update astrocytes for 3.7 nest, kernel 24.04

notebooks/notebooks/astrocytes/astrocyte_brunel.ipynb

@@ -130,7 +130,7 @@
       },
       "outputs": [],
       "source": [
-        "def plot_dynamics(astro_data, neuron_data, start):\n    \"\"\"Plot the dynamics in neurons and astrocytes.\n\n    The dynamics in the given neuron and astrocyte nodes are plotted. The\n    dynamics in clude IP3 and calcium in the astrocytes, and the SIC input to\n    the neurons.\n\n    Parameters\n    ---------\n    astro_data\n        Data of IP3 and calcium dynamics in the astrocytes.\n    neuron_data\n        Data of SIC input to the neurons.\n    start\n        Start time of the plotted dynamics.\n\n    \"\"\"\n    print(\"Plotting dynamics ...\")\n    # astrocyte data\n    astro_mask = astro_data[\"times\"] > start\n    astro_ip3 = astro_data[\"IP3\"][astro_mask]\n    astro_cal = astro_data[\"Ca\"][astro_mask]\n    astro_times = astro_data[\"times\"][astro_mask]\n    astro_times_set = list(set(astro_times))\n    ip3_means = np.array([np.mean(astro_ip3[astro_times == t]) for t in astro_times_set])\n    ip3_sds = np.array([np.std(astro_ip3[astro_times == t]) for t in astro_times_set])\n    cal_means = np.array([np.mean(astro_cal[astro_times == t]) for t in astro_times_set])\n    cal_sds = np.array([np.std(astro_cal[astro_times == t]) for t in astro_times_set])\n    # neuron data\n    neuron_mask = neuron_data[\"times\"] > start\n    neuron_sic = neuron_data[\"I_SIC\"][neuron_mask]\n    neuron_times = neuron_data[\"times\"][neuron_mask]\n    neuron_times_set = list(set(neuron_times))\n    sic_means = np.array([np.mean(neuron_sic[neuron_times == t]) for t in neuron_times_set])\n    sic_sds = np.array([np.std(neuron_sic[neuron_times == t]) for t in neuron_times_set])\n    # set plots\n    fig, axes = plt.subplots(2, 1, sharex=True)\n    color_ip3 = \"tab:blue\"\n    color_cal = \"tab:green\"\n    color_sic = \"tab:purple\"\n    # astrocyte plot\n    axes[0].set_title(f\"{r'IP$_{3}$'} and {r'Ca$^{2+}$'} in astrocytes (n={len(set(astro_data['senders']))})\")\n    axes[0].set_ylabel(r\"IP$_{3}$ ($\\mu$M)\")\n    axes[0].tick_params(axis=\"y\", labelcolor=color_ip3)\n    axes[0].fill_between(\n        astro_times_set, ip3_means + ip3_sds, ip3_means - ip3_sds, alpha=0.3, linewidth=0.0, color=color_ip3\n    )\n    axes[0].plot(astro_times_set, ip3_means, linewidth=2, color=color_ip3)\n    ax = axes[0].twinx()\n    ax.set_ylabel(r\"Ca$^{2+}$ ($\\mu$M)\")\n    ax.tick_params(axis=\"y\", labelcolor=color_cal)\n    ax.fill_between(\n        astro_times_set, cal_means + cal_sds, cal_means - cal_sds, alpha=0.3, linewidth=0.0, color=color_cal\n    )\n    ax.plot(astro_times_set, cal_means, linewidth=2, color=color_cal)\n    # neuron plot\n    axes[1].set_title(f\"SIC in neurons (n={len(set(neuron_data['senders']))})\")\n    axes[1].set_ylabel(\"SIC (pA)\")\n    axes[1].set_xlabel(\"Time (ms)\")\n    axes[1].fill_between(\n        neuron_times_set, sic_means + sic_sds, sic_means - sic_sds, alpha=0.3, linewidth=0.0, color=color_sic\n    )\n    axes[1].plot(neuron_times_set, sic_means, linewidth=2, color=color_sic)"
