Fiber Photometry Example Session¶

In [1]:

from stream_nwbfile import stream_nwbfile
import numpy as np
import matplotlib.pyplot as plt

from stream_nwbfile import stream_nwbfile import numpy as np import matplotlib.pyplot as plt

This notebook showcases one example session from the 000971 dataset containing operant behavior and concurrent fiber photometry recordings.

In [2]:

DANDISET_ID = '000971'
file_path = 'sub-112-283/sub-112-283_ses-FP-PS-2019-06-20T09-32-04_behavior.nwb'
nwbfile, io = stream_nwbfile(DANDISET_ID, file_path)
display(nwbfile)

DANDISET_ID = '000971' file_path = 'sub-112-283/sub-112-283_ses-FP-PS-2019-06-20T09-32-04_behavior.nwb' nwbfile, io = stream_nwbfile(DANDISET_ID, file_path) display(nwbfile)

root (NWBFile)

session_description: RI60 Training with concurrent fiber photometry, rewards delivered on left nose pokes

identifier: 64828a03-4c9b-4212-ad60-d5486717b6df

session_start_time

2019-06-20 09:32:04-05:51

timestamps_reference_time

2019-06-20 09:32:04-05:51

file_create_date

0

2024-06-11 13:06:38.624732-07:00

experimenter

('Seiler, Jillian L.', 'Cosme, Caitlin V.', 'Sherathiya, Venus N.', 'Schaid, Michael D.', 'Bianco, Joseph M.', 'Bridgemohan, Abigael S.', 'Lerner, Talia N.')

related_publications

('https://doi.org/10.1016/j.cub.2022.01.055',)

acquisition

commanded_voltage_series_dls

starting_time: 0.0

rate: 6103.515625

resolution: -1.0

comments: no comments

description: The commanded voltage for the frequency-modulated DLS calcium signal and DLS isosbestic control.

conversion: 1.0

offset: 0.0

unit: volts

data

starting_time_unit: seconds

frequency__unit: hertz

commanded_voltage_series_dms

starting_time: 0.0

rate: 6103.515625

resolution: -1.0

comments: no comments

description: The commanded voltage for the frequency-modulated DMS calcium signal and DMS isosbestic control.

conversion: 1.0

offset: 0.0

unit: volts

data

starting_time_unit: seconds

frequency__unit: hertz

fiber_photometry_response_series

starting_time: 0.0

rate: 1017.2526245117188

resolution: -1.0

comments: no comments

description: The fluorescence from the DMS calcium signal, DMS isosbestic control, DLS calcium signal, and DLS isosbestic control.

conversion: 1.0

offset: 0.0

unit: a.u.

data

starting_time_unit: seconds

fiber_photometry_table_region

description: The region of the FiberPhotometryTable corresponding to the DMS calcium signal, DMS isosbestic control, DLS calcium signal, and DLS isosbestic control.

table

description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.

