green indicator",
model="emission filter model",
center_wavelength_in_nm=505.0,
bandwidth_in_nm=30.0, # 505±15nm
filter_type="Bandpass",
)
edge_optical_filter = EdgeOpticalFilter(
name="edge_optical_filter",
description="emission filter for red indicator",
model="emission filter model",
cut_wavelength_in_nm=585.0,
slope_in_percent_cut_wavelength=1.0,
slope_starting_transmission_in_percent=10.0,
slope_ending_transmission_in_percent=80.0,
filter_type="Longpass",
)
commanded_voltage_series_1 = CommandedVoltageSeries(
name="commanded_voltage_series_1", data=[1.0, 2.0, 3.0], frequency=30.0, rate=30.0, unit="volts"
)
commanded_voltage_series_2 = CommandedVoltageSeries(
name="commanded_voltage_series_2",
data=[4.0, 5.0, 6.0],
rate=30.0,
unit="volts",
)
fiber_photometry_table = FiberPhotometryTable(
name="fiber_photometry_table",
description="fiber photometry table",
)
fiber_photometry_table.add_row(
location="VTA",
coordinates=(3.0, 2.0, 1.0),
indicator=indicator_green,
optical_fiber=optical_fiber_1,
excitation_source=excitation_source_1,
commanded_voltage_series=commanded_voltage_series_1,
photodetector=photodetector_1,
dichroic_mirror=dichroic_mirror_1,
emission_filter=band_optical_filter,
)
fiber_photometry_table.add_row(
location="VTA",
coordinates=(3.0, 2.0, 1.0),
indicator=indicator_red,
optical_fiber=optical_fiber_2,
excitation_source=excitation_source_2,
commanded_voltage_series=commanded_voltage_series_2,
photodetector=photodetector_2,
dichroic_mirror=dichroic_mirror_2,
emission_filter=edge_optical_filter,
)
fiber_photometry_table_region = fiber_photometry_table.create_fiber_photometry_table_region(
region=[0], description="source fibers"
)
fiber_photometry_lab_meta_data = FiberPhotometry(
name="fiber_photometry",
fiber_photometry_table=fiber_photometry_table,
)
fiber_photometry_response_series = FiberPhotometryResponseSeries(
name="fiber_photometry_response_series",
description="my roi response series",
data=np.random.randn(100, 1),
unit="n.a.",
rate=30.0,
fiber_photometry_table_region=fiber_photometry_table_region,
)
nwbfile.add_device(indicator_green)
nwbfile.add_device(indicator_red)
nwbfile.add_device(optical_fiber_1)
nwbfile.add_device(optical_fiber_2)
nwbfile.add_device(excitation_source_1)
nwbfile.add_device(excitation_source_2)
nwbfile.add_device(photodetector_1)
nwbfile.add_device(photodetector_2)
nwbfile.add_device(dichroic_mirror_1)
nwbfile.add_device(dichroic_mirror_2)
nwbfile.add_device(band_optical_filter)
nwbfile.add_device(edge_optical_filter)
nwbfile.add_acquisition(commanded_voltage_series_1)
nwbfile.add_acquisition(commanded_voltage_series_2)
nwbfile.add_lab_meta_data(fiber_photometry_lab_meta_data)
nwbfile.add_acquisition(fiber_photometry_response_series)%%{
init: {
'theme': 'base',
'themeVariables': {
'primaryColor': '#ffffff',
"primaryBorderColor': '#144E73',
'lineColor': '#D96F32'
}
}
}%%
classDiagram
direction BT
class TimeSeries {
attributes
--------------------------------------
name : str
description : str
rate : float
starting_time: float
timestamps : array-like
unit : str
offset : float, optional
conversion : float, optional
}
class DynamicTable{
attributes
--------------------------------------
name : str
description : str
}
class Device{
attributes
--------------------------------------
name : str
description : str
manufacturer : str
}
class FiberPhotometryResponseSeries {
datasets
--------------------------------------
data [ntime, nfibers] : array-like
links
--------------------------------------
fiber_photometry_table_region : DynamicTableRegion
}
