000971/lernerlab/seiler_2024/optogenetics_example_notebook.ipynb

{
 "cells": [
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "# Optogenetics Example Session"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 1,
   "metadata": {},
   "outputs": [],
   "source": [
    "from stream_nwbfile import stream_nwbfile\n",
    "import numpy as np\n",
    "import matplotlib.pyplot as plt"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "This notebook showcases one example session from the 000971 dataset containing operant behavior and concurrent excitatory optogenetic stimulation."
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 2,
   "metadata": {},
   "outputs": [
    {
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       "        <div class='container-wrap'><div class='container-header'><div class='xr-obj-type'><h3>root (NWBFile)</h3></div></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".session_description\">session_description: </span><span class=\"field-value\">FR1 Training with optogenetic stimulation, rewards delivered on both left and right nose pokes, optogenetic stimulation delivered on all rewarded nose pokes</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".identifier\">identifier: </span><span class=\"field-value\">fc40e324-a189-49ed-8e65-81e994c0d698</span></div><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".session_start_time\"><b>session_start_time</b></summary><span class=\"field-key\">2020-10-20 13:00:57-05:51</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".timestamps_reference_time\"><b>timestamps_reference_time</b></summary><span class=\"field-key\">2020-10-20 13:00:57-05:51</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".file_create_date\"><b>file_create_date</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".file_create_date[0]\"><b>0</b></summary><span class=\"field-key\">2024-06-11 13:11:05.817671-07:00</span></details></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".experimenter\"><b>experimenter</b></summary><span class=\"field-key\">('Seiler, Jillian L.', 'Cosme, Caitlin V.', 'Sherathiya, Venus N.', 'Schaid, Michael D.', 'Bianco, Joseph M.', 'Bridgemohan, Abigael S.', 'Lerner, Talia N.')</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".related_publications\"><b>related_publications</b></summary><span class=\"field-key\">('https://doi.org/10.1016/j.cub.2022.01.055',)</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".stimulus\"><b>stimulus</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".stimulus['OptogeneticSeries']\"><b>OptogeneticSeries</b></summary><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].resolution\">resolution: </span><span class=\"field-value\">-1.0</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].comments\">comments: </span><span class=\"field-value\">no comments</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].description\">description: </span><span class=\"field-value\">During operant training (beginning with FR1), each rewarded nosepoke was paired with a train of blue light (460nm, 1 s, 20 Hz, 15 mW) generated by an LED light source and pulse generator (Prizmatix). A subset of mice (\"ChR2 Scrambled\") received the same train of light but paired with random nosepokes on a separate RI60 schedule.</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].conversion\">conversion: </span><span class=\"field-value\">1.0</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].offset\">offset: </span><span class=\"field-value\">0.0</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].unit\">unit: </span><span class=\"field-value\">watts</span></div><details><summary style=\"display: list-item; margin-left: 40px;\" class=\"container-fields field-key\" title=\".stimulus['OptogeneticSeries'].data\"><b>data</b></summary></details><details><summary style=\"display: list-item; margin-left: 40px;\" class=\"container-fields field-key\" title=\".stimulus['OptogeneticSeries'].timestamps\"><b>timestamps</b></summary></details><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].timestamps_unit\">timestamps_unit: </span><span