table

	location	indicator	optical_fiber	excitation_source	photodetector	dichroic_mirror	coordinates	commanded_voltage_series	emission_filter	excitation_filter
id
0	DMS	dms_green_fluorophore abc.Indicator at 0x4963995696\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 0.8 4.7]\n injection_location: medial SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_calcium_signal abc.ExcitationSource at 0x4963998384\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 465.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.8, 1.5, 2.8]	commanded_voltage_series_dms abc.CommandedVoltageSeries at 0x4962263024\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DMS calcium signal and DMS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	excitation_filter abc.BandOpticalFilter at 0x4963994208\nFields:\n bandwidth_in_nm: 30.0\n center_wavelength_in_nm: 475.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n
1	DMS	dms_green_fluorophore abc.Indicator at 0x4963995696\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 0.8 4.7]\n injection_location: medial SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_isosbestic_control abc.ExcitationSource at 0x4963998528\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 405.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.8, 1.5, 2.8]	commanded_voltage_series_dms abc.CommandedVoltageSeries at 0x4962263024\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DMS calcium signal and DMS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	isosbestic_excitation_filter abc.BandOpticalFilter at 0x4963999008\nFields:\n bandwidth_in_nm: 10.0\n center_wavelength_in_nm: 405.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n
2	DLS	dls_green_fluorophore abc.Indicator at 0x4962259616\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 1.3 4.2]\n injection_location: lateral SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_calcium_signal abc.ExcitationSource at 0x4963998384\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 465.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.1, 2.8, 3.5]	commanded_voltage_series_dls abc.CommandedVoltageSeries at 0x4962255920\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DLS calcium signal and DLS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	excitation_filter abc.BandOpticalFilter at 0x4963994208\nFields:\n bandwidth_in_nm: 30.0\n center_wavelength_in_nm: 475.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n
3	DLS	dls_green_fluorophore abc.Indicator at 0x4962259616\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 1.3 4.2]\n injection_location: lateral SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_isosbestic_control abc.ExcitationSource at 0x4963998528\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 405.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.1, 2.8, 3.5]	commanded_voltage_series_dls abc.CommandedVoltageSeries at 0x4962255920\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DLS calcium signal and DLS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	isosbestic_excitation_filter abc.BandOpticalFilter at 0x4963999008\nFields:\n bandwidth_in_nm: 10.0\n center_wavelength_in_nm: 405.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n

keywords

processing

behavior

description: Operant behavioral data from MedPC. MSN = FOOD_RI 60 LEFT TTL Box = 3

data_interfaces

behavioral_epochs

interval_series

reward_port_intervals

resolution: -1.0

comments: no comments

description: Interval of time spent in reward port (1 is entry, -1 is exit)

conversion: 1.0

offset: 0.0

unit: n/a

data

timestamps

timestamps_unit: seconds

interval: 1

left_nose_poke_times

description: Left nose poke times

timestamps

timestamps__unit: seconds

left_reward_times

description: Left reward times

timestamps

timestamps__unit: seconds

right_nose_poke_times

description: Right nose poke times

timestamps

timestamps__unit: seconds

epoch_tags

set()

devices

dichroic_mirror

description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.

manufacturer: Doric Lenses

model: 4 ports Fluorescence Mini Cube - GCaMP

dls_green_fluorophore

description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.

manufacturer: Addgene

label: GCaMP7b

injection_location: lateral SNc

injection_coordinates_in_mm

[3.1 1.3 4.2]

dms_green_fluorophore

description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.

manufacturer: Addgene

label: GCaMP7b

injection_location: medial SNc

injection_coordinates_in_mm

[3.1 0.8 4.7]

emission_filter

description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.

manufacturer: Doric Lenses

center_wavelength_in_nm: 525.0

bandwidth_in_nm: 50.0

filter_type: Bandpass

model: 4 ports Fluorescence Mini Cube - GCaMP

excitation_filter

description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.

manufacturer: Doric Lenses

center_wavelength_in_nm: 475.0

bandwidth_in_nm: 30.0

filter_type: Bandpass

model: 4 ports Fluorescence Mini Cube - GCaMP

excitation_source_calcium_signal

description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.

manufacturer: Doric Lenses

model: Connectorized LED

illumination_type: LED

excitation_wavelength_in_nm: 465.0

excitation_source_isosbestic_control

description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.

manufacturer: Doric Lenses

model: Connectorized LED

illumination_type: LED

excitation_wavelength_in_nm: 405.0

isosbestic_excitation_filter

description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.

manufacturer: Doric Lenses

center_wavelength_in_nm: 405.0

bandwidth_in_nm: 10.0

filter_type: Bandpass

model: 4 ports Fluorescence Mini Cube - GCaMP

optical_fiber

description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.

manufacturer: Doric Lenses

model: Fiber Optic Implant

numerical_aperture: 0.48

core_diameter_in_um: 400.0

photodetector

description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.