+        "def plot_dynamics(astro_data, neuron_data, start):\n    \"\"\"Plot the dynamics in neurons and astrocytes.\n\n    The dynamics in the given neuron and astrocyte nodes are plotted. The\n    dynamics in clude IP3 and calcium in the astrocytes, and the SIC input to\n    the neurons.\n\n    Parameters\n    ---------\n    astro_data\n        Data of IP3 and calcium dynamics in the astrocytes.\n    neuron_data\n        Data of SIC input to the neurons.\n    start\n        Start time of the plotted dynamics.\n\n    \"\"\"\n    print(\"Plotting dynamics ...\")\n    # astrocyte data\n    astro_mask = astro_data[\"times\"] > start\n    astro_ip3 = astro_data[\"IP3\"][astro_mask]\n    astro_cal = astro_data[\"Ca_astro\"][astro_mask]\n    astro_times = astro_data[\"times\"][astro_mask]\n    astro_times_set = list(set(astro_times))\n    ip3_means = np.array([np.mean(astro_ip3[astro_times == t]) for t in astro_times_set])\n    ip3_sds = np.array([np.std(astro_ip3[astro_times == t]) for t in astro_times_set])\n    cal_means = np.array([np.mean(astro_cal[astro_times == t]) for t in astro_times_set])\n    cal_sds = np.array([np.std(astro_cal[astro_times == t]) for t in astro_times_set])\n    # neuron data\n    neuron_mask = neuron_data[\"times\"] > start\n    neuron_sic = neuron_data[\"I_SIC\"][neuron_mask]\n    neuron_times = neuron_data[\"times\"][neuron_mask]\n    neuron_times_set = list(set(neuron_times))\n    sic_means = np.array([np.mean(neuron_sic[neuron_times == t]) for t in neuron_times_set])\n    sic_sds = np.array([np.std(neuron_sic[neuron_times == t]) for t in neuron_times_set])\n    # set plots\n    fig, axes = plt.subplots(2, 1, sharex=True)\n    color_ip3 = \"tab:blue\"\n    color_cal = \"tab:green\"\n    color_sic = \"tab:purple\"\n    # astrocyte plot\n    axes[0].set_title(f\"{r'IP$_{3}$'} and {r'Ca$^{2+}$'} in astrocytes (n={len(set(astro_data['senders']))})\")\n    axes[0].set_ylabel(r\"IP$_{3}$ ($\\mu$M)\")\n    axes[0].tick_params(axis=\"y\", labelcolor=color_ip3)\n    axes[0].fill_between(\n        astro_times_set, ip3_means + ip3_sds, ip3_means - ip3_sds, alpha=0.3, linewidth=0.0, color=color_ip3\n    )\n    axes[0].plot(astro_times_set, ip3_means, linewidth=2, color=color_ip3)\n    ax = axes[0].twinx()\n    ax.set_ylabel(r\"Ca$^{2+}$ ($\\mu$M)\")\n    ax.tick_params(axis=\"y\", labelcolor=color_cal)\n    ax.fill_between(\n        astro_times_set, cal_means + cal_sds, cal_means - cal_sds, alpha=0.3, linewidth=0.0, color=color_cal\n    )\n    