class=\"field-value\">seconds</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].interval\">interval: </span><span class=\"field-value\">1</span></div><details><summary style=\"display: list-item; margin-left: 40px;\" class=\"container-fields field-key\" title=\".stimulus['OptogeneticSeries'].site\"><b>site</b></summary><details><summary style=\"display: list-item; margin-left: 60px;\" class=\"container-fields field-key\" title=\".stimulus['OptogeneticSeries'].site.device\"><b>device</b></summary><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].site.device.description\">description: </span><span class=\"field-value\">Optogenetic stimulus pulses were generated from the Optogenetics-LED-Dual (Prizmatix) driven by the Optogenetics PulserPlus (Prizmatix). Engineered for scaling Optogenetics experiments, the Optogenetics-LED-Dual light source features two independent fiber-coupled LED channels each equipped with independent power and switching control. Optogenetics Pulser / PulserPlus are programmable TTL pulse train generators for pulsing LEDs, lasers and shutters used in Optogenetics activation in neurophysiology and behavioral research.</span></div><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].site.device.manufacturer\">manufacturer: </span><span class=\"field-value\">Prizmatix</span></div></details><div style=\"margin-left: 60px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].site.description\">description: </span><span class=\"field-value\">Mice for DMS excitatory optogenetics experiments received 1 ml of AAV5-EF1a-DIO-hChR2(H134R)-EYFP (3.3e13 GC/mL, Addgene, lot v17652) or the control fluorophore-only virus AAV5-EF1a-DIO-EYFP (3.5e12 virus molecules/mL, UNC Vector Core, lot AV4310K) in medial (AP -3.1, ML 0.8, DV -4.7) and a single fiber optic implant (Prizmatix; 250mm core, 0.66 NA) over ipsilateral DMS (AP 0.8, ML 1.5, DV -2.8). Hemispheres were counterbalanced between mice.</span></div><div style=\"margin-left: 60px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].site.excitation_lambda\">excitation_lambda: </span><span class=\"field-value\">460.0</span></div><div style=\"margin-left: 60px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus['OptogeneticSeries'].site.location\">location: </span><span class=\"field-value\">Injection location: medial SNc (AP -3.1, ML 0.8, DV -4.7) \n",
       " Stimulation location: DMS (AP 0.8, ML 1.5, DV -2.8)</span></div></details></details></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".keywords\"><b>keywords</b></summary></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".processing\"><b>processing</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".processing['behavior']\"><b>behavior</b></summary><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].description\">description: </span><span class=\"field-value\">Operant behavioral data from MedPC.\n",
       "MSN = FR1_BOTH_WStim \n",
       "Box = 3</span></div><details><summary style=\"display: list-item; margin-left: 40px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces\"><b>data_interfaces</b></summary><details><summary style=\"display: list-item; margin-left: 60px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces['reward_port_entry_times']\"><b>reward_port_entry_times</b></summary><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].data_interfaces['reward_port_entry_times'].description\">description: </span><span class=\"field-value\">Reward port entry times</span></div><details><summary style=\"display: list-item; margin-left: 80px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces['reward_port_entry_times'].timestamps\"><b>timestamps</b></summary></details><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].data_interfaces['reward_port_entry_times'].timestamps__unit\">timestamps__unit: </span><span class=\"field-value\">seconds</span></div></details><details><summary style=\"display: list-item; margin-left: 60px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces['right_nose_poke_times']\"><b>right_nose_poke_times</b></summary><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].data_interfaces['right_nose_poke_times'].description\">description: </span><span class=\"field-value\">Right nose poke times</span></div><details><summary style=\"display: list-item; margin-left: 80px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces['right_nose_poke_times'].timestamps\"><b>timestamps</b></summary></details><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].data_interfaces['right_nose_poke_times'].timestamps__unit\">timestamps__unit: </span><span class=\"field-value\">seconds</span></div></details><details><summary style=\"display: list-item; margin-left: 60px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces['right_reward_times']\"><b>right_reward_times</b></summary><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].data_interfaces['right_reward_times'].description\">description: </span><span class=\"field-value\">Right reward times</span></div><details><summary style=\"display: list-item; margin-left: 80px;\" class=\"container-fields field-key\" title=\".processing['behavior'].data_interfaces['right_reward_times'].timestamps\"><b>timestamps</b></summary></details><div style=\"margin-left: 80px;\" class=\"container-fields\"><span class=\"field-key\" title=\".processing['behavior'].data_interfaces['right_reward_times'].timestamps__unit\">timestamps__unit: </span><span class=\"field-value\">seconds</span></div></details></details></details></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".epoch_tags\"><b>epoch_tags</b></summary><span class=\"field-key\">set()</span></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".devices\"><b>devices</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".devices['Optogenetics_LED_Dual']\"><b>Optogenetics_LED_Dual</b></summary><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".devices['Optogenetics_LED_Dual'].description\">description: </span><span class=\"field-value\">Optogenetic stimulus pulses were generated from the Optogenetics-LED-Dual (Prizmatix) driven by the Optogenetics PulserPlus (Prizmatix). Engineered for scaling Optogenetics experiments, the Optogenetics-LED-Dual light source features two independent fiber-coupled LED channels each equipped with independent power and switching control. Optogenetics Pulser / PulserPlus are programmable TTL pulse train generators for pulsing LEDs, lasers and shutters used in Optogenetics activation in neurophysiology and behavioral research.</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".devices['Optogenetics_LED_Dual'].manufacturer\">manufacturer: </span><span class=\"field-value\">Prizmatix</span></div></details></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".ogen_sites\"><b>ogen_sites</b></summary><details><summary style=\"display: list-item; margin-left: 20px;\" class=\"container-fields field-key\" title=\".ogen_sites['OptogeneticStimulusSite']\"><b>OptogeneticStimulusSite</b></summary><details><summary style=\"display: list-item; margin-left: 40px;\" class=\"container-fields field-key\" title=\".ogen_sites['OptogeneticStimulusSite'].device\"><b>device</b></summary><div style=\"margin-left: 60px;\" class=\"container-fields\"><span class=\"field-key\" title=\".ogen_sites['OptogeneticStimulusSite'].device.description\">description: </span><span class=\"field-value\">Optogenetic stimulus pulses were generated from the Optogenetics-LED-Dual (Prizmatix) driven by the Optogenetics PulserPlus (Prizmatix). Engineered for scaling Optogenetics experiments, the Optogenetics-LED-Dual light source features two independent fiber-coupled LED channels each equipped with independent power and switching control. Optogenetics Pulser / PulserPlus are programmable TTL pulse train generators for pulsing LEDs, lasers and shutters used in Optogenetics activation in neurophysiology and behavioral research.