manufacturer: Doric Lenses

model: Newport Visible Femtowatt Photoreceiver Module

detector_type: photodiode

detected_wavelength_in_nm: 525.0

gain: 10000000000.0

subject

age: P10W/

age__reference: birth

description: Male and female WT (C57BL/6J) and (DAT)::IRES-Cre knockin mice (JAX006660) were obtained from The Jackson Laboratory and crossed in house. Only heterozygote transgenic mice, obtained by backcrossing to C57BL/6J wildtypes, were used for experiments. Littermates of the same sex were randomly assigned to experimental groups (fiber photometry-14 males, 22 females; DMS excitatory optogenetics- 20 males, 19 females; DMS inhibitory optogenetics- 13 males, 13 females; DLS excitatory optogenetics- 18 males, 18 females). Adult mice at least 10 weeks of age were used in all experiments. Mice were group housed under a conventional 12 h light cycle (dark from 7:00pm to 7:00am) with ad libitum access to food and water prior to operant training. All experiments were approved by the Northwestern University Institutional Animal Care and Use Committee.

genotype: DAT-IRES-Cre: B6.SJLSlc6a3tm1.1(cre)Bkmn/J

sex: F

species: Mus musculus

subject_id: 112.283

strain: C57BL/6J

lab_meta_data

fiber_photometry

fiber_photometry_table

description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.

