added reporting

reporting/Cognitive States in the gerbil Parietal Cortex/01 - Complex goal-directed cognitive states are supported by PPC population activity.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "0b931cf7",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/Cognitive States in the gerbil Parietal Cortex/02 - PPC evoked responses are shaped by corresponding cognitive state.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "9c3d897c",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/Cognitive States in the gerbil Parietal Cortex/03 - Dynamics of PPC single units depending on AEP states.ipynb

@@ -0,0 +1,43 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "9325c0d5",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# show micro-structure of PPC units depending on the AEP metric states"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4da7a0c9",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/Cognitive States in the gerbil Parietal Cortex/04 - Reversed timing of late AEP components between A1 and PPC.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": 1,
+   "id": "bf9750e6",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# overlap A1 / PPC AEPs on top of each other\n",
+    "# maybe try to infer correlations"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "fe9071d3",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/Cognitive States in the gerbil Parietal Cortex/05 - Different cognitive states in the same behavior.ipynb

@@ -0,0 +1,33 @@
+{
+ "cells": [
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "4e069761",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/State-dependent neural dynamics in the gerbil Auditory Cortex/00 - Highlights.ipynb

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+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "ea835d2f",
+   "metadata": {},
+   "source": [
+    "## - The structure of Auditory Evoked Responses (AEPs) is dynamic in freely-moving gerbils engaged in the auditory task\n",
+    "\n",
+    "## - Dynamics of the AEPs reflect instant behavioral relevance of the auditory stimulus\n",
+    "\n",
+    "## - Single units in AC exhibit micro- and macro- structural tuning to auditory stimulations depending on their relevance\n",
+    "\n",
+    "## - The micro-structure of single unit responses can be broked down into typical phases (On, Off, early and late post-phases)\n",
+    "\n",
+    "## - Coherent single-unit neuronal activity during certain response phases is driving corresponding AEP components (P1, N1, P2, P3)"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "98f36b37",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/State-dependent neural dynamics in the gerbil Auditory Cortex/03 - Evoked responses are driven by neuronal population activity.ipynb

@@ -0,0 +1,116 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "415b1905",
+   "metadata": {},
+   "source": [
+    "## State separation based on AEP metrics "
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "f5666b26",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# just show low / high AEP metric state (red / gray?)"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "df99ba10",
+   "metadata": {},
+   "source": [
+    "## On-responses are modulated by P1 state"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "3fd32391",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# show example neurons and population statistics\n",
+    "# maybe compute strength of the ON response for each neuron and correlate with P1"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "1c0d058f",
+   "metadata": {},
+   "source": [
+    "## Off responses are ? modulated by N1 state"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 5,
+   "id": "c8c86dd4",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# maybe? check"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "2210ad95",
+   "metadata": {},
+   "source": [
+    "## Early responses are modulated by P2 state"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 6,
+   "id": "8cbda6e1",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# same"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "401a9289",
+   "metadata": {},
+   "source": [
+    "## Late responses are modulated by P3 state"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 7,
+   "id": "3d112a37",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# same"
+   ]
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}

reporting/State-dependent neural dynamics in the gerbil Auditory Cortex/04 - Dynamics of the mismatch response depending on the AEP states.ipynb

@@ -0,0 +1,88 @@
+{
+ "cells": [
+  {
+   "cell_type": "markdown",
+   "id": "57a6fc24",
+   "metadata": {},
+   "source": [
+    "## Mismatch response (MMR) as a measure of stimulus change"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 2,
+   "id": "08a235ca",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# introduce MMR"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "675fcd2e",
+   "metadata": {},
+   "source": [
+    "## MMR response depending on P1, N1, P2 and P3 states"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 3,
+   "id": "033b6507",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# show examples for individual session\n",
+    "# compute across sessions?"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "id": "af381ac6",
+   "metadata": {},
+   "source": [
+    "## Behavioral relevance of the MMR for performance in SIT"
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": 4,
+   "id": "4de99e39",
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "# compute..."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "id": "d287fdfa",
+   "metadata": {},
+   "outputs": [],
+   "source": []
+  }
+ ],
+ "metadata": {
+  "kernelspec": {
+   "display_name": "Python 3 (ipykernel)",
+   "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": "3.8.10"
+  }
+ },
+ "nbformat": 4,
+ "nbformat_minor": 5
+}