finalized notebooks

Author: pauladkisson

001259/ephys_example_notebook.ipynb

@@ -9,7 +9,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 3,
+   "execution_count": 1,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -22,12 +22,12 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "This notebook showcases one example session from the 001259 dataset containing operant behavior and concurrent electrophysiology recording."
+    "This notebook showcases one example session from the 001259 dataset containing operant behavior and concurrent OpenEphys recordings in primary auditory cortex (A1)."
    ]
   },
   {
    "cell_type": "code",
-   "execution_count": 4,
+   "execution_count": 2,
    "metadata": {},
    "outputs": [
     {
@@ -94,7 +94,7 @@
        "    <tr>\n",
        "      <th>0</th>\n",
        "      <td>Primary Auditory Cortex (A1)</td>\n",
-       "      <td>ElectrodeGroup pynwb.ecephys.ElectrodeGroup at 0x4995524336\\nFields:\\n  description: ElectrodeGroup for all channels in the recording probe.\\n  device: MasmanidisSiliconMicroprobe128AxN pynwb.device.Device at 0x4995525104\\nFields:\\n  description: Masmanidis Lab dense 128-channel recording probes (https://masmanidislab.neurobio.ucla.edu/technology.html).\\n  manufacturer: Masmanidis Lab\\n\\n  location: Primary Auditory Cortex (A1)\\n</td>\n",
+       "      <td>ElectrodeGroup pynwb.ecephys.ElectrodeGroup at 0x4788585536\\nFields:\\n  description: ElectrodeGroup for all channels in the recording probe.\\n  device: MasmanidisSiliconMicroprobe128AxN pynwb.device.Device at 0x4368008688\\nFields:\\n  description: Masmanidis Lab dense 128-channel recording probes (https://masmanidislab.neurobio.ucla.edu/technology.html).\\n  manufacturer: Masmanidis Lab\\n\\n  location: Primary Auditory Cortex (A1)\\n</td>\n",
        "      <td>ElectrodeGroup</td>\n",
        "      <td>CH16</td>\n",
        "      <td>200.0</td>\n",
@@ -152,7 +152,7 @@
        "    <tr>\n",
        "      <th>0</th>\n",
        "      <td>Primary Auditory Cortex (A1)</td>\n",
-       "      <td>ElectrodeGroup pynwb.ecephys.ElectrodeGroup at 0x4995524336\\nFields:\\n  description: ElectrodeGroup for all channels in the recording probe.\\n  device: MasmanidisSiliconMicroprobe128AxN pynwb.device.Device at 0x4995525104\\nFields:\\n  description: Masmanidis Lab dense 128-channel recording probes (https://masmanidislab.neurobio.ucla.edu/technology.html).\\n  manufacturer: Masmanidis Lab\\n\\n  location: Primary Auditory Cortex (A1)\\n</td>\n",
+       "      <td>ElectrodeGroup pynwb.ecephys.ElectrodeGroup at 0x4788585536\\nFields:\\n  description: ElectrodeGroup for all channels in the recording probe.\\n  device: MasmanidisSiliconMicroprobe128AxN pynwb.device.Device at 0x4368008688\\nFields:\\n  description: Masmanidis Lab dense 128-channel recording probes (https://masmanidislab.neurobio.ucla.edu/technology.html).\\n  manufacturer: Masmanidis Lab\\n\\n  location: Primary Auditory Cortex (A1)\\n</td>\n",
        "      <td>ElectrodeGroup</td>\n",
        "      <td>CH16</td>\n",
        "      <td>200.0</td>\n",
@@ -487,7 +487,7 @@
        "</table><p>... and 231 more rows.</p></details></details><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".experiment_description\">experiment_description: </span><span class=\"field-value\">Identifying mistakes is important for improving performance during acoustic behaviors like speech and musicianship. Although hearing is instrumental for monitoring and adapting these behaviors, the neural circuits that integrate motor, acoustic, and goal-related signals to detect errors and guide ongoing sensorimotor adaptation in mammals remain unidentified. Here, we develop a novel closed-loop, sound-guided behavior that requires mice to use real-time acoustic feedback to guide skilled ongoing forelimb movements. Large scale electrophysiology recordings reveal that the mouse auditory cortex integrates information about sound and movement, as well as encodes error- and learning-related signals during this sound-generating behavior. Distinct groups of auditory cortex neurons signal different error types, and the activity of these neurons predicts both within-trial and across-trial behavioral adaptations. Brief, behavior-triggered optogenetic suppression of auditory cortex during error signaling hinders behavioral corrections on both rapid and long time scales, indicating that cortical error signals are necessary for skilled acoustic behaviors. Together, these experiments identify a cortical role for detecting errors and learning from mistakes and suggest that the auditory cortex plays a critical role in skilled, sound-generating behavior in mammals.</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".session_id\">session_id: </span><span class=\"field-value\">231029</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab\">lab: </span><span class=\"field-value\">Schneider</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".institution\">institution: </span><span class=\"field-value\">New York University</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 v0.6.5</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/schneider_lab_to_nwb_env/lib/python3.12/site-packages/neuroconv/basedatainterface.py</span></div></div>"
       ],
       "text/plain": [
-       "root pynwb.file.NWBFile at 0x4987780608\n",
+       "root pynwb.file.NWBFile at 0x4789700848\n",
        "Fields:\n",
        "  acquisition: {\n",
        "    ElectricalSeries <class 'pynwb.ecephys.ElectricalSeries'>,\n",
@@ -526,7 +526,7 @@
        "  session_start_time: 2023-10-29 16:56:01-04:00\n",
        "  source_script: Created using NeuroConv v0.6.5\n",
        "  source_script_file_name: /opt/anaconda3/envs/schneider_lab_to_nwb_env/lib/python3.12/site-packages/neuroconv/basedatainterface.py\n",
-       "  subject: subject pynwb.file.Subject at 0x4993512896\n",
+       "  subject: subject pynwb.file.Subject at 0x4793637520\n",
        "Fields:\n",
        "  age: P12W/\n",
        "  age__reference: birth\n",
@@ -562,7 +562,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 5,
+   "execution_count": 3,
    "metadata": {},
    "outputs": [],
    "source": [
@@ -604,7 +604,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 6,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -702,7 +702,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 7,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {

001259/opto_example_notebook.ipynb

@@ -284,7 +284,7 @@
        "</table><p>... and 433 more rows.</p></details></details><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".experiment_description\">experiment_description: </span><span class=\"field-value\">Identifying mistakes is important for improving performance during acoustic behaviors like speech and musicianship. Although hearing is instrumental for monitoring and adapting these behaviors, the neural circuits that integrate motor, acoustic, and goal-related signals to detect errors and guide ongoing sensorimotor adaptation in mammals remain unidentified. Here, we develop a novel closed-loop, sound-guided behavior that requires mice to use real-time acoustic feedback to guide skilled ongoing forelimb movements. Large scale electrophysiology recordings reveal that the mouse auditory cortex integrates information about sound and movement, as well as encodes error- and learning-related signals during this sound-generating behavior. Distinct groups of auditory cortex neurons signal different error types, and the activity of these neurons predicts both within-trial and across-trial behavioral adaptations. Brief, behavior-triggered optogenetic suppression of auditory cortex during error signaling hinders behavioral corrections on both rapid and long time scales, indicating that cortical error signals are necessary for skilled acoustic behaviors. Together, these experiments identify a cortical role for detecting errors and learning from mistakes and suggest that the auditory cortex plays a critical role in skilled, sound-generating behavior in mammals.</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".session_id\">session_id: </span><span class=\"field-value\">231013</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".lab\">lab: </span><span class=\"field-value\">Schneider</span></div><div style=\"margin-left: 0px;\" class=\"container-fields\"><span class=\"field-key\" title=\".institution\">institution: </span><span class=\"field-value\">New York University</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 v0.6.5</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/schneider_lab_to_nwb_env/lib/python3.12/site-packages/neuroconv/basedatainterface.py</span></div></div>"
       ],
       "text/plain": [
-       "root pynwb.file.NWBFile at 0x5011575040\n",
+       "root pynwb.file.NWBFile at 0x4956450992\n",
        "Fields:\n",
        "  acquisition: {\n",
        "    video_camera_1 <class 'pynwb.image.ImageSeries'>,\n",
@@ -324,7 +324,7 @@
        "  stimulus: {\n",
        "    optogenetic_series <class 'pynwb.ogen.OptogeneticSeries'>\n",
        "  }\n",
-       "  subject: subject pynwb.file.Subject at 0x5011396256\n",
+       "  subject: subject pynwb.file.Subject at 0x4960712176\n",
        "Fields:\n",
        "  age: P12W/\n",
        "  age__reference: birth\n",
@@ -398,7 +398,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 10,
+   "execution_count": 4,
    "metadata": {},
    "outputs": [
     {
@@ -486,7 +486,7 @@
   },
   {
    "cell_type": "code",
-   "execution_count": 11,
+   "execution_count": 5,
    "metadata": {},
    "outputs": [
     {