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Add support for recording and processing dLight with pyPhotometry (#174)
* Add support for recording dLight with pyPhotometry * Update example metadata files
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‎README.md‎

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## Usage
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1. Open `metadata_example.yaml` in a text editor. Update the paths to point to your data and update the metadata for your experiment.
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1. Open one of the example metadata files in a text editor (`metadata_example_Jose.yaml` for Jose's experiments, or `metadata_example_Tim.yaml` for Tim / Yang-Sun / Stephanie's experiments). Update the paths to point to your data and update the metadata for your experiment. See `metadata_fully_explained.yaml` for an explanation of all metadata fields.
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2. Run the conversion to generate an NWB file (replace `output_dir` with your desired output directory).
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The nwb file will be automatically named based on the animal name and date (i.e. `rat_date.nwb`):

‎metadata_example.yaml‎

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‎metadata_example_Jose.yaml‎

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# Example metadata file for one of Jose's experiments
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# Bilateral injection of gACh4h and rDA3m in NAcc
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# Recording using pyPhotometry in the new maze room
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institution: University of California, San Francisco
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lab: Berke Lab
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experimenter:
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- Figueroa, Jose
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experiment_description: Hex maze task
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animal_name: IM-1891_jimmy
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date: "20250723"
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subject:
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subject_id: IM-1891
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species: Rattus norvegicus
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genotype: Wildtype
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sex: M
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date_of_birth: 2024-10-17
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description: Long Evans Rat
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photometry:
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# Recording was done using pyPhotometry
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ppd_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/RecordingDay17_ProbSwitch_Lhem_CKTL-2025-07-23-123503.ppd"
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# Excitation sources for the new maze room
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excitation_sources:
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- Doric Purple LED
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- Doric Blue LED
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- Doric Green LED
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# Photodetector for the new maze room
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photodetector: Doric ilFMC7-G2 (Integrated LED Fluorescence Mini Cube 5 ports Gen.2)
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# Bilateral optic fibers in NAcc
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optic_fiber_implant_sites:
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- optic_fiber: Doric 0.66mm Flat 40mm Optic Fiber
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targeted_location: NAcc
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ap_in_mm: 1.8
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ml_in_mm: 1.8
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dv_in_mm: -6.0 # 6.0 mm deep for males, 5.8 mm deep for females
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recording: true # Recorded from the right hemisphere
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- optic_fiber: Doric 0.66mm Flat 40mm Optic Fiber
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targeted_location: NAcc
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ap_in_mm: 1.8
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ml_in_mm: -1.8
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dv_in_mm: -6.0 # 6.0 mm deep for males, 5.8 mm deep for females
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# Bilateral injection of cocktail virus in NAcc
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virus_injections:
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# Right Hemisphere
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- virus_name: gACh4h
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targeted_location: NAcc
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ap_in_mm: 1.8
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ml_in_mm: 1.8
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dv_in_mm: -6.2 # 6.2 mm deep for males, 6.0 mm deep for females
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volume_in_uL: 1.0
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titer_in_vg_per_mL: 1.15e13
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- virus_name: rDA3m (AAV9)
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targeted_location: NAcc
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ap_in_mm: 1.8
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ml_in_mm: 1.8
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dv_in_mm: -6.2 # 6.2 mm deep for males, 6.0 mm deep for females
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volume_in_uL: 1.0
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titer_in_vg_per_mL: 5.89e12
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# Left Hemisphere
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- virus_name: gACh4h
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targeted_location: NAcc
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ap_in_mm: 1.8
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ml_in_mm: -1.8
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dv_in_mm: -6.2 # 6.2 mm deep for males, 6.0 mm deep for females
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volume_in_uL: 1.0
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titer_in_vg_per_mL: 1.15e13
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- virus_name: rDA3m (AAV9)
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targeted_location: NAcc
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ap_in_mm: 1.8
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ml_in_mm: -1.8
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dv_in_mm: -6.2 # 6.2 mm deep for males, 6.0 mm deep for females
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volume_in_uL: 1.0
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titer_in_vg_per_mL: 5.89e12
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behavior:
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arduino_text_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/arduinoraw0.txt"
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arduino_timestamps_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/ArduinoStamps0.csv"
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maze_configuration_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/barriers.txt"
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video:
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video_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/Behav_Vid0.avi"
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video_timestamps_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/testvidtimes0.csv"
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dlc_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/Behav_Vid0DLC_resnet50_Triangle_Maze_PhotMar24shuffle1_800000.h5"
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hex_centroids_file_path: "C:/Users/j2fig/OneDrive - UCSF/ACh Rats/IM-1891_jimmy/20250723/IM-1891_jimmy_20250723_hex_coordinates.csv"
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surgery:
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Surgery took place on 2025-05-03.
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Rat was bilaterally injected in the nucleus accumbens core with both ACh3.8 and rDA3m AAV virus.
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Fibers were placed bilaterally, targeting the NAcc.
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No Complications
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virus:
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ACh3.8 and rDA3m AAV virus were injected bilaterally into the nucleus accumbens core on 2024-05-03.
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The titer for rDA3m was 5.89e12 vg/mL and ACh3.8 was 1.15e13 (BrainVTA).
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The injection was done in a cocktail at a volume was 1.0 uL per hemisphere.
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notes:
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Reward used was 30uL sucrose solution (10% sucrose, 0.1% NaCl) at each reward port.
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The rat was water deprived before the experiment.
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keywords:
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- photometry
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- behavior
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- hex maze
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- dopamine
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- acetylcholine
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- reward