class CommandedVoltageSeries {
datasets
--------------------------------------
data [ntime] : array-like
attributes
--------------------------------------
frequency : float
}
class FiberPhotometryTable {
VectorData Columns
--------------------------------------
location : str
coordinates [AP, ML, DV] : [float, float, float]
notes : str
commanded_voltage_series : CommandedVoltageSeries
optical_fiber : OpticalFiber
photodetector : Photodetector
indicator : Indicator
excitation_source : ExcitationSource
dichroic_mirror : DichroicMirror
emission_filter : BandOpticalFilter | EdgeOpticalFilter
excitation_filter : BandOpticalFilter | EdgeOpticalFilter
}
class OpticalFiber{
attributes
--------------------------------------
model : str
numerical_aperture : float
core_diameter_in_um : float
}
class ExcitationSource{
attributes
--------------------------------------
model : str
illumination_type : str
excitation_wavelength_in_nm : float
}
class Photodetector{
attributes
--------------------------------------
model : str
detector_type : str
detected_wavelength_in_nm : float
gain : float
}
class BandOpticalFilter{
attributes
--------------------------------------
model : str
center_wavelength_in_nm : float
bandwidth_in_nm : float
filter_type : str
}
class EdgeOpticalFilter{
attributes
--------------------------------------
model : str
cut_wavelength_in_nm : float
slope_in_percent_cut_wavelength : float
slope_starting_transmission_in_percent : float
slope_ending_transmission_in_percent : float
filter_type : str
}
class DichroicMirror{
attributes
--------------------------------------
model : str
cut_on_wavelength_in_nm : float
cut_off_wavelength_in_nm : float
reflection_band_in_nm : float
angle_of_incidence_in_degrees : float
}
class Indicator{
attributes
--------------------------------------
label : str, optional
injection_location : str
injection_coordinates_in_mm [AP, ML, DV] : [float, float, float]
}
TimeSeries <|-- FiberPhotometryResponseSeries : extends
TimeSeries <|-- CommandedVoltageSeries : extends
DynamicTable <|-- FiberPhotometryTable : extends
Device <|-- OpticalFiber : extends
Device <|-- ExcitationSource : extends
Device <|-- Photodetector : extends
Device <|-- BandOpticalFilter : extends
Device <|-- EdgeOpticalFilter : extends
Device <|-- DichroicMirror : extends
Device <|-- Indicator : extends
CommandedVoltageSeries o-- FiberPhotometryTable : aggregates
OpticalFiber o-- FiberPhotometryTable : aggregates
ExcitationSource o-- FiberPhotometryTable : aggregates
Photodetector o-- FiberPhotometryTable : aggregates
BandOpticalFilter o-- FiberPhotometryTable : aggregates
EdgeOpticalFilter o-- FiberPhotometryTable : aggregates
DichroicMirror o-- FiberPhotometryTable : aggregates
Indicator o-- FiberPhotometryTable : aggregates
FiberPhotometryTable -- FiberPhotometryResponseSeries : links
style Device stroke:blue,stroke-width:5px
style TimeSeries stroke:blue,stroke-width:5px
style DynamicTable stroke:blue,stroke-width:5px
style FiberPhotometryResponseSeries stroke:green,stroke-width:5px
style CommandedVoltageSeries stroke:green,stroke-width:5px
style FiberPhotometryTable stroke:green,stroke-width:5px
style OpticalFiber stroke:green,stroke-width:5px
style ExcitationSource stroke:green,stroke-width:5px
style Photodetector stroke:green,stroke-width:5px
style BandOpticalFilter stroke:green,stroke-width:5px
style EdgeOpticalFilter stroke:green,stroke-width:5px
style DichroicMirror stroke:green,stroke-width:5px
style Indicator stroke:green,stroke-width:5px
This extension was created using ndx-template.