</span></div><div style=\"margin-left: 60px;\" class=\"container-fields\"><span class=\"field-key\" title=\".ogen_sites['OptogeneticStimulusSite'].device.manufacturer\">manufacturer: </span><span class=\"field-value\">Prizmatix</span></div></details><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".ogen_sites['OptogeneticStimulusSite'].description\">description: </span><span class=\"field-value\">Mice for DMS excitatory optogenetics experiments received 1 ml of AAV5-EF1a-DIO-hChR2(H134R)-EYFP (3.3e13 GC/mL, Addgene, lot v17652) or the control fluorophore-only virus AAV5-EF1a-DIO-EYFP (3.5e12 virus molecules/mL, UNC Vector Core, lot AV4310K) in medial (AP -3.1, ML 0.8, DV -4.7) and a single fiber optic implant (Prizmatix; 250mm core, 0.66 NA) over ipsilateral DMS (AP 0.8, ML 1.5, DV -2.8). Hemispheres were counterbalanced between mice.</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".ogen_sites['OptogeneticStimulusSite'].excitation_lambda\">excitation_lambda: </span><span class=\"field-value\">460.0</span></div><div style=\"margin-left: 40px;\" class=\"container-fields\"><span class=\"field-key\" title=\".ogen_sites['OptogeneticStimulusSite'].location\">location: </span><span class=\"field-value\">Injection location: medial SNc (AP -3.1, ML 0.8, DV -4.7) \n",
       " Stimulation location: DMS (AP 0.8, ML 1.5, DV -2.8)</span></div></details></details><details><summary style=\"display: list-item; margin-left: 0px;\" class=\"container-fields field-key\" title=\".subject\"><b>subject</b></summary><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.age\">age: </span><span class=\"field-value\">P10W/</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.age__reference\">age__reference: </span><span class=\"field-value\">birth</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.description\">description: </span><span class=\"field-value\">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.</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.genotype\">genotype: </span><span class=\"field-value\">DAT-IRES-Cre: B6.SJLSlc6a3tm1.1(cre)Bkmn/J</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.sex\">sex: </span><span class=\"field-value\">F</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.species\">species: </span><span class=\"field-value\">Mus musculus</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.subject_id\">subject_id: </span><span class=\"field-value\">119.416</span></div><div style=\"margin-left: 20px;\" class=\"container-fields\"><span class=\"field-key\" title=\".subject.strain\">strain: </span><span class=\"field-value\">C57BL/6J</span></div></details><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".experiment_description\">experiment_description: </span><span class=\"field-value\">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.</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".session_id\">session_id: </span><span class=\"field-value\">Opto-DMS-Excitatory-ChR2-2020-10-20T13-00-57</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab\">lab: </span><span class=\"field-value\">Lerner</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".institution\">institution: </span><span class=\"field-value\">Northwestern Unitersity</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".notes\">notes: </span><span class=\"field-value\">Hemisphere with DMS: Right\n",
       "Experiment: DMS Excitatory\n",
       "Behavior: RI60\n",
       "Punishment Group: nan\n",
       "Did Not Learn: False\n",
       "</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".source_script\">source_script: </span><span class=\"field-value\">Created using NeuroConv v0.4.11</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".source_script_file_name\">source_script_file_name: </span><span class=\"field-value\">/opt/anaconda3/envs/lerner_lab_to_nwb_env/lib/python3.12/site-packages/neuroconv/basedatainterface.py</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".surgery\">surgery: </span><span class=\"field-value\">ChR2 in DMS projecting SNc, probe in DMS</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".stimulus_notes\">stimulus_notes: </span><span class=\"field-value\">Excitatory stimulation on rewarded nosepokes</span></div></div>"
      ],
      "text/plain": [
       "root pynwb.file.NWBFile at 0x5099719552\n",
       "Fields:\n",
       "  devices: {\n",
       "    Optogenetics_LED_Dual <class 'pynwb.device.Device'>\n",