‎metadata_example_Tim.yaml‎

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# Example metadata file for one of Tim's experiments
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# Bilateral injection of dLight in NAcc + 256-ch silicon probe in Hippocampus CA1
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# Recording using LabVIEW in the old maze room
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institution: University of California, San Francisco
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lab: Berke Lab
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experimenter:
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- Tim Krausz
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experiment_description: Hex maze task
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date: 07/19/2022
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subject:
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subject_id: IM-1478
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species: Rattus norvegicus
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genotype: Wildtype
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sex: M
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age: 6mo # exact age unknown
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description: Long Evans Rat
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ephys:
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impedance_file_path: "/Volumes/Tim/Ephys/IM-1478/07192022/impedance.csv"
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openephys_folder_path: "/Volumes/Tim/Ephys/IM-1478/07192022/2022-07-19_13-12-30"
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electrodes_location: "Hippocampus CA1"
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targeted_x: 4.5 # AP in mm
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targeted_y: -2.2 # ML in mm
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targeted_z: -2.0 # DV in mm
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mountain_sort_output_file_path: "/Volumes/Tim/Ephys/IM-1478/07192022/mntsort_output/firings.mda"
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sampling_frequency: 30000
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probe:
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- "256-ch Silicon Probe, 3mm length, 66um pitch"
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photometry:
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# Recording was done using LabVIEW
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phot_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/IM-1478_2022-07-19_13-07-06____Tim_Conditioning.phot"
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box_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/IM-1478_2022-07-19_13-07-06____Tim_Conditioning.box"
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# Excitation sources for the old maze room
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excitation_sources:
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- Thorlabs Purple LED
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- Thorlabs Blue LED
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# Photodetector for the old maze room
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photodetector: Doric iFMC7-G2 (7 ports Fluorescence Mini Cube - Three Fluorophores)
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# Bilateral optic fibers in NAcc
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optic_fiber_implant_sites:
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- optic_fiber: Doric 0.66mm Flat 40mm Optic Fiber
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targeted_location: NAcc
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ap_in_mm: 1.7
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ml_in_mm: 1.7
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dv_in_mm: -6.0
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- optic_fiber: Doric 0.66mm Flat 40mm Optic Fiber
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targeted_location: NAcc
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ap_in_mm: 1.7
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ml_in_mm: -1.7
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dv_in_mm: -6.0
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recording: true # Recorded from left hemisphere
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# Bilateral injection of dLight in NAcc
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virus_injections:
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- virus_name: dLight1.3b
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targeted_location: NAcc
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ap_in_mm: 1.7
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ml_in_mm: 1.7
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dv_in_mm: -6.2
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volume_in_uL: 1.0
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titer_in_vg_per_mL: 2e12
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- virus_name: dLight1.3b
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targeted_location: NAcc
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ap_in_mm: 1.7
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ml_in_mm: -1.7
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dv_in_mm: -6.2
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volume_in_uL: 1.0
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titer_in_vg_per_mL: 2e12
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behavior:
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arduino_text_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/arduinoraw0.txt"
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arduino_timestamps_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/ArduinoStamps0.csv"
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maze_configuration_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/barriers.txt"
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video:
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video_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/Behav_Vid0.avi"
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video_timestamps_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/testvidtimes0.csv"
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dlc_path: "/Volumes/Tim/Photometry/IM-1478/07192022/Behav_Vid0DLC_resnet50_Triangle_Maze_EphysDec7shuffle1_800000.h5"
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hex_centroids_file_path: "/Volumes/Tim/Photometry/IM-1478/07192022/IM-1478_07192022_hex_coordinates.csv"
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surgery:
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Bilateral dLight 1.3b and optic fibers. Fiber implant was .2 mm above injection site (DV -6.0).
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Hippocampal implant was in the left hemisphere.
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virus:
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AAVDJ-CAG-dLight1.3b (Vigene) at a titer of 2x10^12 at AP +1.7, ML +/-1.7, DV -6.2
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notes:
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Reward used was 15uL sucrose solution (10% sucrose, 0.1% NaCl) at each reward port.
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The rat was water deprived before the experiment.
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keywords:
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- photometry
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- ephys
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- behavior
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- video
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- hex maze
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- dopamine
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- reward
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- credit assignment

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