ax.plot(astro_times_set, cal_means, linewidth=2, color=color_cal)\n    # neuron plot\n    axes[1].set_title(f\"SIC in neurons (n={len(set(neuron_data['senders']))})\")\n    axes[1].set_ylabel(\"SIC (pA)\")\n    axes[1].set_xlabel(\"Time (ms)\")\n    axes[1].fill_between(\n        neuron_times_set, sic_means + sic_sds, sic_means - sic_sds, alpha=0.3, linewidth=0.0, color=color_sic\n    )\n    axes[1].plot(neuron_times_set, sic_means, linewidth=2, color=color_sic)"
       ]
     },
     {
@@ -148,7 +148,7 @@
       },
       "outputs": [],
       "source": [
-        "def run_simulation():\n    \"\"\"Run simulation of a neuron-astrocyte network.\"\"\"\n    # NEST configuration\n    nest.ResetKernel()\n    nest.resolution = sim_params[\"dt\"]\n    nest.local_num_threads = sim_params[\"n_threads\"]\n    nest.print_time = True\n    nest.overwrite_files = True\n\n    # use random seed for reproducible sampling\n    random.seed(sim_params[\"seed\"])\n\n    # simulation settings\n    pre_sim_time = sim_params[\"pre_sim_time\"]\n    sim_time = sim_params[\"sim_time\"]\n\n    # create and connect nodes\n    exc, inh, astro, noise = create_astro_network()\n    connect_astro_network(exc, inh, astro, noise)\n\n    # create and connect recorders (multimeter default resolution = 1 ms)\n    sr_neuron = nest.Create(\"spike_recorder\")\n    mm_neuron = nest.Create(\"multimeter\", params={\"record_from\": [\"I_SIC\"]})\n    mm_astro = nest.Create(\"multimeter\", params={\"record_from\": [\"IP3\", \"Ca\"]})\n\n    # select nodes randomly and connect them with recorders\n    print(\"Connecting recorders ...\")\n    neuron_list = (exc + inh).tolist()\n    astro_list = astro.tolist()\n    n_neuron_rec_spk = min(len(neuron_list), sim_params[\"N_rec_spk\"])\n    n_neuron_rec_mm = min(len(neuron_list), sim_params[\"N_rec_mm\"])\n    n_astro_rec = min(len(astro), sim_params[\"N_rec_mm\"])\n    neuron_list_for_sr = neuron_list[: min(len(neuron_list), n_neuron_rec_spk)]\n    neuron_list_for_mm = sorted(random.sample(neuron_list, n_neuron_rec_mm))\n    astro_list_for_mm = sorted(random.sample(astro_list, n_astro_rec))\n    nest.Connect(neuron_list_for_sr, sr_neuron)\n    nest.Connect(mm_neuron, neuron_list_for_mm)\n    nest.Connect(mm_astro, astro_list_for_mm)\n\n    # run pre-simulation\n    print(\"Running pre-simulation ...\")\n    nest.Simulate(pre_sim_time)\n\n    # run simulation\n    print(\"Running simulation ...\")\n    nest.Simulate(sim_time)\n\n    # read out recordings\n    neuron_spikes = sr_neuron.events\n    neuron_data = mm_neuron.events\n    astro_data = mm_astro.events\n\n    # make raster plot\n    nest.raster_plot.from_device(\n        sr_neuron, hist=True, title=f\"Raster plot of neuron {neuron_list_for_sr[0]} to {neuron_list_for_sr[-1]}\"\n    )\n\n    # plot dynamics in astrocytes and neurons\n    plot_dynamics(astro_data, neuron_data, 0.0)\n\n    # show plots\n    plt.show()"