table

	location	indicator	optical_fiber	excitation_source	photodetector	dichroic_mirror	coordinates	commanded_voltage_series	emission_filter	excitation_filter
id
0	DMS	dms_green_fluorophore abc.Indicator at 0x4963995696\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 0.8 4.7]\n injection_location: medial SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_calcium_signal abc.ExcitationSource at 0x4963998384\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 465.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.8, 1.5, 2.8]	commanded_voltage_series_dms abc.CommandedVoltageSeries at 0x4962263024\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DMS calcium signal and DMS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	excitation_filter abc.BandOpticalFilter at 0x4963994208\nFields:\n bandwidth_in_nm: 30.0\n center_wavelength_in_nm: 475.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n
1	DMS	dms_green_fluorophore abc.Indicator at 0x4963995696\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 0.8 4.7]\n injection_location: medial SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_isosbestic_control abc.ExcitationSource at 0x4963998528\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 405.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.8, 1.5, 2.8]	commanded_voltage_series_dms abc.CommandedVoltageSeries at 0x4962263024\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DMS calcium signal and DMS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	isosbestic_excitation_filter abc.BandOpticalFilter at 0x4963999008\nFields:\n bandwidth_in_nm: 10.0\n center_wavelength_in_nm: 405.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n
2	DLS	dls_green_fluorophore abc.Indicator at 0x4962259616\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 1.3 4.2]\n injection_location: lateral SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_calcium_signal abc.ExcitationSource at 0x4963998384\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 465.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.1, 2.8, 3.5]	commanded_voltage_series_dls abc.CommandedVoltageSeries at 0x4962255920\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DLS calcium signal and DLS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	excitation_filter abc.BandOpticalFilter at 0x4963994208\nFields:\n bandwidth_in_nm: 30.0\n center_wavelength_in_nm: 475.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n
3	DLS	dls_green_fluorophore abc.Indicator at 0x4962259616\nFields:\n description: Mice for fiber photometry experiments received infusions of 1ml of AAV5-CAG-FLEX-jGCaMP7b-WPRE (1.02e13 vg/mL, Addgene, lot 18-429) into lateral SNc (AP 3.1, ML 1.3, DV 4.2) in one hemisphere and medial SNc (AP 3.1, ML 0.8, DV 4.7) in the other. Hemispheres were counterbalanced between mice.\n injection_coordinates_in_mm: [3.1 1.3 4.2]\n injection_location: lateral SNc\n label: GCaMP7b\n manufacturer: Addgene\n	optical_fiber abc.OpticalFiber at 0x4963999968\nFields:\n core_diameter_in_um: 400.0\n description: Fiber optic implants (Doric Lenses; 400 um, 0.48 NA) were placed above DMS (AP 0.8, ML 1.5, DV 2.8) and DLS (AP 0.1, ML 2.8, DV 3.5). The DMS implant was placed in the hemisphere receiving a medial SNc viral injection, while the DLS implant was placed in the hemisphere receiving a lateral SNc viral injection. Calcium signals from dopamine terminals in DMS and DLS were recorded during RI30, on the first and last days of RI60/RR20 training as well as on both footshock probes for each mouse. All recordings were done using a fiber photometry rig with optical components from Doric lenses controlled by a real-time processor from Tucker Davis Technologies (TDT; RZ5P). TDT Synapse software was used for data acquisition.\n manufacturer: Doric Lenses\n model: Fiber Optic Implant\n numerical_aperture: 0.48\n	excitation_source_isosbestic_control abc.ExcitationSource at 0x4963998528\nFields:\n description: 465nm and 405nm LEDs were modulated at 211 Hz and 330 Hz, respectively, for DMS probes. 465nm and 405nm LEDs were modulated at 450 Hz and 270 Hz, respectively for DLS probes. LED currents were adjusted in order to return a voltage between 150-200mV for each signal, were offset by 5 mA, were demodulated using a 4 Hz lowpass frequency filter.\n excitation_wavelength_in_nm: 405.0\n illumination_type: LED\n manufacturer: Doric Lenses\n model: Connectorized LED\n	photodetector abc.Photodetector at 0x4964001360\nFields:\n description: This battery-operated photoreceiver has high gain and detects CW light signals in the sub-picowatt to nanowatt range. When used in conjunction with a modulated light source and a lock-in amplifier to reduce the measurement bandwidth, it achieves sensitivity levels in the femtowatt range. Doric offer this Newport product with add-on fiber optic adapter that improves coupling efficiency between the large core, high NA optical fibers used in Fiber Photometry and relatively small detector area. Its output analog voltage (0-5 V) can be monitored with an oscilloscope or with a DAQ board to record the data with a computer.\n detected_wavelength_in_nm: 525.0\n detector_type: photodiode\n gain: 10000000000.0\n manufacturer: Doric Lenses\n model: Newport Visible Femtowatt Photoreceiver Module\n	dichroic_mirror abc.DichroicMirror at 0x4963994496\nFields:\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	[0.1, 2.8, 3.5]	commanded_voltage_series_dls abc.CommandedVoltageSeries at 0x4962255920\nFields:\n comments: no comments\n conversion: 1.0\n data: <HDF5 dataset "data": shape (22570496,), type "<f4">\n description: The commanded voltage for the frequency-modulated DLS calcium signal and DLS isosbestic control.\n frequency__unit: hertz\n offset: 0.0\n rate: 6103.515625\n resolution: -1.0\n starting_time: 0.0\n starting_time_unit: seconds\n unit: volts\n	emission_filter abc.BandOpticalFilter at 0x4963994736\nFields:\n bandwidth_in_nm: 50.0\n center_wavelength_in_nm: 525.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n	isosbestic_excitation_filter abc.BandOpticalFilter at 0x4963999008\nFields:\n bandwidth_in_nm: 10.0\n center_wavelength_in_nm: 405.0\n description: Dual excitation band fiber photometry measurements use a Fluorescence Mini Cube with 4 ports: one port for the functional fluorescence excitation light, one for the isosbestic excitation, one for the fluorescence detection, and one for the sample. The cube has dichroic mirrors to combine isosbestic and fluorescence excitations and separate the fluorescence emission and narrow bandpass filters limiting the excitation fluorescence spectrum.\n filter_type: Bandpass\n manufacturer: Doric Lenses\n model: 4 ports Fluorescence Mini Cube - GCaMP\n

experiment_description: Compulsive behavior is a defining feature of disorders such as substance use disorders. Current evidence suggests that corticostriatal circuits control the expression of established compulsions, but little is known about the mechanisms regulating the development of compulsions. We hypothesized that dopamine, a critical modulator of striatal synaptic plasticity, could control alterations in corticostriatal circuits leading to the development of compulsions (defined here as continued reward seeking in the face of punishment). We used dual-site fiber photometry to measure dopamine axon activity in the dorsomedial striatum (DMS) and the dorsolateral striatum (DLS) as compulsions emerged. Individual variability in the speed with which compulsions emerged was predicted by DMS dopamine axon activity. Amplifying this dopamine signal accelerated animals' transitions to compulsion, whereas inhibition delayed it. In contrast, amplifying DLS dopamine signaling had no effect on the emergence of compulsions. These results establish DMS dopamine signaling as a key controller of the development of compulsive reward seeking.