       "  }\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.\n",
       "  experimenter: ['Seiler, Jillian L.' 'Cosme, Caitlin V.' 'Sherathiya, Venus N.'\n",
       " 'Schaid, Michael D.' 'Bianco, Joseph M.' 'Bridgemohan, Abigael S.'\n",
       " 'Lerner, Talia N.']\n",
       "  file_create_date: [datetime.datetime(2024, 6, 11, 13, 11, 5, 817671, tzinfo=tzoffset(None, -25200))]\n",
       "  identifier: fc40e324-a189-49ed-8e65-81e994c0d698\n",
       "  institution: Northwestern Unitersity\n",
       "  keywords: <StrDataset for HDF5 dataset \"keywords\": shape (9,), type \"|O\">\n",
       "  lab: Lerner\n",
       "  notes: Hemisphere with DMS: Right\n",
       "Experiment: DMS Excitatory\n",
       "Behavior: RI60\n",
       "Punishment Group: nan\n",
       "Did Not Learn: False\n",
       "\n",
       "  ogen_sites: {\n",
       "    OptogeneticStimulusSite <class 'pynwb.ogen.OptogeneticStimulusSite'>\n",
       "  }\n",
       "  processing: {\n",
       "    behavior <class 'pynwb.base.ProcessingModule'>\n",
       "  }\n",
       "  related_publications: ['https://doi.org/10.1016/j.cub.2022.01.055']\n",
       "  session_description: FR1 Training with optogenetic stimulation, rewards delivered on both left and right nose pokes, optogenetic stimulation delivered on all rewarded nose pokes\n",
       "  session_id: Opto-DMS-Excitatory-ChR2-2020-10-20T13-00-57\n",
       "  session_start_time: 2020-10-20 13:00:57-05:51\n",
       "  source_script: Created using NeuroConv v0.4.11\n",
       "  source_script_file_name: /opt/anaconda3/envs/lerner_lab_to_nwb_env/lib/python3.12/site-packages/neuroconv/basedatainterface.py\n",
       "  stimulus: {\n",
       "    OptogeneticSeries <class 'pynwb.ogen.OptogeneticSeries'>\n",
       "  }\n",
       "  stimulus_notes: Excitatory stimulation on rewarded nosepokes\n",
       "  subject: subject pynwb.file.Subject at 0x5099724016\n",
       "Fields:\n",
       "  age: P10W/\n",
       "  age__reference: birth\n",
       "  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.\n",
       "  genotype: DAT-IRES-Cre: B6.SJLSlc6a3tm1.1(cre)Bkmn/J\n",
       "  sex: F\n",
       "  species: Mus musculus\n",
       "  strain: C57BL/6J\n",
       "  subject_id: 119.416\n",
       "\n",
       "  surgery: ChR2 in DMS projecting SNc, probe in DMS\n",
       "  timestamps_reference_time: 2020-10-20 13:00:57-05:51"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "DANDISET_ID = '000971'\n",
    "file_path = 'sub-119-416/sub-119-416_ses-Opto-DMS-Excitatory-ChR2-2020-10-20T13-00-57_ogen.nwb'\n",
    "nwbfile, io = stream_nwbfile(DANDISET_ID, file_path)\n",
    "display(nwbfile)"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Retrieve Optogenetic and Behavioral Data"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 3,
   "metadata": {},
   "outputs": [],
   "source": [
    "# Optogenetic Stimulation\n",
    "optogenetic_stimulation_timestamps = nwbfile.stimulus['OptogeneticSeries'].timestamps[:]\n",
    "optogenetic_stimulation_data = nwbfile.stimulus['OptogeneticSeries'].data[:]\n",
    "opto_onset_times = optogenetic_stimulation_timestamps[optogenetic_stimulation_data == 0.015]\n",
    "opto_offset_times = optogenetic_stimulation_timestamps[optogenetic_stimulation_data == 0]\n",
    "\n",
    "# Behavior\n",
    "right_nose_poke_times = nwbfile.processing['behavior'].data_interfaces['right_nose_poke_times'].timestamps[:]\n",
    "right_reward_times = nwbfile.processing['behavior'].data_interfaces['right_reward_times'].timestamps[:]\n",
    "reward_port_entry_times = nwbfile.processing['behavior'].data_interfaces['reward_port_entry_times'].timestamps[:]"
   ]
  },
  {
   "cell_type": "markdown",
   "metadata": {},
   "source": [
    "Plot"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 4,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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      "text/plain": [
       "<Figure size 1000x500 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "t_start = 1\n",
    "t_end = 3600\n",
    "right_nose_poke_mask = np.logical_and(right_nose_poke_times >= t_start, right_nose_poke_times < t_end)\n",