+        "def run_simulation():\n    \"\"\"Run simulation of a neuron-astrocyte network.\"\"\"\n    # NEST configuration\n    nest.ResetKernel()\n    nest.resolution = sim_params[\"dt\"]\n    nest.local_num_threads = sim_params[\"n_threads\"]\n    nest.print_time = True\n    nest.overwrite_files = True\n\n    # use random seed for reproducible sampling\n    random.seed(sim_params[\"seed\"])\n\n    # simulation settings\n    pre_sim_time = sim_params[\"pre_sim_time\"]\n    sim_time = sim_params[\"sim_time\"]\n\n    # create and connect nodes\n    exc, inh, astro, noise = create_astro_network()\n    connect_astro_network(exc, inh, astro, noise)\n\n    # create and connect recorders (multimeter default resolution = 1 ms)\n    sr_neuron = nest.Create(\"spike_recorder\")\n    mm_neuron = nest.Create(\"multimeter\", params={\"record_from\": [\"I_SIC\"]})\n    mm_astro = nest.Create(\"multimeter\", params={\"record_from\": [\"IP3\", \"Ca_astro\"]})\n\n    # select nodes randomly and connect them with recorders\n    print(\"Connecting recorders ...\")\n    neuron_list = (exc + inh).tolist()\n    astro_list = astro.tolist()\n    n_neuron_rec_spk = min(len(neuron_list), sim_params[\"N_rec_spk\"])\n    n_neuron_rec_mm = min(len(neuron_list), sim_params[\"N_rec_mm\"])\n    n_astro_rec = min(len(astro), sim_params[\"N_rec_mm\"])\n    neuron_list_for_sr = neuron_list[: min(len(neuron_list), n_neuron_rec_spk)]\n    neuron_list_for_mm = sorted(random.sample(neuron_list, n_neuron_rec_mm))\n    astro_list_for_mm = sorted(random.sample(astro_list, n_astro_rec))\n    nest.Connect(neuron_list_for_sr, sr_neuron)\n    nest.Connect(mm_neuron, neuron_list_for_mm)\n    nest.Connect(mm_astro, astro_list_for_mm)\n\n    # run pre-simulation\n    print(\"Running pre-simulation ...\")\n    nest.Simulate(pre_sim_time)\n\n    # run simulation\n    print(\"Running simulation ...\")\n    nest.Simulate(sim_time)\n\n    # read out recordings\n    neuron_spikes = sr_neuron.events\n    neuron_data = mm_neuron.events\n    astro_data = mm_astro.events\n\n    # make raster plot\n    nest.raster_plot.from_device(\n        sr_neuron, hist=True, title=f\"Raster plot of neuron {neuron_list_for_sr[0]} to {neuron_list_for_sr[-1]}\"\n    )\n\n    # plot dynamics in astrocytes and neurons\n    plot_dynamics(astro_data, neuron_data, 0.0)\n\n    # show plots\n    plt.show()"
       ]
     },
     {
@@ -172,9 +172,9 @@
   ],
   "metadata": {
     "kernelspec": {
-      "display_name": "EBRAINS-23.09",
+      "display_name": "EBRAINS-24.04",
       "language": "python",
-      "name": "ebrains-23.09"
+      "name": "ebrains-24.04"
     },
     "language_info": {
       "codemirror_mode": {
@@ -191,4 +191,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}