session_id: FP_PS_2019-06-20T09-32-04

lab: Lerner

institution: Northwestern Unitersity

notes: Hemisphere with DMS: Right Experiment: Fiber Photometry Behavior: RI60 Punishment Group: Punishment Sensitive Did Not Learn: False

source_script: Created using NeuroConv v0.4.11

source_script_file_name: /opt/anaconda3/envs/lerner_lab_to_nwb_env/lib/python3.12/site-packages/neuroconv/basedatainterface.py

surgery: GCaMP7b in DMS & DLS projecting SNc, fiber photometry probes in DMS & DLS

virus: AAV5-CAG-FLEX-jGCaMP7b-WPRE

Retrieve Photometry and Behavioral Data

In [3]:

# Photometry
fiber_photometry_responses = nwbfile.acquisition['fiber_photometry_response_series'].data[:]
dms_calcium_signal = fiber_photometry_responses[:, 0]
dms_isosbestic_control = fiber_photometry_responses[:, 1]
dls_calcium_signal = fiber_photometry_responses[:, 2]
dls_isosbestic_control = fiber_photometry_responses[:, 3]
fs = nwbfile.acquisition['fiber_photometry_response_series'].rate
timestamps = np.arange(0, len(dms_calcium_signal) / fs, 1/fs)

# Behavior
left_nose_poke_times = nwbfile.processing['behavior'].data_interfaces['left_nose_poke_times'].timestamps[:]
left_reward_times = nwbfile.processing['behavior'].data_interfaces['left_reward_times'].timestamps[:]
reward_port_intervals = nwbfile.processing['behavior'].data_interfaces['behavioral_epochs'].interval_series['reward_port_intervals']
reward_port_interval_data = reward_port_intervals.data[:]
reward_port_interval_times = reward_port_intervals.timestamps[:]
reward_port_entry_times = reward_port_interval_times[reward_port_interval_data==1]
reward_port_exit_times = reward_port_interval_times[reward_port_interval_data==-1]

# Photometry fiber_photometry_responses = nwbfile.acquisition['fiber_photometry_response_series'].data[:] dms_calcium_signal = fiber_photometry_responses[:, 0] dms_isosbestic_control = fiber_photometry_responses[:, 1] dls_calcium_signal = fiber_photometry_responses[:, 2] dls_isosbestic_control = fiber_photometry_responses[:, 3] fs = nwbfile.acquisition['fiber_photometry_response_series'].rate timestamps = np.arange(0, len(dms_calcium_signal) / fs, 1/fs) # Behavior left_nose_poke_times = nwbfile.processing['behavior'].data_interfaces['left_nose_poke_times'].timestamps[:] left_reward_times = nwbfile.processing['behavior'].data_interfaces['left_reward_times'].timestamps[:] reward_port_intervals = nwbfile.processing['behavior'].data_interfaces['behavioral_epochs'].interval_series['reward_port_intervals'] reward_port_interval_data = reward_port_intervals.data[:] reward_port_interval_times = reward_port_intervals.timestamps[:] reward_port_entry_times = reward_port_interval_times[reward_port_interval_data==1] reward_port_exit_times = reward_port_interval_times[reward_port_interval_data==-1]