    "right_reward_mask = np.logical_and(right_reward_times >= t_start, right_reward_times < t_end)\n",
    "reward_port_entry_mask = np.logical_and(reward_port_entry_times >= t_start, reward_port_entry_times < t_end)\n",
    "opto_onset_mask = np.logical_and(opto_onset_times >= t_start, opto_onset_times < t_end)\n",
    "opto_offset_mask = np.logical_and(opto_offset_times >= t_start, opto_offset_times < t_end)\n",
    "lineoffsets = 1\n",
    "linelengths = 1\n",
    "alpha = 0.3\n",
    "ylim = [-2, 2]\n",
    "y = np.arange(-1, 0, 0.1)\n",
    "\n",
    "fix, ax = plt.subplots(figsize=(10, 5))\n",
    "ax.eventplot(right_nose_poke_times[right_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Right Nose Poke')\n",
    "ax.eventplot(right_reward_times[right_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Right Reward')\n",
    "for i, (onset_time, offset_time) in enumerate(zip(opto_onset_times[opto_onset_mask], opto_offset_times[opto_offset_mask])):\n",
    "    x1 = onset_time*np.ones(len(y))\n",
    "    x2 = offset_time*np.ones(len(y))\n",
    "    if i == 0:\n",
    "        ax.fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='Optogenetic Stimulation')\n",
    "    else:\n",
    "        ax.fill_betweenx(y, x1, x2, color='b', alpha=alpha)\n",
    "ax.set_ylim(ylim)\n",
    "ax.set_title('DMS Excitatory ChR2')\n",
    "ax.yaxis.set_visible(False)\n",
    "ax.set_xlabel('Time (s)')\n",
    "_ = ax.legend(bbox_to_anchor=(1.01, 1), loc='upper left')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": 5,
   "metadata": {},
   "outputs": [
    {
     "data": {
      "image/png": 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      "text/plain": [
       "<Figure size 1000x500 with 1 Axes>"
      ]
     },
     "metadata": {},
     "output_type": "display_data"
    }
   ],
   "source": [
    "t_start = 2200\n",
    "t_end = 2250\n",
    "right_nose_poke_mask = np.logical_and(right_nose_poke_times >= t_start, right_nose_poke_times < t_end)\n",
    "right_reward_mask = np.logical_and(right_reward_times >= t_start, right_reward_times < t_end)\n",
    "reward_port_entry_mask = np.logical_and(reward_port_entry_times >= t_start, reward_port_entry_times < t_end)\n",
    "opto_onset_mask = np.logical_and(opto_onset_times >= t_start, opto_onset_times < t_end)\n",
    "opto_offset_mask = np.logical_and(opto_offset_times >= t_start, opto_offset_times < t_end)\n",
    "lineoffsets = 1\n",
    "linelengths = 1\n",
    "alpha = 0.3\n",
    "ylim = [-2, 2]\n",
    "y = np.arange(-1, 0, 0.1)\n",
    "\n",
    "fix, ax = plt.subplots(figsize=(10, 5))\n",
    "ax.eventplot(right_nose_poke_times[right_nose_poke_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='r', label='Right Nose Poke')\n",
    "ax.eventplot(right_reward_times[right_reward_mask], lineoffsets=lineoffsets, linelengths=linelengths, color='g', label='Right Reward')\n",
    "for i, (onset_time, offset_time) in enumerate(zip(opto_onset_times[opto_onset_mask], opto_offset_times[opto_offset_mask])):\n",
    "    x1 = onset_time*np.ones(len(y))\n",
    "    x2 = offset_time*np.ones(len(y))\n",
    "    if i == 0:\n",
    "        ax.fill_betweenx(y, x1, x2, color='b', alpha=alpha, label='Optogenetic Stimulation')\n",
    "    else:\n",
    "        ax.fill_betweenx(y, x1, x2, color='b', alpha=alpha)\n",
    "ax.set_ylim(ylim)\n",
    "ax.set_title('DMS Excitatory ChR2')\n",
    "ax.yaxis.set_visible(False)\n",
    "ax.set_xlabel('Time (s)')\n",
    "_ = ax.legend(bbox_to_anchor=(1.01, 1), loc='upper left')"
   ]
  },
  {
   "cell_type": "code",
   "execution_count": null,
   "metadata": {},
   "outputs": [],
   "source": []
  }
 ],
 "metadata": {
  "kernelspec": {
   "display_name": "lerner_notebook_env",
   "language": "python",
   "name": "python3"
  },
  "language_info": {
   "codemirror_mode": {
    "name": "ipython",
    "version": 3
   },
   "file_extension": ".py",
   "mimetype": "text/x-python",
   "name": "python",
   "nbconvert_exporter": "python",
   "pygments_lexer": "ipython3",
   "version": "3.10.0"
  }
 },
 "nbformat": 4,
 "nbformat_minor": 2
}