notebooks/notebooks/astrocytes/astrocyte_brunel.py

@@ -256,7 +256,7 @@ def plot_dynamics(astro_data, neuron_data, start):
     # astrocyte data
     astro_mask = astro_data["times"] > start
     astro_ip3 = astro_data["IP3"][astro_mask]
-    astro_cal = astro_data["Ca"][astro_mask]
+    astro_cal = astro_data["Ca_astro"][astro_mask]
     astro_times = astro_data["times"][astro_mask]
     astro_times_set = list(set(astro_times))
     ip3_means = np.array([np.mean(astro_ip3[astro_times == t]) for t in astro_times_set])
@@ -329,7 +329,7 @@ def run_simulation():
     # create and connect recorders (multimeter default resolution = 1 ms)
     sr_neuron = nest.Create("spike_recorder")
     mm_neuron = nest.Create("multimeter", params={"record_from": ["I_SIC"]})
-    mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+    mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 
     # select nodes randomly and connect them with recorders
     print("Connecting recorders ...")

notebooks/notebooks/astrocytes/astrocyte_interaction.ipynb

@@ -58,7 +58,7 @@
       },
       "outputs": [],
       "source": [
-        "astrocyte = nest.Create(\"astrocyte_lr_1994\", params=params_astro)\nmm_astro = nest.Create(\"multimeter\", params={\"record_from\": [\"IP3\", \"Ca\"]})\nnest.Connect(mm_astro, astrocyte)"
+        "astrocyte = nest.Create(\"astrocyte_lr_1994\", params=params_astro)\nmm_astro = nest.Create(\"multimeter\", params={\"record_from\": [\"IP3\", \"Ca_astro\"]})\nnest.Connect(mm_astro, astrocyte)"
       ]
     },
     {
@@ -130,15 +130,15 @@
       },
       "outputs": [],
       "source": [
-        "fig, ax = plt.subplots(2, 2, sharex=True, figsize=(6.4, 4.8), dpi=100)\naxes = ax.flat\naxes[0].plot(data_pre[\"times\"], data_pre[\"V_m\"])\naxes[1].plot(data_astro[\"times\"], data_astro[\"IP3\"])\naxes[2].plot(data_post[\"times\"], data_post[\"I_SIC\"])\naxes[3].plot(data_astro[\"times\"], data_astro[\"Ca\"])\naxes[0].set_title(f\"Presynaptic neuron\\n(Poisson rate = {poisson_rate_neuro} Hz)\")\naxes[0].set_ylabel(\"Membrane potential (mV)\")\naxes[2].set_title(\"Postsynaptic neuron\")\naxes[2].set_ylabel(\"Slow inward current (pA)\")\naxes[2].set_xlabel(\"Time (ms)\")\naxes[1].set_title(\"Astrocyte\")\naxes[1].set_ylabel(r\"[IP$_{3}$] ($\\mu$M)\")\naxes[3].set_ylabel(r\"[Ca$^{2+}$] ($\\mu$M)\")\naxes[3].set_xlabel(\"Time (ms)\")\nplt.tight_layout()\nplt.show()\nplt.close()"
+        "fig, ax = plt.subplots(2, 2, sharex=True, figsize=(6.4, 4.8), dpi=100)\naxes = ax.flat\naxes[0].plot(data_pre[\"times\"], data_pre[\"V_m\"])\naxes[1].plot(data_astro[\"times\"], data_astro[\"IP3\"])\naxes[2].plot(data_post[\"times\"], data_post[\"I_SIC\"])\naxes[3].plot(data_astro[\"times\"], data_astro[\"Ca_astro\"])\naxes[0].set_title(f\"Presynaptic neuron\\n(Poisson rate = {poisson_rate_neuro} Hz)\")\naxes[0].set_ylabel(\"Membrane potential (mV)\")\naxes[2].set_title(\"Postsynaptic neuron\")\naxes[2].set_ylabel(\"Slow inward current (pA)\")\naxes[2].set_xlabel(\"Time (ms)\")\naxes[1].set_title(\"Astrocyte\")\naxes[1].set_ylabel(r\"[IP$_{3}$] ($\\mu$M)\")\naxes[3].set_ylabel(r\"[Ca$^{2+}$] ($\\mu$M)\")\naxes[3].set_xlabel(\"Time (ms)\")\nplt.tight_layout()\nplt.show()\nplt.close()"
       ]
     }
   ],
   "metadata": {
     "kernelspec": {
-      "display_name": "EBRAINS-23.09",
+      "display_name": "EBRAINS-24.04",
       "language": "python",
-      "name": "ebrains-23.09"
+      "name": "ebrains-24.04"
     },
     "language_info": {
       "codemirror_mode": {
@@ -155,4 +155,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}

notebooks/notebooks/astrocytes/astrocyte_interaction.py

@@ -95,7 +95,7 @@
 # Create and connect the astrocyte and its devices.
 
 astrocyte = nest.Create("astrocyte_lr_1994", params=params_astro)
-mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 nest.Connect(mm_astro, astrocyte)
 
 ###############################################################################
@@ -133,7 +133,7 @@
 axes[0].plot(data_pre["times"], data_pre["V_m"])
 axes[1].plot(data_astro["times"], data_astro["IP3"])
 axes[2].plot(data_post["times"], data_post["I_SIC"])
-axes[3].plot(data_astro["times"], data_astro["Ca"])
+axes[3].plot(data_astro["times"], data_astro["Ca_astro"])
 axes[0].set_title(f"Presynaptic neuron\n(Poisson rate = {poisson_rate_neuro} Hz)")
 axes[0].set_ylabel("Membrane potential (mV)")
 axes[2].set_title("Postsynaptic neuron")

notebooks/notebooks/astrocytes/astrocyte_single.ipynb

@@ -58,7 +58,7 @@
       },
       "outputs": [],
       "source": [
-        "astrocyte = nest.Create(\"astrocyte_lr_1994\", params=params_astro)\nps_astro = nest.Create(\"poisson_generator\", params={\"rate\": poisson_rate})\nmm_astro = nest.Create(\"multimeter\", params={\"record_from\": [\"IP3\", \"Ca\"]})\nnest.Connect(ps_astro, astrocyte, syn_spec={\"weight\": poisson_weight})\nnest.Connect(mm_astro, astrocyte)"
+        "astrocyte = nest.Create(\"astrocyte_lr_1994\", params=params_astro)\nps_astro = nest.Create(\"poisson_generator\", params={\"rate\": poisson_rate})\nmm_astro = nest.Create(\"multimeter\", params={\"record_from\": [\"IP3\", \"Ca_astro\"]})\nnest.Connect(ps_astro, astrocyte, syn_spec={\"weight\": poisson_weight})\nnest.Connect(mm_astro, astrocyte)"
       ]
     },
     {
@@ -94,15 +94,15 @@
       },
       "outputs": [],
       "source": [
-        "fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6.4, 4.8), dpi=100)\naxes[0].plot(data[\"times\"], data[\"IP3\"])\naxes[1].plot(data[\"times\"], data[\"Ca\"])\naxes[0].set_ylabel(r\"[IP$_{3}$] ($\\mu$M)\")\naxes[1].set_ylabel(r\"[Ca$^{2+}$] ($\\mu$M)\")\naxes[1].set_xlabel(\"Time (ms)\")\nplt.tight_layout()\nplt.show()\nplt.close()"
+        "fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6.4, 4.8), dpi=100)\naxes[0].plot(data[\"times\"], data[\"IP3\"])\naxes[1].plot(data[\"times\"], data[\"Ca_astro\"])\naxes[0].set_ylabel(r\"[IP$_{3}$] ($\\mu$M)\")\naxes[1].set_ylabel(r\"[Ca$^{2+}$] ($\\mu$M)\")\naxes[1].set_xlabel(\"Time (ms)\")\nplt.tight_layout()\nplt.show()\nplt.close()"
       ]
     }
   ],
   "metadata": {
     "kernelspec": {
-      "display_name": "EBRAINS-23.09",
+      "display_name": "EBRAINS-24.04",
       "language": "python",
-      "name": "ebrains-23.09"
+      "name": "ebrains-24.04"
     },
     "language_info": {
       "codemirror_mode": {
@@ -119,4 +119,4 @@
   },
   "nbformat": 4,
   "nbformat_minor": 0
-}
+}

notebooks/notebooks/astrocytes/astrocyte_single.py

@@ -78,7 +78,7 @@
 
 astrocyte = nest.Create("astrocyte_lr_1994", params=params_astro)
 ps_astro = nest.Create("poisson_generator", params={"rate": poisson_rate})
-mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca"]})
+mm_astro = nest.Create("multimeter", params={"record_from": ["IP3", "Ca_astro"]})
 nest.Connect(ps_astro, astrocyte, syn_spec={"weight": poisson_weight})
 nest.Connect(mm_astro, astrocyte)
 
@@ -93,7 +93,7 @@
 
 fig, axes = plt.subplots(2, 1, sharex=True, figsize=(6.4, 4.8), dpi=100)
 axes[0].plot(data["times"], data["IP3"])
-axes[1].plot(data["times"], data["Ca"])
+axes[1].plot(data["times"], data["Ca_astro"])
 axes[0].set_ylabel(r"[IP$_{3}$] ($\mu$M)")
 axes[1].set_ylabel(r"[Ca$^{2+}$] ($\mu$M)")
 axes[1].set_xlabel("Time (ms)")