Plot

In [4]:

t_start = 2000
t_end = 2100
photometry_slice = slice(int(t_start * fs), int(t_end * fs))
left_nose_poke_mask = np.logical_and(left_nose_poke_times >= t_start, left_nose_poke_times < t_end)
left_reward_mask = np.logical_and(left_reward_times >= t_start, left_reward_times < t_end)
reward_port_interval_mask = np.logical_and(reward_port_entry_times >= t_start, reward_port_entry_times < t_end)
lineoffsets = 200
linelengths = 50
y = np.arange(170, 180, 0.1)
alpha = 0.3
ylim = [165, 235]

fix, ax = plt.subplots(2, 1, figsize=(10, 10), sharex=True)
ax[0].plot(timestamps[photometry_slice], dms_calcium_signal[photometry_slice], label='Calcium Signal')
ax[0].plot(timestamps[photometry_slice], dms_isosbestic_control[photometry_slice], label='Isosbestic Control')
ax[0].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke')
ax[0].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward')
for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])):
    x1 = reward_port_entry_time*np.ones(len(y))
    x2 = reward_port_exit_time*np.ones(len(y))
    if i == 0:
        ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port')
    else:
        ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha)
ax[0].set_ylim(ylim)
ax[0].set_title('DMS')
ax[0].legend()
ax[0].set_ylabel('Fluorescence (a.u.)')

ax[1].plot(timestamps[photometry_slice], dls_calcium_signal[photometry_slice], label='Calcium Signal')
ax[1].plot(timestamps[photometry_slice], dls_isosbestic_control[photometry_slice], label='Isosbestic Control')
ax[1].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke')
ax[1].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward')
for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])):
    x1 = reward_port_entry_time*np.ones(len(y))
    x2 = reward_port_exit_time*np.ones(len(y))
    if i == 0:
        ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port')
    else:
        ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha)
ax[1].set_ylim(ylim)
ax[1].set_title('DLS')
ax[1].legend()
ax[1].set_xlabel('Time (s)')
_ = ax[1].set_ylabel('Fluorescence (a.u.)')

t_start = 2000 t_end = 2100 photometry_slice = slice(int(t_start * fs), int(t_end * fs)) left_nose_poke_mask = np.logical_and(left_nose_poke_times >= t_start, left_nose_poke_times < t_end) left_reward_mask = np.logical_and(left_reward_times >= t_start, left_reward_times < t_end) reward_port_interval_mask = np.logical_and(reward_port_entry_times >= t_start, reward_port_entry_times < t_end) lineoffsets = 200 linelengths = 50 y = np.arange(170, 180, 0.1) alpha = 0.3 ylim = [165, 235] fix, ax = plt.subplots(2, 1, figsize=(10, 10), sharex=True) ax[0].plot(timestamps[photometry_slice], dms_calcium_signal[photometry_slice], label='Calcium Signal') ax[0].plot(timestamps[photometry_slice], dms_isosbestic_control[photometry_slice], label='Isosbestic Control') ax[0].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke') ax[0].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward') for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])): x1 = reward_port_entry_time*np.ones(len(y)) x2 = reward_port_exit_time*np.ones(len(y)) if i == 0: ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port') else: ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha) ax[0].set_ylim(ylim) ax[0].set_title('DMS') ax[0].legend() ax[0].set_ylabel('Fluorescence (a.u.)') ax[1].plot(timestamps[photometry_slice], dls_calcium_signal[photometry_slice], label='Calcium Signal') ax[1].plot(timestamps[photometry_slice], dls_isosbestic_control[photometry_slice], label='Isosbestic Control') ax[1].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke') ax[1].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward') for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])): x1 = reward_port_entry_time*np.ones(len(y)) x2 = reward_port_exit_time*np.ones(len(y)) if i == 0: ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port') else: ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha) ax[1].set_ylim(ylim) ax[1].set_title('DLS') ax[1].legend() ax[1].set_xlabel('Time (s)') _ = ax[1].set_ylabel('Fluorescence (a.u.)')

Zoom in for more detail

In [5]:

t_start = 2000
t_end = 2020
photometry_slice = slice(int(t_start * fs), int(t_end * fs))
left_nose_poke_mask = np.logical_and(left_nose_poke_times >= t_start, left_nose_poke_times < t_end)
left_reward_mask = np.logical_and(left_reward_times >= t_start, left_reward_times < t_end)
reward_port_interval_mask = np.logical_and(reward_port_entry_times >= t_start, reward_port_entry_times < t_end)
lineoffsets = 200
linelengths = 50
y = np.arange(170, 180, 0.1)
alpha = 0.3
ylim = [165, 235]

fix, ax = plt.subplots(2, 1, figsize=(10, 10), sharex=True)
ax[0].plot(timestamps[photometry_slice], dms_calcium_signal[photometry_slice], label='Calcium Signal')
ax[0].plot(timestamps[photometry_slice], dms_isosbestic_control[photometry_slice], label='Isosbestic Control')
ax[0].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke')
ax[0].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward')
for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])):
    x1 = reward_port_entry_time*np.ones(len(y))
    x2 = reward_port_exit_time*np.ones(len(y))
    if i == 0:
        ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port')
    else:
        ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha)
ax[0].set_ylim(ylim)
ax[0].set_title('DMS')
ax[0].legend()
ax[0].set_ylabel('Fluorescence (a.u.)')

ax[1].plot(timestamps[photometry_slice], dls_calcium_signal[photometry_slice], label='Calcium Signal')
ax[1].plot(timestamps[photometry_slice], dls_isosbestic_control[photometry_slice], label='Isosbestic Control')
ax[1].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke')
ax[1].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward')
for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])):
    x1 = reward_port_entry_time*np.ones(len(y))
    x2 = reward_port_exit_time*np.ones(len(y))
    if i == 0:
        ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port')
    else:
        ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha)
ax[1].set_ylim(ylim)
ax[1].set_title('DLS')
ax[1].legend()
ax[1].set_xlabel('Time (s)')
_ = ax[1].set_ylabel('Fluorescence (a.u.)')

t_start = 2000 t_end = 2020 photometry_slice = slice(int(t_start * fs), int(t_end * fs)) left_nose_poke_mask = np.logical_and(left_nose_poke_times >= t_start, left_nose_poke_times < t_end) left_reward_mask = np.logical_and(left_reward_times >= t_start, left_reward_times < t_end) reward_port_interval_mask = np.logical_and(reward_port_entry_times >= t_start, reward_port_entry_times < t_end) lineoffsets = 200 linelengths = 50 y = np.arange(170, 180, 0.1) alpha = 0.3 ylim = [165, 235] fix, ax = plt.subplots(2, 1, figsize=(10, 10), sharex=True) ax[0].plot(timestamps[photometry_slice], dms_calcium_signal[photometry_slice], label='Calcium Signal') ax[0].plot(timestamps[photometry_slice], dms_isosbestic_control[photometry_slice], label='Isosbestic Control') ax[0].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke') ax[0].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward') for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])): x1 = reward_port_entry_time*np.ones(len(y)) x2 = reward_port_exit_time*np.ones(len(y)) if i == 0: ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port') else: ax[0].fill_betweenx(y, x1, x2, color='b', alpha=alpha) ax[0].set_ylim(ylim) ax[0].set_title('DMS') ax[0].legend() ax[0].set_ylabel('Fluorescence (a.u.)') ax[1].plot(timestamps[photometry_slice], dls_calcium_signal[photometry_slice], label='Calcium Signal') ax[1].plot(timestamps[photometry_slice], dls_isosbestic_control[photometry_slice], label='Isosbestic Control') ax[1].eventplot(left_nose_poke_times[left_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Left Nose Poke') ax[1].eventplot(left_reward_times[left_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Left Reward') for i, (reward_port_entry_time, reward_port_exit_time) in enumerate(zip(reward_port_entry_times[reward_port_interval_mask], reward_port_exit_times[reward_port_interval_mask])): x1 = reward_port_entry_time*np.ones(len(y)) x2 = reward_port_exit_time*np.ones(len(y)) if i == 0: ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='In Reward Port') else: ax[1].fill_betweenx(y, x1, x2, color='b', alpha=alpha) ax[1].set_ylim(ylim) ax[1].set_title('DLS') ax[1].legend() ax[1].set_xlabel('Time (s)') _ = ax[1].set_ylabel('Fluorescence (a.u.)')

In [ ]: