diff --git a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip index ec7294b5a..b1677c38b 100644 Binary files a/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip and b/dev/_downloads/07fcc19ba03226cd3d83d4e40ec44385/auto_examples_python.zip differ diff --git a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip index 9616d9959..0822230f4 100644 Binary files a/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip and b/dev/_downloads/6f1e7a639e0699d6164445b55e6c116d/auto_examples_jupyter.zip differ diff --git a/dev/_downloads/9575eddd15339b520cfc58b84c61894f/optimize_evoked.zip b/dev/_downloads/9575eddd15339b520cfc58b84c61894f/optimize_evoked.zip index 97407b667..1237fc7c2 100644 Binary files a/dev/_downloads/9575eddd15339b520cfc58b84c61894f/optimize_evoked.zip and b/dev/_downloads/9575eddd15339b520cfc58b84c61894f/optimize_evoked.zip differ diff --git a/dev/_downloads/b52c981e7b898beab8949a80ade71521/optimize_rhythmic.zip b/dev/_downloads/b52c981e7b898beab8949a80ade71521/optimize_rhythmic.zip index bf082accb..27e65f110 100644 Binary files a/dev/_downloads/b52c981e7b898beab8949a80ade71521/optimize_rhythmic.zip and b/dev/_downloads/b52c981e7b898beab8949a80ade71521/optimize_rhythmic.zip differ diff --git a/dev/_modules/hnn_core/cell_response.html b/dev/_modules/hnn_core/cell_response.html index becf941a8..b8caa8bbd 100644 --- a/dev/_modules/hnn_core/cell_response.html +++ b/dev/_modules/hnn_core/cell_response.html @@ -151,14 +151,14 @@

Source code for hnn_core.cell_response

 
     Parameters
     ----------
-    spike_times : list (n_trials,) of list (n_spikes,) of float, shape | None
+    spike_times : list (n_trials,) of list (n_spikes,) of float | None
         Each element of the outer list is a trial.
         The inner list contains the time stamps of spikes.
-    spike_gids : list (n_trials,) of list (n_spikes,) of float, shape | None
+    spike_gids : list (n_trials,) of list (n_spikes,) of float | None
         Each element of the outer list is a trial.
         The inner list contains the cell IDs of neurons that
         spiked.
-    spike_types : list (n_trials,) of list (n_spikes,) of float, shape | None
+    spike_types : list (n_trials,) of list (n_spikes,) of float | None
         Each element of the outer list is a trial.
         The inner list contains the type of spike (e.g., evprox1
         or L2_pyramidal) that occurred at the corresponding time stamp.
@@ -172,22 +172,22 @@ 
Source code for hnn_core.cell_response
 
     Attributes
     ----------
-    spike_times : list (n_trials,) of list (n_spikes,) of float, shape
+    spike_times : list (n_trials,) of list (n_spikes,) of float
         Each element of the outer list is a trial.
         The inner list contains the time stamps of spikes.
-    spike_gids : list (n_trials,) of list (n_spikes,) of float, shape
+    spike_gids : list (n_trials,) of list (n_spikes,) of float
         Each element of the outer list is a trial.
         The inner list contains the cell IDs of neurons that
         spiked.
-    spike_types : list (n_trials,) of list (n_spikes,) of float, shape
+    spike_types : list (n_trials,) of list (n_spikes,) of float
         Each element of the outer list is a trial.
         The inner list contains the type of spike (e.g., evprox1
         or L2_pyramidal) that occurred at the corresponding time stamp.
         Each gid corresponds to a type via Network::gid_ranges.
-    vsec : list (n_trials,) of dict, shape
+    vsec : list (n_trials,) of dict
         Each element of the outer list is a trial.
         Dictionary indexed by gids containing voltages for cell sections.
-    isec : list (n_trials,) of dict, shape
+    isec : list (n_trials,) of dict
         Each element of the outer list is a trial.
         Dictionary indexed by gids containing currents for cell sections.
     ca : list (n_trials,) of dict, shape
@@ -276,78 +276,13 @@ 
Source code for hnn_core.cell_response
         return (times_self == times_other and
                 self._spike_gids == other._spike_gids and
                 self._spike_types == other._spike_types and
+                self._vsec == other._vsec and
+                self._isec == other._isec and
+                self._ca == other._ca and
                 self.vsec == other.vsec and
                 self.isec == other.isec and
                 self.ca == other.ca)
 
-
[docs]    def __getitem__(self, gid_item):
-        """Returns a CellResponse object with a copied subset filtered by gid.
-
-        Parameters
-        ----------
-        gid_item : int | slice
-            Subset of gids .
-
-        Returns
-        -------
-        cell_response : instance of CellResponse
-            See below for use cases.
-        """
-
-        if isinstance(gid_item, slice):
-            gid_item = np.arange(gid_item.stop)[gid_item]
-        elif isinstance(gid_item, list):
-            gid_item = np.array(gid_item)
-        elif isinstance(gid_item, np.ndarray):
-            if gid_item.ndim > 1:
-                raise ValueError("ndarray cannot exceed 1 dimension")
-            else:
-                pass
-        elif isinstance(gid_item, int):
-            gid_item = np.array([gid_item])
-        else:
-            raise TypeError("indices must be int, slice, or array-like, "
-                            f"not {type(gid_item).__name__}")
-
-        if not np.issubdtype(gid_item.dtype, np.integer):
-            raise TypeError("gids must be of dtype int, "
-                            f"not {gid_item.dtype.name}")
-
-        n_trials = len(self._spike_times)
-        times_slice = list()
-        gids_slice = list()
-        types_slice = list()
-        vsoma_slice = list()
-        isoma_slice = list()
-        for trial_idx in range(n_trials):
-            gid_mask = np.isin(self._spike_gids[trial_idx], gid_item)
-            times_trial = np.array(
-                self._spike_times[trial_idx])[gid_mask].tolist()
-            gids_trial = np.array(
-                self._spike_gids[trial_idx])[gid_mask].tolist()
-            types_trial = np.array(
-                self._spike_types[trial_idx])[gid_mask].tolist()
-
-            vsoma_trial = {gid: self._vsoma[trial_idx][gid] for gid in gid_item
-                           if gid in self._vsoma[trial_idx].keys()}
-
-            isoma_trial = {gid: self._isoma[trial_idx][gid] for gid in gid_item
-                           if gid in self._isoma[trial_idx].keys()}
-
-            times_slice.append(times_trial)
-            gids_slice.append(gids_trial)
-            types_slice.append(types_trial)
-            vsoma_slice.append(vsoma_trial)
-            isoma_slice.append(isoma_trial)
-
-        cell_response_slice = CellResponse(spike_times=times_slice,
-                                           spike_gids=gids_slice,
-                                           spike_types=types_slice)
-        cell_response_slice._vsoma = vsoma_slice
-        cell_response_slice._isoma = isoma_slice
-
-        return cell_response_slice

-
     @property
     def spike_times(self):
         return self._spike_times
diff --git a/dev/_modules/hnn_core/viz.html b/dev/_modules/hnn_core/viz.html
index 4edab419b..e0b7e2293 100644
--- a/dev/_modules/hnn_core/viz.html
+++ b/dev/_modules/hnn_core/viz.html
@@ -599,7 +599,10 @@ 
Source code for hnn_core.viz
     elif isinstance(color, list):
         color_cycle = cycle(color)
 
-    bins = np.linspace(0, spike_times[-1], 50)
+    if len(cell_response.times) > 0:
+        bins = np.linspace(0, cell_response.times[-1], 50)
+    else:
+        bins = np.linspace(0, spike_times[-1], 50)
 
     # Create dictionary to aggregate spike times that have the same spike_label
     spike_type_times = {spike_label: list() for
diff --git a/dev/_sources/whats_new.rst.txt b/dev/_sources/whats_new.rst.txt
index 7bbe1ca58..d43cf755a 100644
--- a/dev/_sources/whats_new.rst.txt
+++ b/dev/_sources/whats_new.rst.txt
@@ -92,6 +92,9 @@ Changelog
   and interpolation method to smoothen CSD plot,
   by `Katharina Duecker`_ in :gh:`815`
 
+- Cleaned up internal logic in :class:`~hnn_core.CellResponse`,
+  by `Nick Tolley`_ in :gh:`647`.
+
 Bug
 ~~~
 - Fix inconsistent connection mapping from drive gids to cell gids, by
diff --git a/dev/generated/hnn_core.CellResponse.html b/dev/generated/hnn_core.CellResponse.html
index 7c3e521ea..3b848bb39 100644
--- a/dev/generated/hnn_core.CellResponse.html
+++ b/dev/generated/hnn_core.CellResponse.html
@@ -89,7 +89,6 @@
       aria-labelledby="dLabelLocalToc">
    
 
  • hnn_core.CellResponse
      
 
    • CellResponse
        
-
      • CellResponse.__getitem__()
        • 
 
      • CellResponse.__repr__()
        • 
 
      • CellResponse.mean_rates()
        • 
 
      • CellResponse.plot_spikes_hist()
        • 
@@ -161,14 +160,14 @@ 
        hnn_core.CellResponse
 
        Parameters:
        
 
        
-
        spike_timeslist (n_trials,) of list (n_spikes,) of float, shape | None
        Each element of the outer list is a trial.
+
        spike_timeslist (n_trials,) of list (n_spikes,) of float | None
        Each element of the outer list is a trial.
 The inner list contains the time stamps of spikes.
        
 
        
-
        spike_gidslist (n_trials,) of list (n_spikes,) of float, shape | None
        Each element of the outer list is a trial.
+
        spike_gidslist (n_trials,) of list (n_spikes,) of float | None
        Each element of the outer list is a trial.
 The inner list contains the cell IDs of neurons that
 spiked.
        
 
        
-
        spike_typeslist (n_trials,) of list (n_spikes,) of float, shape | None
        Each element of the outer list is a trial.
+
        spike_typeslist (n_trials,) of list (n_spikes,) of float | None
        Each element of the outer list is a trial.
 The inner list contains the type of spike (e.g., evprox1
 or L2_pyramidal) that occurred at the corresponding time stamp.
 Each gid corresponds to a type via Network().gid_ranges.
        
@@ -183,22 +182,22 @@ 
        hnn_core.CellResponse
 
        Attributes:
        
 
        
-
        spike_timeslist (n_trials,) of list (n_spikes,) of float, shape
        Each element of the outer list is a trial.
+
        spike_timeslist (n_trials,) of list (n_spikes,) of float
        Each element of the outer list is a trial.
 The inner list contains the time stamps of spikes.
        
 
        
-
        spike_gidslist (n_trials,) of list (n_spikes,) of float, shape
        Each element of the outer list is a trial.
+
        spike_gidslist (n_trials,) of list (n_spikes,) of float
        Each element of the outer list is a trial.
 The inner list contains the cell IDs of neurons that
 spiked.
        
 
        
-
        spike_typeslist (n_trials,) of list (n_spikes,) of float, shape
        Each element of the outer list is a trial.
+
        spike_typeslist (n_trials,) of list (n_spikes,) of float
        Each element of the outer list is a trial.
 The inner list contains the type of spike (e.g., evprox1
 or L2_pyramidal) that occurred at the corresponding time stamp.
 Each gid corresponds to a type via Network::gid_ranges.
        
 
        
-
        vseclist (n_trials,) of dict, shape
        Each element of the outer list is a trial.
+
        vseclist (n_trials,) of dict
        Each element of the outer list is a trial.
 Dictionary indexed by gids containing voltages for cell sections.
        
 
        
-
        iseclist (n_trials,) of dict, shape
        Each element of the outer list is a trial.
+
        iseclist (n_trials,) of dict
        Each element of the outer list is a trial.
 Dictionary indexed by gids containing currents for cell sections.
        
 
        
 
        calist (n_trials,) of dict, shape
        Each element of the outer list is a trial.
@@ -231,26 +230,6 @@ 
        hnn_core.CellResponse
 
 
-
        
-
        
-__getitem__(gid_item)[source]
        
-
        Returns a CellResponse object with a copied subset filtered by gid.
        
-
        
-
        Parameters:
        
-
        
-
        gid_itemint | slice
        Subset of gids .
        
-
        
-
        
-
        
-
        Returns:
        
-
        
-
        cell_responseinstance of CellResponse
        See below for use cases.
        
-
        
-
        
-
        
-
        
-
        
-
 
        
 
        
 __repr__()[source]
        
diff --git a/dev/genindex.html b/dev/genindex.html
index 82cd71688..ac3f99284 100644
--- a/dev/genindex.html
+++ b/dev/genindex.html
@@ -160,8 +160,6 @@ 
        Index
        
 
        _
        
 
        
   
          
-      
        • __getitem__() (hnn_core.CellResponse method)
-
          • 
       
        • __repr__() (hnn_core.Cell method)
 
       
            
diff --git a/dev/objects.inv b/dev/objects.inv
index f6dd7e477..c6c29c4a2 100644
Binary files a/dev/objects.inv and b/dev/objects.inv differ
diff --git a/dev/searchindex.js b/dev/searchindex.js
index 44b48ed9a..04f969582 100644
--- a/dev/searchindex.js
+++ b/dev/searchindex.js
@@ -1 +1 @@
-Search.setIndex({"docnames": ["api", "auto_examples/howto/index", "auto_examples/howto/optimize_evoked", "auto_examples/howto/optimize_rhythmic", "auto_examples/howto/plot_batch_simulate", "auto_examples/howto/plot_connectivity", "auto_examples/howto/plot_firing_pattern", "auto_examples/howto/plot_hnn_animation", "auto_examples/howto/plot_record_extracellular_potentials", "auto_examples/howto/plot_simulate_mpi_backend", "auto_examples/howto/sg_execution_times", "auto_examples/index", "auto_examples/sg_execution_times", "auto_examples/workflows/index", "auto_examples/workflows/plot_simulate_alpha", "auto_examples/workflows/plot_simulate_beta", "auto_examples/workflows/plot_simulate_evoked", "auto_examples/workflows/plot_simulate_gamma", "auto_examples/workflows/plot_simulate_somato", "auto_examples/workflows/sg_execution_times", "contributing", "generated/hnn_core.Cell", "generated/hnn_core.CellResponse", "generated/hnn_core.Network", "generated/hnn_core.calcium_model", "generated/hnn_core.dipole.Dipole", "generated/hnn_core.dipole.average_dipoles", "generated/hnn_core.extracellular.ExtracellularArray", "generated/hnn_core.gui.HNNGUI", "generated/hnn_core.jones_2009_model", "generated/hnn_core.law_2021_model", "generated/hnn_core.optimization.Optimizer", "generated/hnn_core.parallel_backends.JoblibBackend", "generated/hnn_core.parallel_backends.MPIBackend", "generated/hnn_core.pick_connection", "generated/hnn_core.read_dipole", "generated/hnn_core.read_params", "generated/hnn_core.read_spikes", "generated/hnn_core.simulate_dipole", "generated/hnn_core.viz.NetworkPlotter", "generated/hnn_core.viz.plot_cell_connectivity", "generated/hnn_core.viz.plot_cell_morphology", "generated/hnn_core.viz.plot_cells", "generated/hnn_core.viz.plot_connectivity_matrix", "generated/hnn_core.viz.plot_dipole", "generated/hnn_core.viz.plot_laminar_csd", "generated/hnn_core.viz.plot_laminar_lfp", "generated/hnn_core.viz.plot_psd", "generated/hnn_core.viz.plot_spikes_hist", "generated/hnn_core.viz.plot_spikes_raster", "generated/hnn_core.viz.plot_tfr_morlet", "glossary", "governance", "index", "network_file_desc", "parallel", "roadmap", "sg_execution_times", "whats_new"], "filenames": ["api.rst", "auto_examples/howto/index.rst", "auto_examples/howto/optimize_evoked.rst", "auto_examples/howto/optimize_rhythmic.rst", "auto_examples/howto/plot_batch_simulate.rst", "auto_examples/howto/plot_connectivity.rst", "auto_examples/howto/plot_firing_pattern.rst", "auto_examples/howto/plot_hnn_animation.rst", "auto_examples/howto/plot_record_extracellular_potentials.rst", "auto_examples/howto/plot_simulate_mpi_backend.rst", "auto_examples/howto/sg_execution_times.rst", "auto_examples/index.rst", "auto_examples/sg_execution_times.rst", "auto_examples/workflows/index.rst", "auto_examples/workflows/plot_simulate_alpha.rst", "auto_examples/workflows/plot_simulate_beta.rst", "auto_examples/workflows/plot_simulate_evoked.rst", "auto_examples/workflows/plot_simulate_gamma.rst", "auto_examples/workflows/plot_simulate_somato.rst", "auto_examples/workflows/sg_execution_times.rst", "contributing.rst", "generated/hnn_core.Cell.rst", "generated/hnn_core.CellResponse.rst", "generated/hnn_core.Network.rst", "generated/hnn_core.calcium_model.rst", "generated/hnn_core.dipole.Dipole.rst", "generated/hnn_core.dipole.average_dipoles.rst", "generated/hnn_core.extracellular.ExtracellularArray.rst", "generated/hnn_core.gui.HNNGUI.rst", "generated/hnn_core.jones_2009_model.rst", "generated/hnn_core.law_2021_model.rst", "generated/hnn_core.optimization.Optimizer.rst", "generated/hnn_core.parallel_backends.JoblibBackend.rst", "generated/hnn_core.parallel_backends.MPIBackend.rst", "generated/hnn_core.pick_connection.rst", "generated/hnn_core.read_dipole.rst", "generated/hnn_core.read_params.rst", "generated/hnn_core.read_spikes.rst", "generated/hnn_core.simulate_dipole.rst", "generated/hnn_core.viz.NetworkPlotter.rst", "generated/hnn_core.viz.plot_cell_connectivity.rst", "generated/hnn_core.viz.plot_cell_morphology.rst", "generated/hnn_core.viz.plot_cells.rst", "generated/hnn_core.viz.plot_connectivity_matrix.rst", "generated/hnn_core.viz.plot_dipole.rst", "generated/hnn_core.viz.plot_laminar_csd.rst", "generated/hnn_core.viz.plot_laminar_lfp.rst", "generated/hnn_core.viz.plot_psd.rst", "generated/hnn_core.viz.plot_spikes_hist.rst", "generated/hnn_core.viz.plot_spikes_raster.rst", "generated/hnn_core.viz.plot_tfr_morlet.rst", "glossary.rst", "governance.rst", "index.rst", "network_file_desc.rst", "parallel.rst", "roadmap.rst", "sg_execution_times.rst", "whats_new.rst"], "titles": ["API Documentation", "How to", "05. Optimize simulated evoked response parameters", "08. Optimize simulated rhythmic responses", "07. Batch Simulation", "03. Modifying local connectivity", "01. Plot firing pattern", "06. Animating HNN simulations", "02. Record extracellular potentials", "04. Use MPI backend for parallelization", "Computation times", "Tutorials", "Computation times", "Tutorials", "02. Simulate Alpha and Beta Rhythms", "05. Simulate beta modulated ERP", "01. Simulate Event Related Potentials (ERPs)", "03. Simulate Gamma Rhythms", "04. From MEG sensor-space data to HNN simulation", "Computation times", "Contributions", "hnn_core.Cell", "hnn_core.CellResponse", "hnn_core.Network", "hnn_core.calcium_model", "hnn_core.dipole.Dipole", "hnn_core.dipole.average_dipoles", "hnn_core.extracellular.ExtracellularArray", "hnn_core.gui.HNNGUI", "hnn_core.jones_2009_model", "hnn_core.law_2021_model", "hnn_core.optimization.Optimizer", "hnn_core.parallel_backends.JoblibBackend", "hnn_core.parallel_backends.MPIBackend", "hnn_core.pick_connection", "hnn_core.read_dipole", "hnn_core.read_params", "hnn_core.read_spikes", "hnn_core.simulate_dipole", "hnn_core.viz.NetworkPlotter", "hnn_core.viz.plot_cell_connectivity", "hnn_core.viz.plot_cell_morphology", "hnn_core.viz.plot_cells", "hnn_core.viz.plot_connectivity_matrix", "hnn_core.viz.plot_dipole", "hnn_core.viz.plot_laminar_csd", "hnn_core.viz.plot_laminar_lfp", "hnn_core.viz.plot_psd", "hnn_core.viz.plot_spikes_hist", "hnn_core.viz.plot_spikes_raster", "hnn_core.viz.plot_tfr_morlet", "Glossary", "Project Governance", "hnn-core", "Network File Content", "Parallel backends", "The HNN Roadmap", "Computation times", "What\u2019s new?"], "terms": {"These": [1, 11, 15, 20, 25, 27, 29, 44, 46, 50, 55, 56], "ar": [1, 3, 4, 5, 6, 8, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 29, 32, 33, 34, 36, 38, 44, 46, 47, 48, 50, 52, 53, 54, 55, 56, 58], "short": [1, 11, 25, 47, 51], "exampl": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 48, 54, 55, 56, 57, 58], "show": [1, 2, 3, 4, 5, 6, 8, 11, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 28, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "us": [1, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 30, 33, 39, 42, 44, 45, 46, 48, 50, 52, 53, 54, 55, 56, 57, 58], "hnn": [1, 2, 4, 6, 8, 9, 10, 11, 13, 14, 16, 17, 19, 23, 28, 29, 32, 33, 39, 51, 52, 57, 58], "core": [1, 2, 3, 4, 9, 11, 13, 14, 16, 17, 18, 28, 33, 51, 52, 55, 56, 58], "api": [1, 5, 11, 13, 20, 39, 52, 53], "accomplish": [1, 11], "specif": [1, 5, 11, 15, 20, 21, 23, 24, 25, 44, 51, 52, 54, 56, 58], "task": [1, 4, 11, 18], "01": [1, 2, 10, 11, 13, 15, 17, 18, 19, 57], "plot": [1, 2, 3, 5, 7, 8, 9, 10, 11, 14, 16, 17, 18, 21, 22, 23, 25, 27, 28, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 56, 57, 58], "fire": [1, 5, 10, 11, 17, 22, 23, 54, 57, 58], "pattern": [1, 5, 10, 11, 17, 23, 29, 34, 40, 57, 58], "02": [1, 10, 11, 13, 15, 17, 18, 19, 57], "record": [1, 5, 6, 7, 10, 11, 16, 18, 21, 22, 23, 27, 38, 53, 54, 56, 57, 58], "extracellular": [1, 10, 11, 23, 38, 46, 57, 58], "potenti": [1, 7, 10, 11, 13, 15, 18, 19, 21, 23, 27, 51, 53, 56, 57, 58], "03": [1, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 18, 19, 57], "modifi": [1, 2, 3, 4, 10, 11, 15, 16, 20, 21, 25, 27, 30, 57, 58], "local": [1, 6, 8, 10, 11, 18, 27, 53, 56, 57, 58], "connect": [1, 6, 10, 11, 14, 15, 17, 21, 23, 28, 29, 30, 32, 33, 34, 38, 40, 43, 51, 56, 57, 58], "04": [1, 10, 11, 13, 15, 19, 57], "mpi": [1, 8, 10, 11, 20, 28, 33, 53, 56, 57, 58], "backend": [1, 4, 10, 11, 16, 18, 20, 28, 53, 57, 58], "parallel": [1, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 20, 21, 32, 33, 56, 57, 58], "05": [1, 10, 11, 13, 18, 19, 29, 31, 35, 38, 57], "optim": [1, 10, 11, 29, 35, 38, 47, 56, 57, 58], "simul": [1, 5, 6, 8, 9, 10, 11, 13, 19, 23, 25, 27, 28, 29, 31, 32, 33, 35, 38, 39, 47, 50, 51, 53, 55, 57, 58], "evok": [1, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 18, 22, 23, 24, 29, 31, 35, 38, 48, 54, 57, 58], "respons": [1, 5, 6, 8, 10, 11, 14, 15, 16, 18, 22, 24, 29, 31, 35, 38, 47, 54, 57, 58], "paramet": [1, 3, 4, 5, 7, 10, 11, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54, 57, 58], "06": [1, 10, 11, 18, 55, 57], "anim": [1, 10, 11, 39, 56, 57, 58], "07": [1, 10, 11, 18, 57], "batch": [1, 10, 11, 56, 57, 58], "go": [2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 56], "end": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 23, 25, 47, 50, 52, 54, 55, 56, 58], "download": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 53], "full": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 25, 35, 36, 39, 56], "code": [2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 52, 53, 58], "run": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 28, 31, 33, 52, 53, 54, 55, 56, 58], "thi": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 38, 40, 48, 52, 53, 54, 55, 56], "your": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53], "browser": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "via": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 22, 52, 55, 56, 58], "binder": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "demonstr": [2, 3, 5, 6, 7, 9, 14, 15, 16, 17, 18], "how": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 32, 33, 38, 40, 52, 54, 55, 56], "model": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 22, 24, 29, 30, 32, 33, 39, 53, 58], "match": [2, 5, 18, 23, 29, 34, 53, 55, 58], "an": [2, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 36, 37, 39, 40, 42, 46, 48, 49, 51, 52, 53, 54, 56, 58], "experiment": [2, 25, 31], "dipol": [2, 3, 4, 5, 8, 9, 14, 16, 17, 18, 21, 23, 27, 31, 32, 33, 35, 38, 44, 46, 47, 50, 53, 54, 55, 56, 58], "waveform": [2, 6, 8, 14, 16, 17, 18, 25, 27, 38], "author": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 52], "carolina": [2, 3, 58], "fernandez": [2, 3, 58], "cxf418": [2, 3], "miami": [2, 3], "edu": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 55, 56], "nick": [2, 4, 5, 6, 7, 8, 14, 15, 58], "tollei": [2, 4, 5, 6, 7, 8, 14, 15, 58], "nicholas_tollei": [2, 4, 5, 6, 7, 8, 14, 15], "brown": [2, 4, 5, 6, 7, 8, 9, 14, 15, 16, 18, 53, 56], "ryan": [2, 4, 18, 58], "thorp": [2, 4, 18, 58], "ryan_thorp": [2, 4, 18], "mainak": [2, 4, 6, 8, 9, 14, 16, 17, 18, 58], "ja": [2, 4, 6, 8, 9, 14, 16, 17, 18, 53, 58], "mja": [2, 4, 6, 9, 14, 17], "mgh": [2, 4, 6, 9, 14, 16, 17], "harvard": [2, 4, 6, 9, 14, 16, 17], "import": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 55, 56], "o": [2, 5, 6, 7, 9, 14, 16, 17, 18], "path": [2, 5, 6, 7, 9, 14, 16, 17, 18, 21, 22, 23, 25, 29, 35, 36, 37], "op": [2, 5, 6, 7, 9, 14, 16, 17, 18], "matplotlib": [2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 58], "pyplot": [2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18], "plt": [2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 25, 27, 31, 44, 46], "let": [2, 3, 4, 5, 6, 9, 14, 16, 17, 18, 55], "u": [2, 3, 4, 5, 6, 9, 14, 16, 17, 18, 20, 23, 54], "hnn_core": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 55], "from": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 47, 48, 49, 51, 52, 53, 55, 56, 57, 58], "mpibackend": [2, 3, 9, 28, 55, 58], "jones_2009_model": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 24, 30, 58], "simulate_dipol": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 33, 54, 55, 58], "read_dipol": [2, 58], "hnn_core_root": [2, 17, 18], "join": [2, 6, 17, 18, 52], "dirnam": [2, 17, 18], "__file__": [2, 17, 18], "The": [2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 58], "number": [2, 3, 4, 7, 9, 14, 16, 18, 20, 23, 25, 27, 28, 32, 33, 38, 50, 54, 55, 58], "mai": [2, 3, 4, 8, 16, 20, 23, 27, 46, 52], "need": [2, 3, 4, 6, 7, 9, 18, 20, 23, 28, 52, 53, 55, 56], "depend": [2, 3, 4, 15, 18, 24, 52, 55, 56, 58], "current": [2, 3, 4, 5, 6, 8, 16, 17, 18, 21, 22, 23, 27, 28, 38, 45, 52, 53, 54, 56], "machin": [2, 3, 4, 56], "n_proc": [2, 3, 9, 33, 55], "10": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 24, 27, 29, 30, 39, 53, 56], "first": [2, 3, 5, 6, 7, 11, 13, 14, 15, 16, 17, 18, 21, 23, 25, 39, 40, 53, 54, 55, 56, 58], "we": [2, 3, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 52, 53, 56], "load": [2, 5, 6, 9, 16, 18, 29, 33, 58], "data": [2, 4, 5, 6, 8, 11, 13, 14, 16, 19, 21, 22, 23, 25, 26, 27, 28, 31, 33, 45, 46, 47, 53, 55, 57, 58], "object": [2, 3, 5, 6, 7, 8, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 52, 53, 54, 55, 58], "i": [2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 28, 29, 31, 33, 34, 36, 38, 39, 40, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58], "differ": [2, 4, 5, 6, 14, 15, 16, 17, 20, 22, 23, 30, 37, 40, 55, 58], "experi": [2, 38, 53], "than": [2, 14, 16, 18, 20, 23, 52, 53, 55, 58], "one": [2, 6, 14, 15, 18, 20, 23, 25, 27, 33, 34, 44, 46, 47, 50, 52, 53, 56], "which": [2, 5, 6, 7, 8, 9, 11, 13, 15, 16, 17, 18, 20, 23, 25, 27, 28, 44, 46, 47, 50, 51, 53, 55, 56, 58], "base": [2, 11, 13, 15, 16, 18, 20, 21, 52, 53, 56, 58], "were": [2, 3, 25, 27, 46, 53, 58], "tune": [2, 53], "so": [2, 3, 9, 16, 18, 20, 25, 52, 53, 58], "initi": [2, 14, 23, 54, 56], "rmse": [2, 58], "larg": [2, 8, 56], "give": [2, 20, 52, 53], "procedur": [2, 56], "lot": [2, 5, 20], "work": [2, 20, 52, 53, 55, 56], "urllib": 2, "request": [2, 33, 51, 52], "urlretriev": 2, "data_url": 2, "http": [2, 15, 18, 20, 27, 39, 53, 55, 56], "raw": [2, 18, 25, 27, 44, 46, 50], "githubusercont": 2, "com": [2, 4, 8, 14, 16, 17, 18, 20, 53, 56], "jonescompneurolab": [2, 20, 53, 56], "master": [2, 20, 53], "meg_detection_data": 2, "s1_suprat": 2, "txt": [2, 6, 22, 25, 35, 37], "exp_dpl": 2, "": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 37, 50, 52, 54, 55, 56], "some": [2, 5, 8, 17, 18, 53, 56], "tstop": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 31, 32, 33, 38, 54, 58], "time": [2, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 28, 30, 32, 33, 38, 39, 45, 46, 47, 50, 52, 54, 55, 58], "1": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 24, 25, 27, 29, 30, 32, 33, 52, 54, 55, 56], "scale_factor": [2, 3, 31], "3000": [2, 3, 5, 14, 16], "smooth_window_len": [2, 3, 31], "30": [2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 28, 39], "net_init": 2, "proxim": [2, 3, 4, 6, 14, 15, 16, 17, 18, 21, 23, 28, 34, 51, 54], "weights_ampa_p1": [2, 6, 15, 16], "l2_basket": [2, 4, 5, 6, 15, 16, 18, 23, 30, 34], "0": [2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 29, 38, 39, 41, 47, 50, 55, 56, 57], "2913": 2, "l2_pyramid": [2, 3, 4, 6, 9, 14, 15, 16, 17, 18, 22, 23, 34], "9337": 2, "l5_basket": [2, 4, 5, 6, 15, 16, 18, 22, 23, 30, 34], "1951": 2, "l5_pyramid": [2, 3, 4, 5, 6, 9, 14, 15, 16, 17, 18, 22, 23, 30, 34], "3602": 2, "weights_nmda_p1": 2, "9240": 2, "0845": 2, "5849": 2, "65105": 2, "synaptic_delays_p": [2, 18], "add_evoked_dr": [2, 4, 6, 15, 16, 18, 23, 58], "evprox1": [2, 6, 15, 16, 18, 22, 37], "mu": [2, 4, 6, 8, 14, 15, 16, 18, 23, 29, 54], "5": [2, 3, 4, 5, 6, 8, 9, 14, 15, 17, 18, 19, 21, 23, 27, 30], "6813": 2, "sigma": [2, 4, 6, 15, 16, 18, 23, 54, 58], "20": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 39, 55], "3969": 2, "numspik": [2, 3, 4, 6, 9, 14, 15, 16, 18, 23], "locat": [2, 3, 4, 5, 6, 9, 14, 15, 16, 17, 18, 21, 23, 28, 34, 51, 54], "weights_ampa": [2, 3, 4, 6, 9, 14, 15, 16, 17, 18, 23, 54], "weights_nmda": [2, 6, 15, 16, 18, 23, 54], "synaptic_delai": [2, 3, 4, 6, 14, 15, 16, 17, 18, 23, 54], "distal": [2, 3, 5, 6, 9, 14, 15, 16, 18, 21, 23, 28, 30, 34, 51, 54], "weights_ampa_d1": [2, 6, 15, 16], "8037": 2, "5738": 2, "3626": 2, "weights_nmda_d1": [2, 6, 15, 16], "2492": 2, "6183": 2, "1121": 2, "synaptic_delays_d1": [2, 6, 16], "evdist1": [2, 6, 15, 16, 18, 22, 23, 37], "58": [2, 6, 18], "6539": 2, "5810": 2, "2": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 30, 52, 54, 55], "weights_ampa_p2": [2, 6, 15, 16], "weights_nmda_p2": 2, "evprox2": [2, 6, 15, 16, 18], "80": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 58], "mpi_cmd": [2, 3, 9, 33, 55], "mpiexec": [2, 3, 9, 33, 55], "init_dpl": 2, "n_trial": [2, 3, 5, 9, 14, 16, 17, 18, 22, 23, 27, 32, 33, 38, 55], "scale": [2, 3, 5, 14, 16, 17, 18, 25, 27, 31, 38, 46, 56, 58], "smooth": [2, 3, 5, 8, 14, 15, 16, 18, 25, 27, 31, 38, 45, 52, 58], "now": [2, 3, 6, 8, 14, 15, 16, 17, 18, 20, 58], "start": [2, 5, 9, 11, 13, 14, 20, 21, 22, 23, 25, 32, 33, 47, 50, 53, 54, 55, 56, 58], "defin": [2, 3, 4, 5, 6, 8, 16, 18, 21, 22, 23, 27, 29, 41, 46, 48, 55, 56, 58], "function": [2, 3, 4, 14, 15, 20, 23, 25, 27, 28, 44, 46, 50, 54, 56, 58], "tell": [2, 3], "routin": [2, 3, 31, 56], "network": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 24, 27, 28, 29, 30, 32, 33, 34, 38, 39, 40, 42, 43, 51, 55, 56, 58], "drive": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 28, 29, 40, 51, 56, 58], "take": [2, 3, 17, 28, 52], "attach": [2, 3, 8, 21, 23], "dictionari": [2, 3, 4, 5, 6, 8, 21, 22, 23, 27, 28, 36, 37, 48, 54, 56, 58], "wish": [2, 3, 23], "def": [2, 3, 4, 5, 15], "set_param": [2, 3, 4, 31], "net": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 24, 27, 28, 29, 30, 32, 33, 34, 38, 39, 40, 42, 43, 48, 49, 54, 55, 58], "param": [2, 3, 17, 18, 23, 24, 28, 29, 30, 36, 38, 56, 58], "evprox2_ampa_l2_basket": 2, "evprox2_ampa_l2_pyramid": 2, "evprox2_ampa_l5_basket": 2, "evprox2_ampa_l5_pyramid": 2, "evprox2_nmda_l2_basket": 2, "evprox2_nmda_l2_pyramid": 2, "evprox2_nmda_l5_basket": 2, "evprox2_nmda_l5_pyramid": 2, "evprox2_mu": 2, "evprox2_sigma": 2, "Then": [2, 3, 8, 16, 18], "constraint": [2, 3, 31], "must": [2, 3, 9, 21, 22, 23, 25, 27, 34, 37, 38, 40, 41, 48, 52, 53, 54], "tupl": [2, 3, 21, 23, 25, 27, 29, 31, 39, 41, 44, 47, 54, 58], "where": [2, 3, 5, 15, 18, 21, 23, 27, 52, 55, 56, 58], "valu": [2, 3, 4, 8, 11, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 34, 35, 36, 38, 43, 44, 46, 50, 54, 58], "each": [2, 3, 4, 5, 6, 8, 9, 11, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 31, 32, 33, 37, 38, 46, 48, 50, 51, 53, 54, 55, 58], "lower": [2, 3, 14, 17, 18, 27, 31, 39, 45], "bound": [2, 3, 27, 45], "second": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 25, 39], "upper": [2, 3, 18, 27, 39, 45], "correspond": [2, 3, 14, 15, 17, 18, 22, 23, 27, 34, 40, 56, 58], "follow": [2, 3, 9, 11, 13, 15, 16, 18, 20, 23, 28, 52, 53, 56], "synapt": [2, 3, 21, 23, 34, 38, 40, 43, 54, 56, 58], "weight": [2, 3, 5, 6, 15, 16, 18, 23, 28, 30, 31, 40, 43, 54, 58], "rang": [2, 3, 6, 8, 14, 17, 18, 22, 23, 25, 34, 37, 50, 58], "unit": [2, 3, 23, 25, 27, 46, 53, 56, 58], "micro": [2, 3, 21, 54], "siemen": [2, 3], "chosen": [2, 3], "keep": [2, 3, 52], "physiolog": [2, 3, 18], "realist": [2, 3, 8, 14, 15, 29], "regim": [2, 3], "dict": [2, 3, 4, 18, 21, 22, 23, 25, 28, 29, 37, 41, 48, 54], "100": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 28, 39, 41], "120": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17], "fit": [2, 3, 18, 25, 31], "max_it": 31, "40": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "final": [2, 3, 5, 6, 7, 8, 9, 15, 16, 17, 18, 20, 52, 53, 55], "can": [2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 20, 21, 23, 25, 27, 28, 29, 39, 41, 44, 46, 47, 50, 52, 53, 54, 55, 56, 58], "alongsid": 2, "post": [2, 18, 56], "well": [2, 5, 17, 18, 23, 25, 51, 53, 55, 56, 58], "converg": [2, 3, 31, 58], "opt_dpl": [2, 3], "net_": [2, 3], "fig": [2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 25, 27, 31, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50], "ax": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58], "subplot": [2, 3, 5, 6, 8, 14, 15, 16, 17, 18, 40], "sharex": [2, 5, 6, 8, 15, 16, 17, 18], "true": [2, 4, 5, 6, 8, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 28, 29, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 58], "figsiz": [2, 3, 4, 5, 6, 8, 15, 16, 17, 18], "6": [2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 30], "origin": [2, 11, 13, 15, 18, 20, 23, 51, 53, 54, 56, 58], "layer": [2, 3, 5, 8, 15, 16, 17, 18, 23, 25, 29, 44, 47, 50, 54, 56, 58], "agg": [2, 3, 4, 5, 15, 16, 25, 26, 44, 47, 50], "fals": [2, 3, 4, 5, 8, 14, 15, 16, 17, 18, 21, 23, 24, 25, 28, 29, 30, 32, 33, 38, 43, 44, 50, 54, 58], "color": [2, 3, 6, 14, 15, 18, 21, 22, 25, 27, 28, 39, 41, 43, 44, 45, 46, 47, 48, 50, 58], "tab": [2, 3], "blue": [2, 27, 45], "orang": 2, "green": [2, 3, 18], "legend": [2, 3, 4, 5, 15, 18], "cell_respons": [2, 5, 6, 8, 14, 15, 16, 17, 18, 22, 23, 37, 48, 49, 54, 58], "plot_spikes_hist": [2, 5, 6, 14, 15, 16, 18, 22, 58], "fig1": [2, 3], "plot_converg": [2, 3, 31], "jupyt": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 28, 56], "notebook": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 28, 56], "optimize_evok": [2, 10, 57, 58], "ipynb": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "python": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 20, 53, 55, 56, 58], "sourc": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 58], "py": [2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 53, 55, 56, 57, 58], "zip": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18], "galleri": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 57], "gener": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 20, 23, 51, 52, 53, 54, 56, 58], "sphinx": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 20], "do": [4, 6, 14, 18, 20, 52, 53, 56], "allow": [4, 5, 7, 8, 9, 16, 18, 23, 52, 54, 58], "user": [4, 8, 11, 13, 18, 33, 52, 53, 56, 58], "effici": [4, 56], "multipl": [4, 16, 23, 27, 34, 55, 56, 58], "comprehens": 4, "analysi": [4, 8, 14, 15, 17, 29, 56, 58], "abdul": [4, 58], "samad": [4, 58], "siddiqui": [4, 58], "abdulsamadsid1": 4, "gmail": [4, 8, 14, 16, 17, 18], "numpi": [4, 15, 17, 20, 22, 45, 46, 53, 58], "np": [4, 15, 17, 55, 58], "batch_simul": 4, "batchsimul": [4, 58], "n_job": [4, 16, 18, 32, 55, 58], "param_valu": 4, "none": [4, 6, 15, 16, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 58], "set": [4, 5, 8, 11, 13, 16, 17, 18, 21, 23, 27, 29, 38, 43, 45, 52, 53, 55, 56, 58], "instanc": [4, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 58], "option": [4, 16, 18, 21, 23, 25, 27, 31, 33, 38, 44, 45, 46, 50, 54, 55, 58], "If": [4, 16, 20, 21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54], "new": [4, 5, 15, 18, 20, 22, 23, 26, 27, 39, 42, 48, 49, 51, 55], "creat": [4, 5, 15, 16, 17, 18, 20, 21, 22, 23, 27, 29, 35, 38, 39, 42, 48, 49, 51, 56, 58], "specifi": [4, 5, 6, 8, 9, 20, 21, 22, 23, 28, 32, 33, 38, 41, 48, 55, 58], "type": [4, 6, 16, 17, 20, 21, 22, 23, 28, 34, 37, 48, 49, 55, 56, 58], "weight_basket": 4, "weight_pyr": 4, "add": [4, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 23, 27, 28, 29, 51, 54, 55, 58], "evprox": [4, 5, 16, 18, 22, 48], "grid": [4, 8, 21, 23, 29], "param_grid": 4, "logspac": 4, "4": [3, 4, 5, 6, 8, 15, 17, 18, 29, 30], "calcul": [4, 6, 8, 18, 22, 23, 25, 27, 50, 56, 58], "summari": 4, "statist": [4, 56], "summary_func": 4, "min": 4, "max": [4, 18], "peak": [4, 15], "list": [4, 5, 8, 14, 16, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 37, 38, 40, 41, 44, 45, 46, 47, 48, 49, 50, 52, 54, 58], "contain": [4, 11, 13, 15, 21, 22, 23, 25, 26, 27, 36, 37, 54, 56, 58], "return": [4, 5, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 55, 58], "summary_stat": 4, "dpl_data": 4, "dpl": [4, 5, 6, 7, 8, 9, 14, 16, 17, 18, 25, 26, 28, 32, 33, 35, 38, 44, 47, 50, 55, 58], "min_peak": 4, "max_peak": 4, "append": [4, 22, 23], "collect": [4, 22, 37, 54], "comment": [4, 52], "off": [4, 53, 58], "dask": 4, "distribut": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 24, 53, 54, 55, 56, 58], "packag": [4, 7, 9, 16, 18, 20, 53], "instal": [4, 9, 18, 25, 55], "client": 4, "threads_per_work": 4, "n_worker": 4, "process": [4, 9, 18, 20, 23, 33, 55, 56, 58], "simulation_result": 4, "combin": [4, 16, 17, 18], "multiprocess": 4, "print": [4, 5, 6, 8, 15, 16, 17, 55], "multiprocessingbackend": 4, "concurr": 4, "worker": 4, "done": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 25, 55], "elaps": [4, 18], "29": [4, 6, 10, 18], "9": [3, 4, 6, 18, 25], "001242556683917088": 4, "004900589999999999": 4, "03665290820701789": 4, "02352069470140582": 4, "038695414756536456": 4, "022995093327209466": 4, "03373821891133495": 4, "03047248131934011": 4, "re": [4, 17, 23, 52, 56], "figur": [4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 22, 23, 25, 27, 31, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58], "label": [4, 18, 25, 44, 45, 46, 47, 58], "xlabel": [4, 6, 18], "index": [4, 6, 14, 21, 22, 23, 39, 40, 43, 48, 49, 54, 56, 58], "ylabel": [4, 6, 18], "magnitud": 4, "titl": [4, 6, 20], "across": [4, 6, 9, 16, 18, 22, 23, 25, 34, 44, 47, 48, 51, 55, 56, 58], "tight_layout": [4, 7, 8, 14], "total": [4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 25, 57], "script": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 53, 56], "minut": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "612": [4, 10], "plot_batch_simul": [4, 10, 57], "sphinx_gallery_thumbnail_numb": [5, 8, 16, 17, 18], "To": [5, 6, 7, 8, 14, 15, 16, 17, 18, 20, 23, 25, 27, 28, 44, 46, 50, 53, 55, 56], "explor": [5, 40, 58], "chang": [5, 7, 8, 14, 15, 20, 21, 23, 24, 40, 56], "instanti": [5, 7, 15, 18, 23, 24, 29, 30, 56, 58], "note": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 23, 24, 25, 27, 29, 30, 34, 38, 40, 47, 53, 55, 56], "add_drives_from_param": [5, 23, 24, 29, 30, 58], "predefin": 5, "without": [5, 9, 14, 15, 16, 18, 20, 23, 27, 32, 56, 58], "shown": [5, 20, 40, 52, 53], "previous": [5, 20, 58], "net_erp": [5, 15], "come": 5, "reflect": [5, 15, 25, 52, 58], "canon": 5, "neocort": [5, 15, 17, 18, 24, 52, 53], "microcircuit": 5, "detail": [5, 6, 7, 8, 11, 13, 14, 16, 17, 18, 20, 24, 52, 53, 56], "everi": [5, 21, 23, 41, 55], "cell": [5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 37, 38, 40, 41, 42, 48, 49, 51, 53, 56, 58], "visual": [5, 7, 8, 11, 13, 14, 16, 18, 28, 39, 40, 43, 58], "plot_connectivity_weight": 5, "plot_cell_connect": [5, 58], "search": [5, 21, 34, 58], "pick_connect": [5, 58], "indic": [5, 21, 23, 34, 41, 58], "provid": [5, 11, 13, 15, 16, 22, 23, 25, 27, 28, 34, 36, 44, 46, 48, 50, 51, 52, 53, 56, 58], "viz": [3, 5, 7, 14, 15, 16, 17, 18, 28], "plot_connectivity_matrix": [5, 58], "len": 5, "conn_indic": [5, 34], "src_gid": [5, 23, 34, 40, 54, 58], "target_gid": [5, 23, 34, 54, 58], "loc": [5, 15, 21, 23, 34, 54], "soma": [5, 6, 8, 15, 21, 23, 24, 34, 38, 41, 51, 58], "receptor": [5, 15, 16, 21, 23, 34, 54], "gabaa": [5, 15, 17, 23, 30, 34], "conn_idx": [5, 40, 43], "here": [5, 6, 14, 18], "pop": 5, "method": [5, 7, 8, 14, 16, 18, 21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 38, 39, 45, 47, 54, 56, 58], "sampl": [5, 8, 18, 22, 23, 25, 27, 45, 46, 54, 58], "random": [5, 9, 14, 23, 54, 58], "element": [5, 21, 22, 23, 27, 28, 40, 41, 48, 52], "copi": [5, 14, 15, 16, 20, 21, 22, 23, 25, 27, 58], "38": [5, 6, 18], "count": [5, 15], "35": [5, 6, 15, 24], "src": [5, 15, 18, 23, 54], "target": [2, 5, 15, 21, 23, 31, 34, 40, 54, 58], "probabl": [5, 15, 23, 28, 54, 58], "025": [5, 15, 38], "delai": [5, 15, 23, 39, 54, 58], "lamtha": [5, 15, 21, 23, 54], "70": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "dure": [5, 8, 15, 23, 55, 56, 58], "store": [5, 6, 8, 21, 23, 24, 29, 30, 54, 58], "under": [5, 8, 23, 52, 58], "spike": [5, 6, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 37, 48, 49, 53, 54, 58], "activ": [5, 6, 8, 14, 15, 17, 18, 22, 23, 27, 37, 39, 48, 49, 52, 55, 56, 58], "after": [5, 8, 11, 13, 15, 17, 18, 20, 27, 29, 53, 55, 58], "plot_spikes_rast": [5, 6, 8, 15, 17, 18, 22, 58], "dpl_erp": 5, "170": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "joblib": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 56, 58], "trial": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 22, 23, 25, 27, 28, 32, 33, 37, 38, 39, 48, 49, 50, 53, 55, 58], "over": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 22, 23, 25, 26, 33, 47, 52, 56, 58], "job": [5, 6, 7, 8, 14, 15, 16, 17, 18, 32], "build": [5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 21, 24, 56, 58], "neuron": [5, 6, 7, 8, 9, 14, 15, 16, 17, 21, 22, 23, 24, 27, 34, 53, 54, 55, 56, 58], "m": [5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 21, 23, 25, 27, 32, 33, 38, 45, 46, 47, 52, 54], "50": [3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 27, 28, 39, 46, 58], "60": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 28], "90": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "110": [5, 6, 7, 8, 9, 14, 15, 16, 17], "130": [5, 6, 7, 8, 9, 14, 15, 16, 17], "140": [5, 6, 7, 8, 9, 14, 15, 16, 17], "150": [5, 6, 7, 8, 9, 14, 15, 16, 17, 21, 28, 41], "160": [5, 6, 7, 8, 9, 14, 15, 16, 17], "size": [5, 6, 7, 8, 9, 15, 16, 17, 18, 21, 23, 28], "640x480": [5, 6, 7, 8, 9, 16, 17], "also": [5, 6, 7, 20, 22, 23, 27, 46, 48, 52, 53, 55, 56, 58], "our": [5, 11, 13, 14, 15, 16, 17, 18, 20, 52, 53, 56], "own": [5, 8, 20], "test": [5, 28, 52, 53, 55, 56, 58], "effect": [5, 14, 15, 17, 18, 23], "clear_connect": [5, 23], "clear": [5, 17, 23, 28, 56], "all": [5, 6, 7, 11, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28, 29, 33, 34, 38, 40, 43, 44, 48, 49, 52, 53, 54, 55, 56, 57, 58], "By": [5, 8, 15, 17, 24, 25, 44, 58], "default": [5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 25, 27, 29, 30, 31, 33, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 50, 53, 54, 55, 58], "retain": [5, 23], "remov": [5, 6, 15, 23, 30, 52, 53, 58], "clear_driv": [5, 23, 58], "add_connect": [5, 23, 58], "custom": [5, 9, 16, 58], "between": [5, 8, 15, 17, 20, 21, 23, 27, 29, 30, 33, 39, 52, 54, 55, 56, 58], "l5": [5, 8, 14, 15, 16, 17, 24, 25, 26, 29, 30, 44, 47, 50, 58], "pyramid": [5, 6, 8, 14, 15, 17, 21, 23, 24, 25, 29, 30, 34, 56], "l2": [5, 8, 14, 15, 16, 25, 26, 29, 30, 34, 44, 47, 50, 58], "basket": [5, 15, 17, 29, 58], "either": [5, 55, 58], "name": [5, 18, 20, 21, 22, 23, 25, 27, 33, 40, 43, 48, 50, 54, 56], "id": [5, 6, 18, 21, 22, 37, 40, 51], "gid": [5, 6, 21, 22, 23, 34, 51, 58], "directli": [5, 53, 56, 58], "get_network": 5, "ampa": [5, 6, 14, 15, 16, 23, 34, 54], "conn_se": [5, 23, 54, 58], "3": [5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 23, 27, 29, 30, 41, 53, 54], "net_al": 5, "dpl_all": 5, "addition": [5, 6, 56], "argument": [5, 22, 23, 34, 48, 58], "spars": 5, "instead": [5, 16, 20, 25, 38, 58], "try": [5, 16, 17, 18], "same": [5, 6, 8, 17, 18, 22, 23, 26, 28, 48, 55, 58], "chanc": 5, "other": [5, 6, 20, 23, 51, 52, 53, 55, 56, 58], "net_spars": 5, "dpl_spars": 5, "With": 5, "previou": [5, 15, 23, 27], "appear": [5, 40], "synchron": [5, 16, 17, 18, 23, 58], "rhythmic": [1, 5, 11, 23, 29, 31, 38, 47, 57, 58], "period": [5, 14, 17, 52], "visibl": 5, "vertic": 5, "line": [5, 23, 25, 27, 47, 52, 53, 55, 56], "sever": [5, 15, 18, 30, 56, 58], "simultan": [5, 14, 15, 53, 56], "produc": [5, 6, 7, 14, 21, 23, 25, 52], "more": [5, 6, 7, 11, 13, 17, 18, 20, 24, 52, 53, 55, 56, 58], "popul": [5, 17, 23, 55, 58], "sparsiti": 5, "addit": [5, 8, 15, 20, 22, 30, 48, 52, 56], "decai": [5, 17, 21], "distanc": [5, 8, 21, 23, 24, 27, 58], "In": [5, 8, 18, 20, 52, 55, 56], "still": [5, 56], "smaller": [5, 14, 18, 40, 56], "As": [5, 23, 52, 56], "step": [5, 8, 14, 15, 17, 18, 20, 28, 32, 33, 38, 56], "see": [5, 7, 8, 15, 16, 18, 20, 21, 22, 23, 24, 25, 27, 48, 53, 54, 55, 56], "impact": [5, 56], "aggreg": [5, 8, 16, 18, 22, 25, 49], "plot_dipol": [5, 14, 15, 16, 58], "constrained_layout": [5, 6, 14, 15, 16, 17, 18], "window_len": [5, 8, 14, 16, 25, 27], "scaling_factor": [5, 16, 17], "spike_typ": [5, 6, 16, 18, 22, 48], "evdist": [5, 16, 18, 22, 48], "600x600": [5, 16, 17, 18], "24": [5, 6, 10, 18], "217": [5, 6, 10], "plot_connect": [5, 10, 57], "inspect": [6, 14, 15, 58], "tempfil": [6, 16], "read_spik": [6, 58], "have": [6, 8, 20, 21, 34, 41, 52, 53, 54, 56, 58], "doe": [6, 23, 53], "ani": [6, 22, 23, 34, 48, 52, 53, 54, 55, 58], "input": [6, 15, 16, 18, 21, 22, 23, 26, 35, 37, 48, 52, 54, 58], "onli": [6, 14, 15, 16, 17, 18, 23, 25, 34, 38, 53, 55, 56, 58], "ahead": 6, "nmda": [6, 15, 16, 23, 30, 34, 54, 58], "normal": [6, 9, 14, 18, 20], "certain": [6, 20], "mean": [6, 15, 22, 23, 58], "standard": [6, 9, 14, 18, 23, 27, 46], "deviat": [6, 9, 14, 23], "006562": [6, 16], "7e": 6, "142300": [6, 16], "019482": [6, 16], "004317": [6, 16], "080074": [6, 16], "63": [6, 16, 18], "53": [6, 15, 16, 18], "85": [6, 16, 18, 21], "event_se": [6, 9, 14, 15, 16, 17, 18, 23, 54, 58], "274": [6, 15, 16], "reason": 6, "call": [6, 20, 25, 33, 58], "resembl": [6, 18, 25, 47], "two": [6, 8, 15, 16, 21, 29, 46, 52, 55, 58], "up": [6, 7, 8, 18, 25, 47, 55, 56], "dendrit": [6, 8, 14, 15, 21, 23, 24, 27, 30, 34, 51], "down": [6, 8, 54], "neg": [6, 18, 58], "deflect": [6, 18], "08831": [6, 16], "01525": [6, 16], "19934": [6, 16], "00865": [6, 16], "synaptic_delays_prox": [6, 16], "zero": [6, 15, 16, 18, 23, 25, 50], "pass": [6, 15, 16, 18, 22, 23, 25, 33, 34, 45, 46, 47, 48, 55, 58], "explicitli": [6, 15, 16, 18, 22, 58], "26": [6, 16], "61": [6, 16, 18], "47": [6, 16, 18, 19], "544": [6, 15, 16], "dynam": [6, 8, 15, 16, 18, 20, 23, 24, 53, 54, 56], "somat": [6, 30, 38, 58], "voltag": [6, 7, 21, 22, 23, 27, 38, 39, 46, 54, 58], "enabl": [6, 20, 21, 23, 29, 44, 53, 54, 56, 58], "000003": [6, 16], "438840": [6, 16], "008958": [6, 16], "684013": [6, 16], "omit": [6, 15, 16, 17, 18, 23], "137": [6, 16], "12": [6, 16, 17, 18], "8": [3, 6, 7, 8, 9, 16, 18, 20, 53, 58], "33": [6, 16, 18], "814": [6, 15, 16, 58], "record_vsec": [6, 7, 21, 38, 54, 58], "explain": [6, 18], "about": [6, 20, 52, 54], "structur": [6, 7, 18, 21, 23, 56], "thei": [6, 20, 52, 53], "better": [6, 7, 18, 53], "interpret": [6, 18, 53, 56], "uniqu": [6, 9, 14, 21, 22, 23, 27, 51, 53, 54, 56, 58], "gid_rang": [6, 22, 23, 37, 54], "ordereddict": 6, "135": [6, 8, 15], "270": [6, 9, 14, 15, 23], "505": 6, "775": 6, "1045": 6, "section": [6, 7, 15, 21, 22, 23, 38, 41, 52, 53, 58], "cellrespons": [6, 23, 37, 48, 49, 55, 58], "individu": [6, 21, 22, 41, 48, 52, 56, 58], "includ": [6, 11, 13, 14, 16, 22, 25, 30, 33, 34, 39, 40, 43, 45, 47, 48, 50, 52, 55, 56, 58], "trial_idx": [6, 8, 9, 14, 16, 17, 22, 39, 48, 49], "vsec": [6, 21, 22, 54, 58], "kei": [6, 15, 20, 21, 22, 23, 25, 37, 40, 41, 48, 52, 54, 58], "dict_kei": [6, 15], "7": [6, 10, 15, 16, 17, 18, 25, 50, 53, 55], "11": [3, 6, 18], "13": [6, 17, 18, 25, 27, 44, 46, 50, 57], "14": [6, 18], "15": [3, 6, 14, 15], "16": [6, 15, 18], "17": [6, 18], "18": [6, 18], "19": [3, 6, 18, 19, 24], "21": [3, 6, 9, 10, 18], "22": [6, 18], "23": 6, "25": [6, 8, 14, 15, 18], "27": [6, 16, 18], "28": [6, 18], "31": [6, 18], "32": [6, 18, 30], "34": [6, 14, 18, 19], "36": [6, 18], "37": 6, "39": [6, 18, 21], "41": [6, 8, 10, 18], "42": [6, 18], "43": 6, "44": [6, 18, 58], "45": [3, 6, 7, 15, 18], "46": 6, "48": [6, 18], "49": [6, 18], "51": [6, 18], "52": [6, 18], "54": 6, "55": [3, 6, 18], "56": [6, 18], "57": [6, 15, 19], "59": [6, 16, 18, 19], "62": [6, 18], "64": [6, 18], "65": [6, 17, 18], "66": [6, 18], "67": [6, 18], "68": [6, 18], "69": [6, 18], "71": [6, 18], "72": [6, 8, 18], "73": [6, 18], "74": [6, 18], "75": [6, 15, 18], "76": [6, 18], "77": [6, 18, 58], "78": [6, 18], "79": [6, 18, 58], "81": [6, 18], "82": [6, 18], "83": [6, 14, 18], "84": [6, 18], "86": [6, 18, 58], "87": [6, 18], "88": [6, 18], "89": [6, 18], "91": [6, 18], "92": [6, 18, 53], "93": [6, 18], "94": [6, 18], "95": [6, 18], "96": [6, 18, 28, 58], "97": [6, 18], "98": [6, 18, 58], "99": [6, 18], "101": 6, "102": [6, 8, 14, 15, 29, 58], "103": [6, 8], "104": [6, 56], "105": [6, 58], "106": 6, "107": 6, "108": 6, "109": 6, "111": [6, 18, 56], "112": [6, 18], "113": 6, "114": 6, "115": 6, "116": 6, "117": 6, "118": [6, 14], "119": 6, "121": 6, "122": 6, "123": 6, "124": [6, 56], "125": [6, 15], "126": 6, "127": 6, "128": 6, "129": [6, 56], "131": 6, "132": 6, "133": 6, "134": [6, 18], "136": 6, "138": 6, "139": 6, "141": 6, "142": 6, "143": [6, 58], "144": 6, "145": [6, 58], "146": [6, 58], "147": 6, "148": 6, "149": 6, "151": 6, "152": 6, "153": [6, 14, 19], "154": 6, "155": [6, 58], "156": [6, 58], "157": [6, 58], "158": 6, "159": 6, "161": [6, 17, 18, 19], "162": [6, 58], "163": 6, "164": 6, "165": 6, "166": 6, "167": 6, "168": 6, "169": 6, "171": [6, 58], "172": 6, "173": 6, "174": 6, "175": 6, "176": 6, "177": 6, "178": 6, "179": 6, "180": [6, 9, 14, 15, 17], "181": 6, "182": 6, "183": 6, "184": 6, "185": 6, "186": 6, "187": 6, "188": [6, 58], "189": [6, 18], "190": [6, 9, 14, 15, 17, 19, 58], "191": [6, 58], "192": 6, "193": 6, "194": 6, "195": 6, "196": 6, "197": 6, "198": 6, "199": [6, 58], "200": [6, 9, 14, 15, 17, 21, 27, 28, 31, 39, 46], "201": 6, "202": 6, "203": 6, "204": [6, 18, 58], "205": 6, "206": 6, "207": [6, 58], "208": 6, "209": [6, 58], "210": [6, 9, 14, 15, 17], "211": 6, "212": [6, 8, 10], "213": 6, "214": 6, "215": 6, "216": 6, "218": 6, "219": 6, "220": [6, 9, 14, 15, 17], "221": [6, 58], "222": 6, "223": 6, "224": 6, "225": [6, 7], "226": 6, "227": 6, "228": 6, "229": 6, "230": [6, 9, 14, 15, 17], "231": [6, 58], "232": 6, "233": 6, "234": 6, "235": [6, 16, 19], "236": 6, "237": 6, "238": 6, "239": 6, "240": [6, 9, 14, 15, 17], "241": 6, "242": [6, 18], "243": 6, "244": 6, "245": 6, "246": [6, 18, 19], "247": 6, "248": 6, "249": 6, "250": [6, 9, 14, 15, 17, 21, 41], "251": 6, "252": 6, "253": 6, "254": 6, "255": 6, "256": 6, "257": 6, "258": 6, "259": 6, "260": [6, 9, 14, 15], "261": 6, "262": 6, "263": 6, "264": [6, 58], "265": 6, "266": [6, 18], "267": 6, "268": 6, "269": 6, "d": [6, 15, 18, 20, 22, 55], "gid_to_typ": [6, 23], "mv": [6, 21, 39], "write": [6, 22, 23, 25, 55, 58], "them": [6, 16, 20, 23, 33, 52, 56], "text": [6, 15], "file": [6, 9, 10, 12, 16, 17, 18, 19, 20, 22, 23, 25, 28, 29, 35, 36, 37, 38, 56, 57, 58], "format": [6, 18, 22, 23, 54, 58], "syntax": 6, "filenam": [6, 39, 58], "written": [6, 55], "spk_1": 6, "spk_2": 6, "read": [6, 16, 17, 18, 20, 23, 28, 35, 36, 37, 38, 53, 55, 58], "back": [6, 17, 20, 55], "wildcard": [6, 37], "express": [6, 37], "temporarydirectori": 6, "tmp_dir_nam": 6, "spk_": [6, 22, 37], "home": [6, 7, 8, 9, 14, 16, 18], "circleci": [6, 7, 8, 9, 14, 16, 18, 20], "project": [6, 8, 14, 15, 18, 55], "howto": [6, 8, 10, 57], "plot_firing_pattern": [6, 10, 57], "deprecationwarn": 6, "deprec": [6, 23, 29, 56, 58], "futur": [6, 23, 29, 52, 56], "version": [6, 18, 20, 53, 55, 56, 58], "pleas": [6, 20, 51, 53], "save": [6, 23, 54, 58], "along": [6, 8, 24, 27, 53, 56], "tmp": 6, "tmph4ypzpfi": 6, "spk_0": 6, "rate": [6, 8, 22, 23, 27, 58], "class": [6, 7, 9, 21, 22, 23, 25, 27, 28, 31, 32, 33, 35, 39, 56, 58], "window": [6, 8, 14, 18, 21, 25, 27, 28, 31, 39, 41, 47, 53, 56], "tstart": [3, 6, 9, 14, 15, 22, 23], "all_rat": 6, "mean_rat": [6, 22], "mean_typ": [6, 22], "trial_rat": 6, "243697478991596": 6, "705882352941176": 6, "126050420168063": 6, "176470588235297": 6, "raster": [6, 8, 15, 16], "histogram": [6, 15, 16, 18, 22, 48, 58], "idx": [6, 23], "per": [6, 22, 25, 39, 50], "g": [6, 15, 16, 17, 20, 21, 22, 23, 25, 27, 30, 37, 46, 48, 50, 54, 56, 58], "r": [6, 8, 14, 15, 16, 17, 18, 21, 22, 27, 29, 41, 45, 48, 58], "500x700": 6, "868": [6, 10], "ll": [7, 8, 14, 17, 20], "necessari": [7, 15, 20, 52], "modul": [7, 8, 11, 13, 14, 19, 20, 23, 29, 30, 56, 57], "would": [7, 18, 52, 55], "like": [7, 15, 20, 22, 25, 27, 45, 46, 56], "read_param": [7, 17, 58], "network_model": [7, 8], "add_erp_drives_to_jones_model": [7, 8], "begin": [7, 15, 20, 21, 23, 55, 56], "For": [7, 8, 9, 18, 20, 23, 24, 25, 34, 52, 53, 54, 55], "reduc": [7, 15, 18, 55, 58], "speed": [7, 8, 20], "mesh_shap": [7, 23, 24, 29, 30], "move": 7, "further": [7, 51, 52, 53, 56], "apart": [7, 8, 9, 14], "inplane_dist": [7, 8, 21, 23], "\u00b5m": 7, "set_cell_posit": [7, 8, 23, 29, 58], "300": [3, 7, 9, 14, 15, 39], "networkplott": [7, 58], "3d": [7, 18, 21, 39, 40, 41, 43], "net_plot": 7, "miniconda": [7, 9, 16], "env": [7, 9, 16], "testenv": [7, 9, 16], "lib": [7, 9, 16, 55], "python3": [7, 9, 16], "site": [7, 9, 16], "959": 7, "userwarn": [7, 8, 14, 55], "layout": [7, 8, 14, 28], "ha": [7, 8, 14, 15, 20, 21, 23, 25, 54, 55, 56, 58], "tight": [7, 8, 14], "anoth": [7, 15, 33], "angl": 7, "adjust": [7, 18, 20, 25, 29, 39, 40, 43, 45, 50, 58], "azimuth": [7, 39], "elev": [7, 39], "azim": [7, 39], "next": [7, 14, 15, 20, 23, 27], "event": [7, 8, 11, 13, 14, 15, 18, 19, 23, 30, 52, 53, 54, 57, 58], "relat": [7, 8, 9, 11, 13, 15, 19, 28, 52, 53, 56, 57, 58], "erp": [7, 8, 11, 13, 18, 19, 30, 53, 56, 57], "membran": [7, 8, 21, 23, 27, 54, 56], "turn": [7, 58], "reiniti": 7, "plotter": 7, "export_movi": [7, 39], "xyz": 7, "limit": [7, 18, 21, 23, 25, 27, 31, 39, 41, 50, 52, 56], "xlim": [7, 18, 21, 39, 41], "400": [7, 15], "1600": 7, "ylim": [7, 21, 39, 41], "zlim": [7, 21, 39, 41], "500": [7, 39], "animation_demo": 7, "gif": 7, "dpi": [7, 28, 39], "fp": [7, 39], "interv": [7, 39], "funcanim": 7, "0x7f7fef2fdb80": 7, "965": [7, 10], "plot_hnn_anim": [7, 10, 57], "main": [8, 56], "output": [8, 18, 22, 23, 25, 28, 29, 55, 58], "e": [8, 14, 16, 17, 18, 20, 21, 22, 23, 25, 27, 37, 46, 50, 52, 54, 56, 58], "intracellular": 8, "flow": [8, 18], "apic": [8, 15, 21], "At": [8, 18, 55], "eeg": [8, 11, 13, 18, 52, 53, 56], "sensor": [8, 11, 13, 19, 56, 57], "primari": [8, 18, 53, 56], "contributor": [8, 20, 53, 55], "measur": [8, 23, 27, 53, 56], "field": [8, 18, 27, 53, 56, 58], "close": [8, 53], "lfp": [8, 45, 53, 58], "result": [8, 14, 17, 23, 30, 32, 33, 52, 53, 58], "leak": 8, "medium": 8, "through": [8, 11, 13, 22, 48, 52, 56, 58], "passiv": 8, "channel": [8, 15, 18, 24, 30, 45, 52, 58], "simplifi": 8, "assumpt": 8, "approxim": [8, 14, 18, 23, 25, 27, 54], "virtual": [8, 52, 53], "electrod": [8, 23, 27, 46, 54, 58], "place": [8, 14, 16, 17, 20, 25, 27, 58], "around": 8, "christoph": [8, 14, 16, 17, 58], "bailei": [8, 14, 16, 17, 58], "cjb": [8, 16], "cfin": [8, 16], "au": [8, 16], "dk": [8, 16], "mainakja": [8, 18], "jone": [8, 14, 15, 16, 17, 18, 24, 29, 30, 58], "et": [8, 14, 15, 16, 24, 29, 30, 53, 56], "al": [8, 14, 15, 16, 24, 29, 30, 53, 56], "2009": [8, 14, 15, 24, 29, 30], "consist": [8, 9, 14, 15, 20, 33, 54, 58], "squar": [8, 21, 23, 29, 40], "plane": [8, 21, 23, 29, 58], "influenc": [8, 15, 17], "moment": [8, 16, 17, 18, 23, 25, 58], "space": [8, 9, 11, 13, 14, 19, 21, 23, 41, 56, 57], "um": [8, 21, 23, 27, 29, 54], "three": [8, 15, 20, 56], "requir": [8, 16, 17, 18, 20, 23, 53, 55, 56], "posit": [8, 15, 18, 21, 23, 27, 41, 54], "It": [8, 15, 21, 40, 55], "decid": [8, 52], "placement": 8, "plot_cel": [8, 16, 23, 58], "within": [8, 14, 18, 23, 56], "arrang": [8, 23, 29], "regular": [8, 17, 18, 52, 58], "align": [8, 21], "z": [8, 21, 23, 27, 39, 41, 54, 58], "axi": [8, 21, 22, 23, 25, 27, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "linear": [8, 20, 56], "multielectrod": 8, "arrai": [8, 22, 23, 25, 27, 45, 46, 50, 52, 58], "intercontact": 8, "x": [8, 21, 23, 25, 27, 39, 41, 45, 54], "y": [8, 21, 23, 27, 39, 41, 54, 55, 58], "coordin": [8, 18, 21, 23, 27, 54], "triplet": 8, "extend": [8, 23, 27, 56], "2000": 8, "resid": 8, "1300": [8, 28], "2300": 8, "center": [8, 23, 27], "constant": [8, 15, 17, 23, 30, 43, 58], "conduct": [8, 15, 23, 24, 27, 54, 58], "point": [8, 18, 22, 23, 27, 29, 39, 54, 55, 58], "add_electrode_arrai": [8, 23, 27, 58], "depth": [8, 18, 58], "325": 8, "2150": 8, "electrode_po": [8, 23], "dep": 8, "shank1": 8, "rec_arrai": [8, 23, 27, 54, 58], "electrodearrai": 8, "comput": [8, 16, 17, 18, 20, 26, 51, 53, 56, 58], "resourc": [8, 56], "thu": [8, 18, 25, 53], "slightli": 8, "slow": 8, "consider": 8, "extracellulararrai": [8, 23, 58], "psa": [8, 23, 27], "yet": [8, 21, 54], "both": [8, 16, 20, 56, 58], "trace": [8, 14, 18, 25, 27, 44, 46, 50], "decim": [8, 25, 27, 39, 44, 46, 50], "factor": [8, 14, 18, 23, 25, 27, 31, 39, 44, 46, 50], "khz": 8, "appli": [8, 14, 17, 18, 23, 25, 27, 29, 32, 33, 38, 44, 45, 46, 47, 50, 54, 56, 58], "significantli": 8, "40k": 8, "8k": 8, "2k": 8, "gridspec_kw": 8, "height_ratio": 8, "seri": [8, 18, 27, 46], "its": [8, 17, 18, 23, 52, 53, 56], "comparison": [8, 14, 15, 16], "plot_lfp": [8, 27, 58], "major": [8, 15, 52, 56], "set_xlabel": 8, "csd": [8, 27, 45, 53, 58], "bottom": 8, "plot_csd": [8, 27, 58], "plot_record_extracellular_potenti": [8, 10, 57], "quantit": [8, 14, 15, 29], "biophys": [8, 14, 15, 16, 18, 29, 52, 53, 56, 58], "neural": [8, 14, 15, 16, 18, 24, 29, 53, 56], "meg": [8, 11, 13, 14, 15, 19, 29, 52, 53, 56, 57], "rhythm": [8, 11, 13, 15, 19, 29, 53, 56, 57], "rhythmogenesi": [8, 14, 15, 29], "sensori": [8, 14, 15, 29, 56], "j": [8, 14, 15, 16, 18, 29], "neurophysiol": [8, 14], "3554": [8, 14, 15, 29], "3572": [8, 14, 15, 29], "kajikawa": 8, "schroeder": 8, "c": [8, 15, 18, 20, 53, 55], "847": 8, "858": 8, "2011": 8, "even": [9, 51, 53], "singl": [9, 14, 17, 18, 28, 34, 52, 53, 56, 58], "you": [9, 11, 13, 14, 16, 17, 18, 20, 23, 25, 27, 51, 53, 55], "softwar": [9, 18, 52, 53, 56], "want": [9, 16, 18, 20, 52, 53], "configur": [9, 17, 18, 23, 28, 58], "blake": [9, 16, 58], "caldwel": [9, 16, 18, 58], "blake_caldwel": [9, 16], "alpha": [3, 9, 11, 13, 17, 18, 19, 53, 57], "hz": [3, 9, 14, 15, 17, 18, 22, 23, 25, 47], "bursti": [9, 14, 23, 40, 54], "continu": [9, 14, 22, 52, 53, 55, 56], "burst": [9, 14, 23], "pair": [9, 14, 23, 54], "occurr": [9, 14, 23], "jitter": [9, 14, 23, 58], "amount": [9, 14, 27, 46], "repeat": [9, 14, 20, 58], "train": [9, 14, 23, 54, 58], "4e": [3, 9, 14], "add_bursty_dr": [3, 9, 14, 15, 16, 23, 58], "burst_rat": [3, 9, 14, 15, 23], "burst_std": [3, 9, 14, 15, 23], "spike_isi": [3, 9, 14, 15, 23], "n_drive_cel": [3, 9, 14, 15, 16, 18, 23, 54, 58], "278": 9, "processor": [9, 55], "launcher": [9, 33], "openmpi": [9, 33, 53, 55], "system": [9, 11, 13, 53, 55], "310": [9, 14, 15], "sequenti": [9, 28, 53, 56], "numproc": [9, 55], "mechan": [9, 15, 16, 17, 20, 21, 24, 30, 54, 56], "mod": [9, 16, 20, 21, 54], "x86_64": [9, 16], "libnrnmech": [9, 16], "280": [9, 14, 15], "290": [9, 14, 15], "527": [9, 10], "plot_simulate_mpi_backend": [9, 10, 57], "401": 10, "execut": [10, 12, 19, 33, 53, 55, 57], "auto_exampl": [10, 12, 19, 56], "mem": [10, 12, 19, 57], "mb": [10, 12, 18, 19, 57], "00": [10, 12, 18, 19, 57], "000": [10, 12, 18, 57], "workflow": [11, 13, 14, 16, 17, 18, 19, 20, 56, 57, 58], "commonli": [11, 13, 53, 56], "studi": [11, 13, 16, 18, 30, 53, 56], "signal": [3, 11, 13, 14, 17, 18, 52, 53, 55, 56], "low": [11, 13, 17, 52, 53, 56], "frequenc": [3, 11, 13, 14, 15, 17, 18, 25, 31, 47, 50, 53, 56, 58], "beta": [3, 11, 13, 17, 19, 30, 53, 57], "gamma": [11, 13, 19, 53, 57], "band": [3, 11, 13, 18, 31], "gui": [11, 13, 14, 16, 17, 23, 29, 58], "websit": [11, 13, 52, 56], "reproduc": [11, 13, 15, 18, 30, 56, 58], "subset": [11, 13, 22, 23, 58], "elabor": [11, 13], "strongli": [11, 13], "recommend": [11, 13, 14, 16, 17, 18, 20, 23, 25, 27, 44, 46, 50, 52, 53], "background": [11, 13, 18, 39, 52], "inform": [11, 13, 15, 20, 23, 53, 54, 58], "instruct": [11, 13, 20, 53], "clearer": [11, 13], "prior": [11, 13, 14, 18, 56, 58], "public": [11, 13, 15, 18, 53], "investig": [11, 13, 56], "brain": [11, 13, 18, 24, 53, 56], "somatosensori": [11, 13, 18], "help": [11, 13, 15, 18, 20, 53, 56], "get": [11, 13, 16, 18, 23, 53, 54, 55], "auto_examples_python": 11, "auto_examples_jupyt": 11, "n": [12, 15, 18], "A": [12, 15, 21, 23, 25, 26, 27, 28, 31, 33, 46, 51, 52, 53, 55, 56, 58], "complex": [14, 56], "si": 14, "tutori": [14, 16, 17, 18], "review": [14, 16, 17, 20, 52], "below": [14, 16, 17, 20, 22, 54, 55], "recreat": [14, 16, 17], "similar": [14, 15, 17, 20, 23, 56], "albeit": [14, 16], "spectrogram": 14, "sam": [14, 16, 17], "neymotin": [14, 15, 16, 17, 18], "samnemo": [14, 16, 17], "cj": [14, 17], "excit": [14, 17], "synaps": [14, 15, 17, 21, 23, 34, 54, 58], "weights_ampa_p": [3, 14, 18], "syn_delays_p": [3, 14], "alpha_prox": [3, 14], "284": 14, "automat": [14, 22, 27, 45, 53, 58], "choos": [14, 56], "emul": 14, "larger": [14, 18, 52], "patch": [14, 18], "cortex": [14, 15, 18, 27, 30], "simpl": [14, 25, 44, 53, 55], "0x7f7ff43d7df0": 14, "oper": [14, 16, 18, 25, 27, 28, 34, 52], "alter": [14, 15, 25, 27], "insid": [14, 16, 25, 50], "summat": 14, "greater": [14, 23, 52], "volum": [14, 23, 27], "confirm": [14, 17], "what": [14, 15, 16, 33], "inde": 14, "power": [3, 14, 25, 47, 50, 58], "spectral": [3, 14, 25, 47, 58], "densiti": [3, 14, 25, 27, 45, 47, 53, 56, 58], "psd": [3, 14, 25, 47], "plot_psd": [3, 14, 17, 25, 58], "tmin": [14, 15, 17, 18, 25, 27, 44, 46, 47, 50, 58], "tmax": [14, 18, 25, 27, 44, 46, 47, 50, 58], "exclud": 14, "burn": 14, "make": [14, 16, 53, 55, 56, 58], "befor": [14, 16, 17, 20, 23, 38, 52, 53, 55, 56, 58], "order": [14, 18, 25, 55], "compar": [14, 15, 17, 20, 53, 55, 56], "convolv": [14, 25, 27], "long": [14, 15, 56], "ham": [14, 18, 25, 27, 47], "dpl_smooth": 14, "overlai": 14, "onc": [14, 20, 21, 52, 53, 55, 56], "b": [14, 15, 18, 21, 22, 27, 41, 45, 48], "set_xlim": 14, "399": [14, 58], "fmin": [14, 17, 25, 47], "fmax": [3, 14, 17, 25, 47], "1e3": [14, 18], "set_xscal": 14, "log": [14, 20, 28], "plot_simulate_alpha": [14, 19, 57], "spread": [14, 33], "arriv": [14, 15, 52], "opposit": 14, "tend": 14, "known": 14, "weights_ampa_d": [3, 14, 18], "syn_delays_d": [3, 14], "alpha_dist": [3, 14], "296": 14, "verifi": [14, 55], "wa": [14, 15, 18, 33, 56, 58], "most": [14, 15, 18, 25, 47, 53, 56], "recent": [14, 56], "domin": [14, 17], "shift": 14, "abov": [14, 15, 17, 52, 53], "lead": [14, 15, 17, 18, 22, 23, 48], "absolut": 14, "again": [14, 52], "smooth_dpl": 14, "plot_": 14, "avail": [14, 18, 23, 55, 56], "prestimulu": 15, "law": [15, 30], "2021": [15, 30, 56], "modif": [15, 58], "transient": [15, 30], "neocortex": 15, "suppress": 15, "percept": [15, 30], "incom": 15, "law_2021_model": [15, 58], "describ": [15, 23, 29, 30, 53, 54], "One": [15, 27], "signific": [3, 15], "substanti": [15, 52, 56], "increas": [15, 17, 20, 30], "rise": [15, 21], "fall": 15, "gabab": [15, 23, 30, 34], "calcium": [15, 21, 22, 24, 30, 38, 56, 58], "basal": [15, 30], "properti": [15, 27, 28, 54, 58], "cell_typ": [15, 16, 17, 23, 54, 58], "attribut": [15, 21, 22, 23, 25, 27, 28, 32, 33, 39, 41, 54, 58], "geometri": 15, "net_jon": 15, "jones_ris": 15, "tau1": [15, 21, 54], "law_ris": 15, "f": [15, 55], "jones_fal": 15, "tau2": [15, 17, 21, 54], "law_fal": 15, "apical_1": 15, "mech": [15, 54], "nbasal": 15, "ca": [15, 21, 22, 58], "miss": [15, 51, 58], "basal_1": 15, "hh2": 15, "cad": 15, "kca": 15, "km": 15, "cat": 15, "martinotti": 15, "recurr": 15, "tuft": 15, "inhibit": [15, 30], "remain": [15, 18, 52], "replac": [15, 30, 58], "nconnect": 15, "0002": 15, "001": [15, 18], "depress": 15, "consid": [15, 18, 20, 25, 27, 51, 52], "case": [15, 20, 22, 52, 56, 58], "tactil": [15, 16, 18, 30], "stimulu": [15, 18], "deliv": 15, "later": [15, 23, 54], "cortic": [15, 16, 18, 51], "column": [15, 23, 25, 37, 51, 54, 56, 58], "direct": [15, 16, 24, 51, 52, 58], "thalam": [15, 51, 56], "nuclei": [15, 51], "repres": [15, 18, 23, 25, 26, 54, 56], "indirect": [15, 51], "late": [15, 18], "due": [15, 17, 23, 58], "add_erp_dr": 15, "stimulus_start": 15, "0005": [15, 18], "004": [15, 18], "syn_delays_d1": 15, "002": [15, 18], "0011": 15, "syn_delays_prox": 15, "nb": [15, 16, 23, 25, 29], "005": 15, "induc": 15, "just": [15, 21, 38, 58], "strong": [15, 17], "enough": 15, "caus": [15, 55, 58], "mediat": 15, "ultim": [15, 56], "detect": [15, 16, 18, 21, 33], "add_beta_dr": 15, "beta_start": 15, "00032": 15, "00008": 15, "00004": 15, "beta_dist": 15, "tstart_std": [15, 23], "00002": 15, "syn_delays_p1": 15, "beta_prox": 15, "distinct": 15, "net_beta": 15, "net_beta_erp": 15, "And": 15, "been": [15, 20, 25, 56, 58], "observ": [15, 16, 17, 18], "cours": [15, 17, 18, 20, 25, 47, 50], "dpls_beta": 15, "dpls_erp": 15, "dpls_beta_erp": 15, "320": 15, "330": [15, 58], "340": 15, "350": [15, 58], "360": 15, "370": [15, 58], "380": 15, "390": 15, "occur": [15, 18, 22, 23], "exclus": [15, 58], "gaussian": [15, 23, 54, 58], "sustain": 15, "pyrmaid": 15, "asymmetr": 15, "tail": 15, "set_titl": 15, "fix": [15, 17, 20, 23, 25, 50, 52, 58], "tile": [15, 17], "freq": [15, 17, 25, 50], "arang": [15, 17], "plot_tfr_morlet": [15, 17, 25, 58], "n_cycl": [15, 17, 25, 50], "700x700": 15, "happen": [15, 16], "when": [15, 16, 20, 23, 28, 29, 33, 44, 52, 53, 56, 58], "hand": 15, "roughli": 15, "understand": [15, 18], "stimuli": 15, "associ": [15, 18, 23, 45, 46, 56, 58], "amplitud": [15, 16, 17, 18, 21, 23, 54, 58], "puglies": [15, 58], "shin": 15, "h": [15, 21, 32, 33, 38, 54, 55], "sliva": 15, "lee": [15, 17], "moor": [15, 18], "thalamocort": [15, 30, 53], "regul": [15, 30], "relationship": [15, 30], "human": [15, 17, 18, 24, 30, 52, 53, 56], "biorxiv": 15, "440210": 15, "doi": [15, 18, 27, 53, 56], "org": [15, 18, 27, 39, 53, 56], "1101": 15, "pritchett": [15, 18], "l": [15, 18, 21, 54], "sikora": 15, "stufflebeam": [15, 18], "h\u00e4m\u00e4l\u00e4inen": [15, 18], "journal": [15, 16, 29, 53], "neurophysiologi": [15, 29, 53], "1152": [15, 27], "jn": [15, 27], "00535": 15, "silberberg": 15, "markram": 15, "2007": [15, 16, 18], "disynapt": 15, "735": 15, "746": [15, 58], "1016": 15, "012": 15, "394": [15, 19], "plot_simulate_beta": [15, 19, 57], "threshold": [16, 17, 21, 23, 54], "level": [16, 52, 53, 56], "neurosci": [16, 17, 18, 51], "mmja": 16, "plot_morphologi": [16, 21, 58], "axes3d": [16, 21, 23, 39, 40, 41, 42, 43], "extern": [16, 23, 56, 58], "prescrib": 16, "separ": [16, 23, 25, 29, 50, 55, 56, 58], "possibl": [16, 23, 25, 38, 50, 52], "click": [16, 40], "link": [16, 17, 20], "document": [16, 52, 56, 58], "add_poisson_dr": [16, 17, 23, 58], "000007": 16, "could": [16, 28, 33, 56], "equal": [16, 27, 56], "joblibbackend": [16, 18, 33, 55, 58], "rather": [16, 18, 56], "explicit": [16, 18, 20], "analyz": 16, "contribut": [16, 18, 23, 52, 54, 56], "featur": [16, 20, 52, 53, 56, 58], "averag": [16, 18, 22, 25, 26, 44, 47, 50, 58], "exogen": [16, 17, 18, 51, 54, 56], "achiev": [16, 25, 27, 44, 46, 50], "cell_specif": [16, 18, 23, 54, 58], "ad": [16, 20, 23, 27, 28, 29, 58], "net_sync": 16, "interrog": [16, 53], "external_dr": [16, 23, 54, 58], "dpls_sync": 16, "alwai": 16, "look": [16, 17, 20, 55], "conjunct": 16, "avoid": [16, 20, 23, 27, 55], "misinterpret": 16, "seed": [16, 23, 54, 58], "draw": 16, "conclus": 16, "stephani": [16, 29, 58], "correl": [16, 18], "magnetoencephalographi": [16, 18, 53], "10751": [16, 18], "10764": [16, 18], "plot_simulate_evok": [16, 19, 53, 57], "establish": 17, "interneuron": 17, "weak": 17, "params_fnam": [17, 18, 28, 36], "gamma_l5weak_l2weak": 17, "json": [17, 18, 23, 29, 36, 58], "gbar_l": 17, "gbar_l2basket_l2basket": 17, "gbar_l2basket_l2pyr_gabaa": 17, "007": 17, "gbar_l2basket_l2pyr_gabab": 17, "gbar_l2basket_l5pyr": 17, "gbar_l2pyr_l2basket": 17, "0012": 17, "gbar_l2pyr_l2pyr_ampa": 17, "gbar_l2pyr_l2pyr_nmda": 17, "gbar_l2pyr_l5basket": 17, "gbar_l2pyr_l5pyr": 17, "gbar_l5basket_l5basket": 17, "0075": 17, "gbar_l5basket_l5pyr_gabaa": 17, "08": [1, 11, 17, 18, 19, 29, 31, 38, 47, 57], "gbar_l5basket_l5pyr_gabab": 17, "gbar_l5pyr_l5basket": 17, "00091": 17, "gbar_l5pyr_l5pyr_ampa": 17, "gbar_l5pyr_l5pyr_nmda": 17, "tonic": [17, 21, 22, 23, 48, 54, 58], "poisson": [17, 22, 23, 40, 48, 58], "0008": 17, "rate_const": [17, 23, 58], "1349": 17, "30000": 17, "respond": 17, "while": [17, 20, 52, 53], "rel": [17, 23], "displai": [17, 25, 28, 58], "vari": [17, 53], "fraction": 17, "reach": [17, 52], "oscil": 17, "represent": [17, 18, 21, 25, 50, 54, 58], "togeth": [17, 55], "steadi": 17, "state": [17, 21, 58], "henc": [17, 18, 20], "pick": [17, 18], "bia": [17, 21, 23, 58], "notic": 17, "less": [17, 58], "nois": [17, 18], "fact": [17, 51], "depolar": 17, "entir": [17, 20, 21, 25, 39, 41, 47, 50, 53], "durat": [17, 25, 47], "add_tonic_bia": [17, 23, 58], "nearli": 17, "inhibitori": [17, 29, 34, 56], "latenc": 17, "ipsp": 17, "onto": 17, "bring": 17, "ping": 17, "sometim": 17, "although": 17, "mechanist": [17, 53], "decreas": [17, 24, 30], "shorten": 17, "refactori": 17, "distinguish": [17, 52], "laminar": [17, 27, 45, 46, 56, 58], "frontier": 17, "2013": 17, "plot_simulate_gamma": [17, 19, 57], "invers": [18, 23, 56], "solut": 18, "median": [18, 56], "nerv": [18, 56], "s1": 18, "mne": [18, 25, 55, 56, 58], "dataset": [18, 56], "expound": 18, "came": 18, "sequenc": [18, 55, 56], "implement": [18, 20], "those": [18, 23, 52, 56], "who": [18, 52, 56], "articul": 18, "present": [18, 22, 23, 27, 29, 33, 34, 48], "part": [18, 55], "motiv": 18, "nibabel": 18, "pip": [18, 20, 53, 55, 56], "somato": 18, "minimum_norm": 18, "apply_invers": 18, "make_inverse_oper": 18, "subject": [18, 52, 56], "data_path": 18, "raw_fnam": 18, "sub": [18, 52, 58], "_task": 18, "_meg": 18, "fif": 18, "fwd_fname": 18, "deriv": 18, "fwd": 18, "subjects_dir": 18, "freesurf": 18, "mne_data": 18, "tar": 18, "gz": 18, "osf": 18, "io": [18, 56], "tp4sg": 18, "611m": 18, "08m": 18, "8mb": 18, "6m": 18, "9mb": 18, "8m": 18, "3mb": 18, "2m": 18, "4mb": 18, "5m": 18, "5mb": 18, "6mb": 18, "0m": 18, "3m": 18, "0mb": 18, "7mb": 18, "106m": 18, "115m": 18, "125m": 18, "134m": 18, "1mb": 18, "144m": 18, "153m": 18, "163m": 18, "172m": 18, "182m": 18, "191m": 18, "201m": 18, "210m": 18, "220m": 18, "229m": 18, "239m": 18, "248m": 18, "258m": 18, "267m": 18, "277m": 18, "286m": 18, "296m": 18, "305m": 18, "315m": 18, "324m": 18, "334m": 18, "2mb": 18, "343m": 18, "352m": 18, "359m": 18, "367m": 18, "373m": 18, "379m": 18, "388m": 18, "396m": 18, "405m": 18, "412m": 18, "420m": 18, "429m": 18, "437m": 18, "445m": 18, "453m": 18, "459m": 18, "466m": 18, "473m": 18, "481m": 18, "491m": 18, "500m": 18, "510m": 18, "519m": 18, "528m": 18, "537m": 18, "546m": 18, "554m": 18, "563m": 18, "572m": 18, "581m": 18, "590m": 18, "599m": 18, "607m": 18, "78tb": 18, "untar": 18, "content": [18, 20], "attempt": [18, 33], "complet": [18, 20, 55, 56], "582": 18, "estim": [18, 27, 45], "filter": [18, 22, 25, 27, 58], "read_raw_fif": 18, "preload": 18, "l_freq": 18, "h_freq": [18, 25], "identifi": [18, 21, 23, 34, 54, 56], "find_ev": 18, "stim_channel": 18, "sti": 18, "014": 18, "epoch": 18, "event_id": 18, "baselin": [18, 56], "reject": 18, "grad": 18, "4000e": 18, "eog": 18, "350e": 18, "read_forward_solut": 18, "cov": 18, "compute_covari": 18, "inv": 18, "info": [18, 54], "open": [18, 20, 51, 52, 53, 55, 56], "01_task": 18, "somato_meg": 18, "237600": 18, "506999": 18, "791": 18, "1688": 18, "sec": 18, "readi": [18, 20, 55], "269399": 18, "897": 18, "077": 18, "contigu": 18, "segment": [18, 21, 23, 27], "fir": [18, 25], "design": [18, 52, 53, 56], "phase": 18, "non": [18, 23, 53, 55, 56, 58], "causal": 18, "bandpass": 18, "domain": [18, 56], "firwin": 18, "0194": 18, "passband": 18, "rippl": 18, "db": 18, "stopband": 18, "attenu": 18, "edg": 18, "transit": 18, "bandwidth": 18, "cutoff": [18, 25], "length": [18, 21, 25, 27, 31, 54, 55], "993": 18, "307": 18, "287": 18, "found": [18, 20, 39, 58], "stim": 18, "Not": [18, 23], "metadata": 18, "No": 18, "correct": [18, 52, 53], "item": [18, 34, 58], "bad": 18, "drop": 18, "forward": 18, "desir": 18, "matrix": [18, 43], "kind": 18, "3523": 18, "8155": 18, "306": 18, "free": [18, 20], "orient": [18, 53], "transform": [18, 56], "frame": [18, 39], "rank": [18, 55, 58], "toler": 18, "5e": 18, "2e": 18, "ep": 18, "dim": 18, "singular": 18, "mag": 18, "projector": 18, "plot_simulate_somato": [18, 19, 57], "runtimewarn": 18, "someth": 18, "went": 18, "wrong": 18, "driven": 18, "exce": [18, 58], "theoret": 18, "auto": 18, "integ": [18, 21, 25, 27, 44, 46, 50], "covari": 18, "empir": [18, 56], "12432": 18, "convert": [18, 20, 21, 27, 56, 58], "surfac": 18, "emploi": [18, 56], "rotat": 18, "out": [18, 55], "select": [18, 20, 28, 40, 58], "planar": 18, "7615": 18, "004172": 18, "17919e": 18, "exp": [18, 23], "loos": 18, "whiten": 18, "small": 18, "eigenvalu": 18, "pca": 18, "svd": 18, "largest": 18, "42284": 18, "86104e": 18, "nchan": 18, "nzero": 18, "There": [18, 33, 53, 56], "reconstruct": 18, "wherea": 18, "offer": 18, "techniqu": 18, "best": [18, 20, 56], "howev": [18, 20, 25, 47], "assum": [18, 23, 27], "pick_ori": 18, "appropri": [18, 52], "snr": 18, "lambda2": 18, "stc": 18, "return_residu": 18, "verbos": 18, "prepar": 18, "nave": [18, 25], "invert": 18, "vector": [18, 25], "eigenlead": 18, "residu": 18, "varianc": 18, "extract": [18, 55], "postcentr": 18, "gyru": 18, "hemi": 18, "rh": 18, "label_tag": 18, "g_postcentr": 18, "label_s1": 18, "read_labels_from_annot": 18, "parc": 18, "aparc": 18, "a2009": 18, "regexp": 18, "parcel": 18, "annot": [18, 58], "geometr": 18, "mri": 18, "framework": [18, 20, 56], "upward": 18, "deep": 18, "superfici": 18, "downward": 18, "respect": [18, 58], "uncom": 18, "interact": [18, 40, 52, 53, 56, 58], "render": [18, 20, 28, 44], "pyvista": 18, "librari": 18, "should": [18, 20, 21, 23, 27, 52, 53, 55, 58], "central": 18, "040": 18, "imag": [18, 25, 50, 53], "get_brain_class": 18, "brain_label": 18, "white": 18, "add_label": 18, "stc_label": 18, "in_label": 18, "view_layout": 18, "horizont": 18, "initial_tim": 18, "nbrain": 18, "nbrain_label": 18, "nstc_label": 18, "region": [18, 51], "mode": [18, 58], "pca_flip": 18, "promin": 18, "compon": [3, 18, 26, 56, 58], "posterior": 18, "wall": 18, "sulcu": 18, "sinc": [18, 25], "dipolar": 18, "travel": 18, "flip_data": 18, "extract_label_time_cours": 18, "dipole_tc": 18, "1e9": 18, "ro": 18, "nam": [18, 25, 58], "axhlin": 18, "k": [18, 25, 44], "n20": 18, "average_dipol": [18, 58], "implic": 18, "earli": 18, "0036": 18, "0039": 18, "0019": 18, "0020": 18, "weights_nmda_p": 18, "0029": 18, "0030": 18, "276": [18, 58], "003": 18, "0043": 18, "0032": 18, "0009": 18, "weights_nmda_d": 18, "0051": 18, "0010": 18, "synaptic_delays_d": 18, "277": 18, "0041": 18, "0018": 18, "0017": 18, "evdist2": 18, "275": 18, "noisier": 18, "accur": [18, 24, 58], "macroscop": 18, "dpl_smooth_win": 18, "dpl_scalefctr": 18, "_nolegend_": 18, "set_ylabel": 18, "sa": 18, "daniel": [18, 58], "mcdougal": 18, "ra": [18, 21, 54], "carneval": 18, "nt": 18, "ci": [18, 55, 58], "hine": 18, "ml": 18, "sr": 18, "neurosolv": [18, 24, 52, 53], "tool": [18, 52, 53, 56], "cellular": [18, 20, 52, 53, 56], "elif": [18, 56], "e51214": 18, "2020": [18, 56], "7554": [18, 56], "51214": 18, "guid": [20, 52, 53], "until": [20, 54], "welcom": [20, 53], "form": [20, 21, 23, 27, 52], "piec": 20, "bug": [20, 52], "properli": [20, 28], "doc": 20, "incorpor": 20, "branch": 20, "few": [20, 53], "book": 20, "page": [20, 52, 53], "typic": [20, 55], "made": [20, 23, 34, 52, 56], "fork": 20, "repositori": [20, 52, 53, 56], "usual": [20, 27, 46], "clone": [20, 58], "person": 20, "push": 20, "github": [20, 52, 53, 56], "share": [20, 52], "upstream": 20, "codebas": [20, 52], "offici": 20, "remot": 20, "url": 20, "usernam": 20, "account": [20, 53, 56], "button": [20, 28], "top": [20, 27, 46], "right": [20, 40, 52], "corner": [20, 27, 46], "On": 20, "termin": [20, 33, 55], "cd": [20, 55], "check": [20, 33, 53, 58], "correctli": 20, "v": [20, 53], "fetch": 20, "exist": [20, 23, 28, 58], "cool_featur": 20, "checkout": 20, "relev": [20, 23, 34, 52, 56], "commit": [20, 52], "stage": 20, "area": [20, 56], "ensur": [20, 52, 55, 56], "statu": [20, 28, 52], "messag": [20, 53, 55, 58], "tip": 20, "merg": [20, 52], "prefix": 20, "mrg": 20, "flag": 20, "dev": [20, 55], "setup": [20, 58], "build_mod": 20, "extra": [20, 28], "access": [20, 28, 56, 58], "perform": [20, 56], "last": [20, 25, 28, 39], "compil": 20, "rebuilt": 20, "command": [20, 28, 33, 53, 55, 56], "pytest": [20, 55], "simpli": [20, 53], "skip": [20, 55], "mpi4pi": [20, 33, 53, 55], "highli": 20, "encourag": [20, 52], "suit": 20, "whether": [20, 23, 54], "html": [20, 39, 56], "given": [20, 23, 25, 38, 50, 53], "rst": 20, "whats_new": 20, "credit": [20, 55], "releas": [20, 23, 29, 56], "conflict": 20, "built": [20, 52, 56], "noplot": 20, "view": [20, 39, 56], "histori": 20, "therefor": [20, 54], "resolv": [20, 52], "articl": 20, "delet": 20, "easiest": 20, "approach": [20, 52, 56], "editor": [20, 53], "frequent": 20, "awar": 20, "being": [20, 55, 56, 58], "face": 20, "difficult": 20, "easier": 20, "squash": 20, "action": [20, 21, 51], "circl": 20, "autom": 20, "cach": 20, "don": 20, "t": [20, 55, 58], "worri": 20, "But": 20, "rebuild": 20, "build_cach": 20, "md5": 20, "monoton": 20, "v2": 20, "v3": 20, "po": [21, 41, 54], "sect_loc": [21, 23, 54], "cell_tre": [21, 54], "str": [21, 22, 23, 25, 27, 28, 29, 33, 34, 35, 36, 37, 39, 40, 41, 43, 44, 45, 46, 47, 48, 50, 54], "int": [21, 22, 23, 25, 27, 28, 29, 32, 33, 34, 38, 39, 40, 41, 43, 44, 46, 48, 49, 50, 54, 58], "global": [21, 51], "n_cell": [21, 23, 54], "cannot": [21, 52, 58], "tree": [21, 54, 56], "root": 21, "node": 21, "sec_nam": 21, "node_po": 21, "adjac": 21, "parent": 21, "children": 21, "section_soma": 21, "diam": [21, 54], "cm": [21, 27, 54], "end_pt": [21, 54], "nest": 21, "parametr": 21, "morphologi": [21, 39, 41, 58], "insert": [21, 54], "dipole_pp": [21, 54], "record_vsoma": [21, 54], "isec": [21, 22, 54, 58], "soma_gabaa": [21, 54], "soma_gabab": [21, 54], "etc": [21, 22, 23, 27, 37, 38, 40, 52, 54, 55, 56], "record_isec": [21, 38, 54, 58], "record_isoma": [21, 54], "speicifc": 21, "concentr": [21, 22, 38], "record_ca": [21, 38, 58], "tonic_bias": [21, 54], "iclamp": [21, 54], "clamp": [21, 23, 54], "bias": [21, 23, 54, 58], "assign": [21, 23, 51, 54, 58], "__repr__": [21, 22, 23, 27, 31], "repr": [21, 22, 23, 27, 31], "self": [21, 22, 23, 27, 31], "sec_name_ap": 21, "applic": [21, 56], "belong": [21, 58], "create_tonic_bia": [21, 58], "t0": [21, 23, 54], "float": [21, 22, 23, 25, 27, 31, 32, 33, 38, 39, 41, 44, 45, 46, 47, 50, 54, 58], "define_shap": 21, "redefin": 21, "accord": [21, 22, 23, 49, 54, 58], "subtre": 21, "distance_sect": 21, "target_sec_nam": 21, "curr_nod": 21, "find": 21, "string": [21, 22, 27, 36, 46, 48, 55, 58], "mid": 21, "modify_sect": [21, 58], "micron": [21, 54], "diamet": [21, 23, 27, 54], "capacit": [21, 54], "farad": [21, 54], "axial": [21, 54], "resist": [21, 54], "ohm": [21, 54], "leav": 21, "parconnect_from_src": 21, "gid_presyn": 21, "nc_dict": [21, 54], "postsyn": 21, "centric": 21, "presyn": 21, "TO": 21, "presynapt": 21, "pos_src": 21, "a_weight": 21, "a_delai": 21, "exp2syn": 21, "postsynapt": 21, "nc": 21, "netcon": 21, "1200": [21, 41], "ex": [21, 22, 40, 41, 48], "apical_trunk": [21, 41], "bool": [21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54], "handl": [21, 22, 23, 25, 27, 31, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50], "setup_source_netcon": 21, "_pc": 21, "syn_creat": 21, "secloc": 21, "nrn": 21, "revers": [21, 23], "syn": [21, 54], "kinet": 21, "scheme": 21, "to_dict": [21, 22, 23, 27], "spike_tim": 22, "spike_gid": 22, "cell_type_nam": 22, "n_spike": 22, "shape": [22, 23, 25, 27, 29, 45, 46, 58], "outer": 22, "inner": 22, "stamp": 22, "vsoma": 22, "isoma": 22, "n_time": [22, 25, 27, 45, 46], "reset": [22, 58], "empti": [22, 58], "update_typ": 22, "updat": [3, 22, 25, 52, 56, 58], "fname": [22, 23, 25, 35, 37, 39], "__getitem__": 22, "gid_item": 22, "slice": [22, 27], "stop": [22, 28, 32, 33, 38, 54, 58], "spike_r": 22, "kwargs_hist": [22, 48], "valid": [22, 23, 33, 34, 40, 48, 58], "group": [22, 23, 48, 58], "otherwis": [22, 23, 48], "charact": [22, 48], "ev": [22, 48], "equival": [22, 23, 34, 48], "cycl": [22, 23, 25, 48, 50, 58], "keyword": [22, 23, 48], "hist": [22, 48], "legacy_mod": [23, 24, 29, 30, 58], "construct": [23, 28, 29, 56, 58], "mainli": [23, 29], "backward": [23, 29], "compat": [23, 29, 56], "suitabl": [23, 29], "Will": [23, 27, 28, 29, 33, 45], "n_x": [23, 29], "n_y": [23, 29], "ignor": 23, "real": [23, 58], "templat": [23, 58], "artifici": [23, 51, 54, 58], "categori": 23, "272": 23, "542": 23, "pos_dict": [23, 42, 54], "external_bias": [23, 54], "somata": 23, "space_const": [23, 54], "apical_tuft": 23, "cyclic": 23, "doublet": 23, "isi": 23, "independ": [23, 54, 58], "denot": 23, "dispers": [23, 54], "map": [23, 58], "physic": [23, 52], "xy": 23, "randomli": 23, "allow_autaps": [23, 54], "itself": [23, 54], "gid_pair": [23, 40, 54], "min_dist": [23, 27], "infinit": [23, 27], "homogen": [23, 27], "conductor": [23, 27], "treat": [23, 27], "junction": [23, 27], "lsa": [23, 27], "flank": [23, 27], "numer": [23, 27], "error": [23, 27, 53, 55, 58], "minimum": [23, 25, 27, 47, 58], "contact": [23, 27, 45, 46], "act": [23, 27], "behavior": 23, "increment": [23, 55], "exact": [23, 25], "lambda": 23, "renew": 23, "suppli": 23, "intrins": 23, "iter": [23, 58], "net_copi": 23, "lookup": 23, "layer_separ": 23, "impli": 23, "affect": [23, 38], "write_configur": 23, "overwrit": [23, 25], "hierarch": 23, "hdf5": [23, 25, 35, 54, 58], "boolean": 23, "throw": [23, 53], "alreadi": [23, 53, 58], "yield": 23, "improv": [24, 56, 58], "kohl": [24, 58], "topragr": 24, "2022": [24, 30], "biolog": [24, 52], "introduc": [24, 58], "maximum": [24, 25, 47], "gbar": 24, "linearli": 24, "refer": [24, 25, 29, 30, 51, 53, 58], "carmen": [24, 58], "underli": [24, 53, 56], "auditori": 24, "reveal": 24, "topographi": 24, "timecours": 25, "1e": 25, "amper": [25, 53, 56], "meter": [25, 53, 56], "n_layer": 25, "dipl": 25, "sfreq": [25, 27], "scale_appli": 25, "dpl_copi": 25, "rgba": [25, 27, 44, 46], "black": [25, 39, 40, 44], "periodogram": [25, 47], "scipi": [25, 27, 44, 46, 47, 50, 53], "welch": [25, 47], "nyquist": [25, 47], "pad": [25, 50], "colormap": [25, 39, 40, 43, 46, 50, 58], "inferno": [25, 50], "colorbar": [25, 27, 39, 40, 43, 45, 50], "colorbar_insid": [25, 50], "morlet": [25, 50, 58], "tfr_array_morlet": 25, "interest": [25, 50, 52], "millisecond": [25, 50], "higher": [25, 27, 31, 44, 46, 50], "success": [25, 27, 44, 46, 50], "beyond": [25, 50], "mirror": [25, 50], "viridi": [25, 39, 40, 50], "put": [25, 28, 50], "heatmap": [25, 50], "savgol_filt": [25, 58], "savitzki": [25, 58], "golai": [25, 58], "prefer": [25, 27, 38], "high": [25, 56], "polynomi": 25, "iir": 25, "determin": [25, 40, 52], "5th": 25, "multipli": 25, "convolut": [25, 27], "member": [26, 52], "precomput": 27, "n_electrod": 27, "tabl": [27, 52], "00122": 27, "2010": 27, "rat": 27, "array_copi": 27, "vmin": [27, 39, 45], "vmax": [27, 39, 45], "interpol": [27, 45, 58], "spline": [27, 45], "sink": [27, 45, 58], "red": [27, 40, 45], "smoothen": [27, 45, 58], "trial_no": 27, "contact_no": 27, "cividi": [27, 46], "voltage_offset": [27, 46], "voltage_scalebar": [27, 46], "overlaid": 27, "offset": [27, 46, 58], "listedcolormap": [27, 46], "quadruplet": [27, 46], "height": [27, 28, 46], "uv": [27, 46], "bar": [27, 28, 43, 46], "left": [27, 28, 40, 46], "extracellular_copi": 27, "theme_color": 28, "8a2be2": 28, "total_height": 28, "800": 28, "total_width": 28, "header_height": 28, "button_height": 28, "operation_box_height": 28, "drive_widget_width": 28, "left_sidebar_width": 28, "576": 28, "log_window_height": 28, "status_height": 28, "theme": 28, "whole": [28, 55], "dashboard": 28, "pixel": 28, "width": 28, "header": 28, "box": 28, "sidebad": 28, "screen": 28, "style": 28, "simulation_data": 28, "widget_tstop": 28, "widget": [28, 58], "widget_dt": 28, "widget_ntri": 28, "control": [28, 58], "widget_backend_select": 28, "widget_viz_layout_select": 28, "widget_mpi_cmd": 28, "widget_n_job": 28, "multi": [28, 56], "widget_drive_type_select": 28, "widget_location_select": 28, "add_drive_button": 28, "clickabl": 28, "run_button": 28, "trigger": 28, "load_button": 28, "receiv": [28, 33, 55], "upload": [28, 58], "delete_drive_button": 28, "plot_outputs_dict": 28, "panel": 28, "plot_dropdown_types_dict": 28, "dropdown": 28, "menu": 28, "drive_widget": 28, "drive_box": 28, "connectivity_textfield": 28, "add_logging_window_logg": 28, "analysis_config": 28, "everyth": [28, 53], "except": 28, "captur": 28, "extra_margin": 28, "screenshot": 28, "ifram": 28, "snapshot": 28, "margin": 28, "compos": [28, 29, 52], "return_layout": 28, "ipython": [28, 53], "easi": [28, 53, 58], "get_cell_parameters_dict": 28, "cell_parameters_dict": 28, "purpos": [28, 52], "static": 28, "load_paramet": 28, "run_notebook_cel": 28, "penultim": 28, "init": 28, "hit": 28, "twice": 28, "neurophi": 29, "1307": 29, "ratio": [3, 29], "expans": 30, "cereb": 30, "robert": 30, "cerebr": 30, "668": 30, "688": 30, "initial_net": 31, "solver": [31, 58], "cobyla": [], "obj_fun": [3, 31], "dipole_rms": 31, "dt": [32, 33, 38, 58], "postproc": [32, 33, 38, 58], "integr": [32, 33, 38, 56, 58], "cvode": [32, 33, 38], "postprocess": [32, 33, 58], "hyperthread": 33, "actual": [33, 58], "proc": [33, 55], "popen": [33, 55], "expected_data_length": 33, "sent": [33, 55], "proc_queu": 33, "thread": 33, "queue": [33, 55], "hold": 33, "safe": 33, "wai": [33, 38, 52, 53, 55], "\u00e5simul": 33, "logic": [34, 58], "OR": 34, "AND": 34, "file_cont": 36, "pars": 36, "pathnam": 37, "3rd": 37, "dipole_smooth_win": 38, "dipole_scalefctr": 38, "bg_color": 39, "voltage_colormap": 39, "3100": 39, "2200": 39, "time_idx": 39, "helper": 39, "viewpoint": [39, 52], "frame_start": 39, "frame_stop": 39, "writer": 39, "pillow": 39, "export": [39, 55], "movi": 39, "dot": 39, "inch": 39, "altern": [39, 55, 56], "stabl": [39, 56], "animation_api": 39, "cross": 40, "show_weight": 43, "grei": 43, "gradient": 43, "contact_label": [45, 46], "n_channel": 45, "set_yticklabel": [45, 46], "dimension": [46, 56], "n_contact": 46, "jetblu": 46, "definit": 51, "vocabulari": 51, "concept": 51, "think": 51, "term": 51, "issu": [51, 52, 53, 58], "pull": [51, 52], "anatom": [51, 53], "awai": 51, "extrins": 51, "often": 51, "excitatori": 51, "perturb": 51, "split": [51, 55], "closer": 51, "formal": [52, 53], "clarifi": 52, "variou": [52, 54], "commun": [52, 55, 56], "goal": 52, "hypothesi": 52, "research": [52, 53], "upon": 52, "principl": 52, "circuit": [52, 53, 56], "bridg": 52, "macroscal": [52, 56], "magneto": 52, "electro": 52, "encephalographi": 52, "foundat": [52, 56], "transpar": 52, "institut": 52, "neutral": 52, "aim": 52, "support": [52, 58], "collabor": 52, "acknowledg": 52, "divers": 52, "skill": 52, "scientif": [52, 53], "neuro": 52, "mind": 52, "advanc": [52, 56], "invit": 52, "anyon": 52, "particip": [52, 56], "philosophi": [52, 56], "pathwai": 52, "becom": 52, "deeper": 52, "engag": [52, 56], "talent": 52, "team": [52, 56], "toward": 52, "involv": [52, 58], "propos": 52, "onlin": 52, "discuss": [52, 53, 56], "among": [52, 56], "steer": 52, "outlin": [52, 55, 56], "concret": 52, "mani": 52, "submit": 52, "weekli": 52, "meet": 52, "email": 52, "hackathon": 52, "behalf": 52, "strive": 52, "barrier": 52, "dedic": [52, 58], "ongo": 52, "Being": 52, "easili": 52, "expect": [52, 55], "approv": 52, "host": 52, "qualiti": 52, "quantiti": 52, "elig": 52, "elect": 52, "consensu": 52, "extenu": 52, "circumst": 52, "revok": 52, "inact": 52, "year": 52, "reinstat": 52, "resum": 52, "membership": 52, "nomin": 52, "least": 52, "vote": 52, "third": 52, "strateg": 52, "plan": 52, "overal": 52, "basi": 52, "aspect": 52, "expertis": [52, 53], "effort": [52, 56], "attend": 52, "deem": 52, "scope": [52, 56], "vision": 52, "organ": [52, 56], "technic": 52, "servic": 52, "manag": [52, 58], "benefit": 52, "polici": 52, "inquir": 52, "grant": 52, "grace": 52, "former": 52, "retir": 52, "li": 52, "sole": 52, "seek": 52, "purview": 52, "minor": 52, "typo": 52, "sentenc": 52, "confid": 52, "agre": 52, "resolut": 52, "amongst": 52, "held": 52, "facilit": [52, 56], "guidanc": 52, "rais": 52, "taken": 52, "opportun": 52, "address": [52, 58], "logist": 52, "matter": 52, "yearli": 52, "revisit": 52, "draft": 52, "suggest": 52, "leaner": 53, "cleaner": 53, "clinician": 53, "conveni": 53, "modular": 53, "evalu": 53, "hypothes": [53, 56], "electroencephalographi": 53, "intracrani": 53, "electrocorticographi": 53, "ecog": 53, "electr": 53, "nano": 53, "precis": 53, "characterist": 53, "multimod": 53, "flexibl": [53, 56], "serv": 53, "visit": 53, "veri": 53, "ipywidget": [53, 56, 58], "voila": 53, "ipympl": 53, "ipykernel": 53, "scikit": 53, "learn": [53, 56], "platform": [53, 56], "psutil": [53, 55], "anaconda": 53, "tradit": 53, "unset": [53, 55], "pythonpath": 53, "pythonhom": 53, "becaus": 53, "environ": [53, 55], "ones": 53, "conda": [53, 55], "track": 53, "latest": 53, "develop": 53, "nightli": 53, "upgrad": 53, "repo": 53, "zipbal": 53, "fine": 53, "bayesian": [31, 53], "opt": 53, "tweak": 53, "zsh": 53, "maco": [53, 55], "usag": [53, 55], "cpu": [53, 55], "precompil": 53, "sure": 53, "encount": 53, "forum": 53, "block": [53, 55], "magic": 53, "manner": 53, "spyder": 53, "tracker": 53, "question": 53, "joss": 53, "2023": 53, "5848": 53, "21105": 53, "05848": 53, "broken": 54, "object_typ": 54, "n_pyr_x": 54, "nr": 54, "n_pyr_i": 54, "celsiu": 54, "temperatur": 54, "degre": 54, "co": 54, "ordint": 54, "cell_nam": 54, "tempor": 54, "whose": [3, 54], "target_typ": 54, "num_target": 54, "src_type": 54, "num_src": 54, "runtim": [55, 58], "embarrassingli": 55, "interfac": [55, 56, 58], "linux": 55, "sudo": 55, "apt": 55, "libopenmpi": 55, "bin": 55, "dyld_fallback_library_path": 55, "conda_prefix": 55, "shell": 55, "mkdir": 55, "p": 55, "deactiv": 55, "echo": 55, "old_dyld_fallback_library_path": 55, "env_var": 55, "sh": 55, "nrniv": 55, "hello": 55, "comm_world": 55, "get_rank": 55, "quit": 55, "2b7985ba": 55, "2019": 55, "duke": 55, "yale": 55, "bluebrain": 55, "copyright": 55, "1984": 55, "2018": 55, "launch": 55, "binari": 55, "subprocess": 55, "child": 55, "mpisimul": 55, "carri": 55, "stdin": 55, "base64": 55, "encod": 55, "pickl": 55, "mark": 55, "unpickl": 55, "stdout": 55, "stderr": 55, "consol": 55, "progress": 55, "warn": [55, 58], "send": 55, "byte": 55, "know": 55, "doesn": 55, "proccess": 55, "wait": 55, "exit": 55, "successfulli": 55, "decod": 55, "caller": 55, "flush": 55, "whenev": 55, "immedi": 55, "side": 55, "util": 55, "special": 55, "decor": 55, "conftest": 55, "failur": 55, "subsequ": 55, "fail": [55, 58], "generaliz": 56, "circuitri": 56, "am": 56, "friendli": 56, "teach": 56, "graphic": 56, "essenti": 56, "intuit": 56, "gain": 56, "chose": 56, "dive": 56, "utili": 56, "priorit": 56, "practic": 56, "interoper": 56, "netpyn": 56, "entail": 56, "reorgan": 56, "creation": [56, 58], "march": 56, "adopt": 56, "abil": [56, 58], "web": 56, "cli": 56, "extens": 56, "clean": 56, "minim": 56, "pertain": 56, "spectra": 56, "lanalysi": 56, "feb": 56, "sep": 56, "gh": [56, 58], "expand": 56, "renam": 56, "predict": 56, "invas": 56, "fundament": 56, "profil": 56, "inher": 56, "difficulti": 56, "focuss": 56, "snpe": 56, "gon\u00e7alv": 56, "56261": 56, "adapt": 56, "sweep": 56, "architectur": 56, "hhn": 56, "amng": 56, "challeng": 56, "development": 56, "begun": 56, "bed": 56, "hnn2": 56, "multicompart": 56, "seamlessli": 56, "beamform": 56, "dual": 56, "metacel": 56, "ui": 56, "convers": [56, 58], "elimin": 56, "enhanc": 56, "advantag": 56, "meaning": 56, "rigor": 56, "quickli": 56, "motor": 56, "stimul": 56, "footnot": 56, "claim": 56, "understood": 56, "knowledg": 56, "591": [], "thrown": 58, "dylan": 58, "818": 58, "646": 58, "manual": 58, "640": 58, "678": 58, "v8": 58, "georg": 58, "dang": 58, "696": 58, "703": 58, "705": 58, "overlap": 58, "camilo": 58, "diaz": 58, "741": 58, "739": 58, "invalid": 58, "744": 58, "kwarg": 58, "732": 58, "pre": 58, "disabl": 58, "750": 58, "csv": 58, "753": 58, "rajat": 58, "partani": 58, "757": 58, "649": 58, "773": 58, "katharina": 58, "duecker": 58, "769": 58, "convert_to_json": 58, "legaci": 58, "772": 58, "capabl": 58, "782": 58, "754": 58, "806": 58, "815": 58, "inconsist": 58, "642": 58, "scalar": 58, "670": 58, "695": 58, "overwritten": 58, "795": 58, "isin": 58, "in1d": 58, "799": 58, "810": 58, "812": 58, "644": 58, "648": 58, "constrain": 58, "pujol": 58, "_": 58, "652": 58, "766": 58, "which_driv": 58, "moham": 58, "sherif": 58, "478": 58, "mattan": 58, "pelah": 58, "492": 58, "481": 58, "419": 58, "checkpoint": 58, "too": 58, "546": 58, "orsolya": 58, "beatrix": 58, "kolozsvari": 58, "516": 58, "502": 58, "unweight": 58, "kaisu": 58, "lankinen": 58, "610": 58, "458": 58, "456": 58, "462": 58, "longer": 58, "446": 58, "472": 58, "huzi": 58, "cheng": 58, "475": 58, "did": 58, "515": 58, "runtimeerror": 58, "oversubscrib": 58, "session": 58, "545": 58, "559": 58, "611": 58, "614": 58, "606": 58, "479": 58, "calculate_csd2d": 58, "steven": 58, "brandt": 58, "517": 58, "619": 58, "conncetr": 58, "804": 58, "mostafa": 58, "khalil": 58, "publish": 58, "plot_cell_morphologi": 58, "319": 58, "hard": 58, "327": 58, "321": 58, "318": 58, "339": 58, "329": 58, "348": 58, "376": 58, "calcium_model": 58, "sarah": 58, "383": 58, "queri": 58, "367": 58, "conn": 58, "369": 58, "accept": 58, "416": 58, "round": 58, "reposit": 58, "314": 58, "common": 58, "swap": 58, "352": 58, "kenneth": 58, "loi": 58, "368": 58, "wasn": 58, "382": 58, "intend": 58, "397": 58, "421": 58, "l2pyr": 58, "l5pyr": 58, "l2basket": 58, "l5basket": 58, "favor": 58, "322": 58, "readabl": 58, "354": 58, "wherebi": 58, "372": 58, "add_xxx_driv": 58, "sync_within_tri": 58, "436": 58, "alex": 58, "rockhil": 58, "reader": 58, "plot_hist_input": 58, "feed": 58, "visualis": 58, "autaps": 58, "incorrectli": 58, "ident": 58, "samika": 58, "kanekar": 58, "context": 58, "behaviour": 58, "forc": 58, "fam": 58, "regardless": 58, "alpha_prox_weight": 3, "alpha_prox_tstart": 3, "alpha_prox_burst_r": 3, "alpha_prox_burst_std": 3, "alpha_dist_weight": 3, "alpha_dist_tstart": 3, "alpha_dist_burst_r": 3, "alpha_dist_burst_std": 3, "maximize_psd": [3, 31], "maxim": 3, "f_band": [3, 31], "relative_bandpow": [3, 31], "optimize_rhythm": [3, 57], "obj_fun_kwarg": 31, "673": 58}, "objects": {"hnn_core": [[21, 0, 1, "", "Cell"], [22, 0, 1, "", "CellResponse"], [23, 0, 1, "", "Network"], [24, 2, 1, "", "calcium_model"], [29, 2, 1, "", "jones_2009_model"], [30, 2, 1, "", "law_2021_model"], [34, 2, 1, "", "pick_connection"], [35, 2, 1, "", "read_dipole"], [36, 2, 1, "", "read_params"], [37, 2, 1, "", "read_spikes"], [38, 2, 1, "", "simulate_dipole"]], "hnn_core.Cell": [[21, 1, 1, "", "__repr__"], [21, 1, 1, "", "build"], [21, 1, 1, "", "copy"], [21, 1, 1, "", "create_tonic_bias"], [21, 1, 1, "", "define_shape"], [21, 1, 1, "", "distance_section"], [21, 1, 1, "", "modify_section"], [21, 1, 1, "", "parconnect_from_src"], [21, 1, 1, "", "plot_morphology"], [21, 1, 1, "", "record"], [21, 1, 1, "", "setup_source_netcon"], [21, 1, 1, "", "syn_create"], [21, 1, 1, "", "to_dict"]], "hnn_core.CellResponse": [[22, 1, 1, "", "__getitem__"], [22, 1, 1, "", "__repr__"], [22, 1, 1, "", "mean_rates"], [22, 1, 1, "", "plot_spikes_hist"], [22, 1, 1, "", "plot_spikes_raster"], [22, 1, 1, "", "to_dict"], [22, 1, 1, "", "update_types"], [22, 1, 1, "", "write"]], "hnn_core.Network": [[23, 1, 1, "", "__repr__"], [23, 1, 1, "", "add_bursty_drive"], [23, 1, 1, "", "add_connection"], [23, 1, 1, "", "add_electrode_array"], [23, 1, 1, "", "add_evoked_drive"], [23, 1, 1, "", "add_poisson_drive"], [23, 1, 1, "", "add_tonic_bias"], [23, 1, 1, "", "clear_connectivity"], [23, 1, 1, "", "clear_drives"], [23, 1, 1, "", "copy"], [23, 1, 1, "", "gid_to_type"], [23, 1, 1, "", "plot_cells"], [23, 1, 1, "", "set_cell_positions"], [23, 1, 1, "", "write_configuration"]], "hnn_core.dipole": [[25, 0, 1, "", "Dipole"], [26, 2, 1, "", "average_dipoles"]], "hnn_core.dipole.Dipole": [[25, 1, 1, "", "copy"], [25, 1, 1, "", "plot"], [25, 1, 1, "", "plot_psd"], [25, 1, 1, "", "plot_tfr_morlet"], [25, 1, 1, "", "savgol_filter"], [25, 1, 1, "", "scale"], [25, 1, 1, "", "smooth"], [25, 1, 1, "", "write"]], "hnn_core.extracellular": [[27, 0, 1, "", "ExtracellularArray"]], "hnn_core.extracellular.ExtracellularArray": [[27, 1, 1, "", "__repr__"], [27, 1, 1, "", "copy"], [27, 1, 1, "", "plot_csd"], [27, 1, 1, "", "plot_lfp"], [27, 3, 1, "", "sfreq"], [27, 1, 1, "", "smooth"], [27, 1, 1, "", "to_dict"]], "hnn_core.gui": [[28, 0, 1, "", "HNNGUI"]], "hnn_core.gui.HNNGUI": [[28, 3, 1, "", "analysis_config"], [28, 1, 1, "", "capture"], [28, 1, 1, "", "compose"], [28, 3, 1, "", "data"], [28, 1, 1, "", "get_cell_parameters_dict"], [28, 1, 1, "", "load_parameters"], [28, 1, 1, "", "run_notebook_cells"]], "hnn_core.optimization": [[31, 0, 1, "", "Optimizer"]], "hnn_core.optimization.Optimizer": [[31, 1, 1, "", "__repr__"], [31, 1, 1, "", "fit"], [31, 1, 1, "", "plot_convergence"]], "hnn_core.parallel_backends": [[32, 0, 1, "", "JoblibBackend"], [33, 0, 1, "", "MPIBackend"]], "hnn_core.parallel_backends.JoblibBackend": [[32, 1, 1, "", "simulate"]], "hnn_core.parallel_backends.MPIBackend": [[33, 1, 1, "", "simulate"], [33, 1, 1, "", "terminate"]], "hnn_core.viz": [[39, 0, 1, "", "NetworkPlotter"], [40, 2, 1, "", "plot_cell_connectivity"], [41, 2, 1, "", "plot_cell_morphology"], [42, 2, 1, "", "plot_cells"], [43, 2, 1, "", "plot_connectivity_matrix"], [44, 2, 1, "", "plot_dipole"], [45, 2, 1, "", "plot_laminar_csd"], [46, 2, 1, "", "plot_laminar_lfp"], [47, 2, 1, "", "plot_psd"], [48, 2, 1, "", "plot_spikes_hist"], [49, 2, 1, "", "plot_spikes_raster"], [50, 2, 1, "", "plot_tfr_morlet"]], "hnn_core.viz.NetworkPlotter": [[39, 1, 1, "", "export_movie"]]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:function", "3": "py:property"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "function", "Python function"], "3": ["py", "property", "Python property"]}, "titleterms": {"api": [0, 56, 58], "document": [0, 20, 53], "simul": [0, 2, 3, 4, 7, 14, 15, 16, 17, 18, 56], "hnn_core": [0, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "network": [0, 23, 54], "model": [0, 52, 56], "optim": [0, 2, 3, 31, 53], "dipol": [0, 25, 26], "extracellulararrai": [0, 27], "extracellular": [0, 8, 27, 54], "visual": [0, 56], "viz": [0, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "parallel": [0, 9, 53, 55], "backend": [0, 9, 55], "parallel_backend": [0, 32, 33], "input": 0, "output": 0, "gui": [0, 28, 53, 56], "how": [1, 11, 20], "05": [2, 15], "evok": 2, "respons": [2, 3, 52], "paramet": [2, 56], "07": 4, "batch": 4, "extract": 4, "plot": [4, 6], "result": 4, "03": [5, 17], "modifi": 5, "local": [5, 20], "connect": [5, 54], "01": [6, 16], "fire": 6, "pattern": 6, "06": 7, "anim": 7, "hnn": [7, 18, 20, 53, 56], "02": [8, 14], "record": 8, "potenti": [8, 16], "refer": [8, 14, 15, 16, 17, 18], "04": [9, 18], "us": [9, 29, 31, 35, 38, 47], "mpi": [9, 55], "comput": [10, 12, 19, 57], "time": [10, 12, 19, 57], "tutori": [11, 13, 56], "alpha": 14, "beta": [14, 15], "rhythm": [14, 17], "modul": 15, "erp": [15, 16], "event": 16, "relat": 16, "gamma": 17, "from": 18, "meg": 18, "sensor": 18, "space": 18, "data": [18, 56], "contribut": [20, 53, 58], "set": 20, "up": 20, "your": 20, "develop": [20, 52, 56], "environ": 20, "configur": 20, "git": 20, "make": [20, 52], "first": 20, "pull": 20, "request": 20, "instal": [20, 53, 56], "edit": 20, "core": [20, 53], "run": 20, "test": 20, "updat": 20, "build": 20, "rebas": 20, "continu": 20, "integr": 20, "cell": [21, 54], "cellrespons": 22, "exampl": [29, 31, 35, 38, 47, 53], "calcium_model": 24, "average_dipol": 26, "hnngui": 28, "jones_2009_model": 29, "law_2021_model": 30, "joblibbackend": 32, "mpibackend": 33, "pick_connect": 34, "read_dipol": 35, "read_param": 36, "read_spik": 37, "simulate_dipol": 38, "networkplott": 39, "plot_cell_connect": 40, "plot_cell_morphologi": 41, "plot_cel": 42, "plot_connectivity_matrix": 43, "plot_dipol": 44, "plot_laminar_csd": 45, "plot_laminar_lfp": 46, "plot_psd": 47, "plot_spikes_hist": 48, "plot_spikes_rast": 49, "plot_tfr_morlet": 50, "glossari": 51, "project": [52, 56], "govern": [52, 53], "mission": 52, "role": 52, "contributor": 52, "maintain": 52, "council": 52, "decis": 52, "process": [52, 53], "chang": [52, 58], "about": 53, "depend": 53, "option": 53, "bug": [53, 58], "report": 53, "interest": 53, "structur": 53, "cite": 53, "file": 54, "content": 54, "descript": 54, "type": 54, "section": 54, "gid": 54, "rang": 54, "extern": 54, "drive": 54, "bia": 54, "arrai": 54, "joblib": 55, "The": 56, "roadmap": 56, "vision": 56, "timelin": 56, "overview": 56, "short": 56, "term": 56, "goal": 56, "modular": 56, "code": 56, "simplifi": 56, "mainten": 56, "new": [56, 58], "lfp": 56, "csd": 56, "comparison": 56, "estim": 56, "expans": 56, "differ": 56, "cortic": 56, "templat": 56, "choic": 56, "longer": 56, "what": 58, "": 58, "current": 58, "changelog": 58, "0": 58, "3": 58, "peopl": 58, "who": 58, "thi": 58, "releas": 58, "alphabet": 58, "order": 58, "2": 58, "notabl": 58, "1": 58, "08": 3, "rhythmic": 3}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.intersphinx": 1, "sphinx": 58}, "alltitles": {"07. Batch Simulation": [[4, "batch-simulation"]], "Extract and Plot Results": [[4, "extract-and-plot-results"]], "03. Modifying local connectivity": [[5, "modifying-local-connectivity"]], "01. Plot firing pattern": [[6, "plot-firing-pattern"]], "06. Animating HNN simulations": [[7, "animating-hnn-simulations"]], "02. Record extracellular potentials": [[8, "record-extracellular-potentials"]], "References": [[8, "references"], [14, "references"], [15, "references"], [16, "references"], [17, "references"], [18, "references"]], "04. Use MPI backend for parallelization": [[9, "use-mpi-backend-for-parallelization"]], "Computation times": [[10, "computation-times"], [12, "computation-times"], [19, "computation-times"], [57, "computation-times"]], "Tutorials": [[13, "tutorials"], [11, "tutorials"]], "02. Simulate Alpha and Beta Rhythms": [[14, "simulate-alpha-and-beta-rhythms"]], "05. Simulate beta modulated ERP": [[15, "simulate-beta-modulated-erp"]], "01. Simulate Event Related Potentials (ERPs)": [[16, "simulate-event-related-potentials-erps"]], "03. Simulate Gamma Rhythms": [[17, "simulate-gamma-rhythms"]], "04. From MEG sensor-space data to HNN simulation": [[18, "from-meg-sensor-space-data-to-hnn-simulation"]], "API Documentation": [[0, "api-documentation"]], "Simulation (hnn_core):": [[0, "simulation-hnn-core"]], "Network Models (hnn_core):": [[0, "network-models-hnn-core"]], "Optimization (hnn_core.optimization):": [[0, "optimization-hnn-core-optimization"]], "Dipole (hnn_core.dipole):": [[0, "dipole-hnn-core-dipole"]], "ExtracellularArray (hnn_core.extracellular):": [[0, "extracellulararray-hnn-core-extracellular"]], "Visualization (hnn_core.viz):": [[0, "visualization-hnn-core-viz"]], "Parallel backends (hnn_core.parallel_backends):": [[0, "parallel-backends-hnn-core-parallel-backends"]], "Input and Output:": [[0, "input-and-output"]], "GUI (hnn_core.gui):": [[0, "gui-hnn-core-gui"]], "How to": [[1, "how-to"], [11, "how-to"]], "05. Optimize simulated evoked response parameters": [[2, "optimize-simulated-evoked-response-parameters"]], "08. Optimize simulated rhythmic responses": [[3, "optimize-simulated-rhythmic-responses"]], "Contributions": [[20, "contributions"]], "Setting up your local development environment": [[20, "setting-up-your-local-development-environment"]], "Configuring git": [[20, "configuring-git"]], "Making your first pull request": [[20, "making-your-first-pull-request"]], "Installing editable hnn-core": [[20, "installing-editable-hnn-core"]], "Running tests": [[20, "running-tests"]], "Updating documentation": [[20, "updating-documentation"]], "Building the documentation": [[20, "building-the-documentation"]], "How to rebase": [[20, "how-to-rebase"]], "Continuous Integration": [[20, "continuous-integration"]], "hnn_core.Cell": [[21, "hnn-core-cell"]], "hnn_core.CellResponse": [[22, "hnn-core-cellresponse"]], "hnn_core.Network": [[23, "hnn-core-network"]], "hnn_core.calcium_model": [[24, "hnn-core-calcium-model"]], "hnn_core.dipole.Dipole": [[25, "hnn-core-dipole-dipole"]], "hnn_core.dipole.average_dipoles": [[26, "hnn-core-dipole-average-dipoles"]], "hnn_core.extracellular.ExtracellularArray": [[27, "hnn-core-extracellular-extracellulararray"]], "hnn_core.gui.HNNGUI": [[28, "hnn-core-gui-hnngui"]], "hnn_core.jones_2009_model": [[29, "hnn-core-jones-2009-model"]], "Examples using hnn_core.jones_2009_model": [[29, "examples-using-hnn-core-jones-2009-model"]], "hnn_core.law_2021_model": [[30, "hnn-core-law-2021-model"]], "hnn_core.optimization.Optimizer": [[31, "hnn-core-optimization-optimizer"]], "Examples using hnn_core.optimization.Optimizer": [[31, "examples-using-hnn-core-optimization-optimizer"]], "hnn_core.parallel_backends.JoblibBackend": [[32, "hnn-core-parallel-backends-joblibbackend"]], "hnn_core.parallel_backends.MPIBackend": [[33, "hnn-core-parallel-backends-mpibackend"]], "hnn_core.pick_connection": [[34, "hnn-core-pick-connection"]], "hnn_core.read_dipole": [[35, "hnn-core-read-dipole"]], "Examples using hnn_core.read_dipole": [[35, "examples-using-hnn-core-read-dipole"]], "hnn_core.read_params": [[36, "hnn-core-read-params"]], "hnn_core.read_spikes": [[37, "hnn-core-read-spikes"]], "hnn_core.simulate_dipole": [[38, "hnn-core-simulate-dipole"]], "Examples using hnn_core.simulate_dipole": [[38, "examples-using-hnn-core-simulate-dipole"]], "hnn_core.viz.NetworkPlotter": [[39, "hnn-core-viz-networkplotter"]], "hnn_core.viz.plot_cell_connectivity": [[40, "hnn-core-viz-plot-cell-connectivity"]], "hnn_core.viz.plot_cell_morphology": [[41, "hnn-core-viz-plot-cell-morphology"]], "hnn_core.viz.plot_cells": [[42, "hnn-core-viz-plot-cells"]], "hnn_core.viz.plot_connectivity_matrix": [[43, "hnn-core-viz-plot-connectivity-matrix"]], "hnn_core.viz.plot_dipole": [[44, "hnn-core-viz-plot-dipole"]], "hnn_core.viz.plot_laminar_csd": [[45, "hnn-core-viz-plot-laminar-csd"]], "hnn_core.viz.plot_laminar_lfp": [[46, "hnn-core-viz-plot-laminar-lfp"]], "hnn_core.viz.plot_psd": [[47, "hnn-core-viz-plot-psd"]], "Examples using hnn_core.viz.plot_psd": [[47, "examples-using-hnn-core-viz-plot-psd"]], "hnn_core.viz.plot_spikes_hist": [[48, "hnn-core-viz-plot-spikes-hist"]], "hnn_core.viz.plot_spikes_raster": [[49, "hnn-core-viz-plot-spikes-raster"]], "hnn_core.viz.plot_tfr_morlet": [[50, "hnn-core-viz-plot-tfr-morlet"]], "Glossary": [[51, "glossary"]], "Project Governance": [[52, "project-governance"]], "Mission": [[52, "mission"]], "Roles and Responsibilities": [[52, "roles-and-responsibilities"]], "Contributors*": [[52, "contributors"]], "Maintainers**": [[52, "maintainers"]], "Developer Council": [[52, "developer-council"]], "Decision-Making Process": [[52, "decision-making-process"]], "Governance Model Changes": [[52, "governance-model-changes"]], "hnn-core": [[53, "hnn-core"]], "About": [[53, "about"]], "Dependencies": [[53, "dependencies"]], "Optional dependencies": [[53, "optional-dependencies"]], "GUI": [[53, "gui"]], "Optimization": [[53, "optimization"]], "Parallel processing": [[53, "parallel-processing"]], "Installation": [[53, "installation"]], "Documentation and examples": [[53, "documentation-and-examples"]], "Bug reports": [[53, "bug-reports"]], "Interested in Contributing?": [[53, "interested-in-contributing"]], "Governance Structure": [[53, "governance-structure"]], "Citing": [[53, "citing"]], "Network File Content": [[54, "network-file-content"]], "File Content Description": [[54, "file-content-description"]], "Cell Type Description": [[54, "cell-type-description"]], "Section Description": [[54, "section-description"]], "Gid Range Description": [[54, "gid-range-description"]], "External Drive Description": [[54, "external-drive-description"]], "External Bias Description": [[54, "external-bias-description"]], "Connection Description": [[54, "connection-description"]], "Extracellular Array Description": [[54, "extracellular-array-description"]], "Parallel backends": [[55, "parallel-backends"]], "Joblib": [[55, "joblib"]], "MPI": [[55, "mpi"]], "The HNN Roadmap": [[56, "the-hnn-roadmap"]], "Project Vision": [[56, "project-vision"]], "Timeline Overview": [[56, "timeline-overview"]], "Short-Term Goals": [[56, "short-term-goals"]], "Modularize HNN code to simplify installation, development and maintenance": [[56, "modularize-hnn-code-to-simplify-installation-development-and-maintenance"]], "Develop a New HNN GUI": [[56, "develop-a-new-hnn-gui"]], "LFP/CSD Simulation, Visualization and Data Comparison": [[56, "lfp-csd-simulation-visualization-and-data-comparison"]], "Parameter Estimation Expansion": [[56, "parameter-estimation-expansion"]], "Different Cortical Model Template Choices": [[56, "different-cortical-model-template-choices"]], "API and Tutorial development": [[56, "api-and-tutorial-development"]], "Longer-Term Goals": [[56, "longer-term-goals"]], "What\u2019s new?": [[58, "what-s-new"]], "Current": [[58, "current"]], "Changelog": [[58, "changelog"], [58, "id5"], [58, "id10"], [58, "id17"]], "Bug": [[58, "bug"], [58, "id6"], [58, "id12"], [58, "id37"]], "API": [[58, "api"], [58, "id7"], [58, "id13"], [58, "id46"]], "0.3": [[58, "id3"]], "People who contributed to this release (in alphabetical order):": [[58, "people-who-contributed-to-this-release-in-alphabetical-order"], [58, "id14"], [58, "id55"]], "0.2": [[58, "id8"]], "Notable Changes": [[58, "notable-changes"]], "0.1": [[58, "id15"]]}, "indexentries": {"cell (class in hnn_core)": [[21, "hnn_core.Cell"]], "__repr__() (hnn_core.cell method)": [[21, "hnn_core.Cell.__repr__"]], "build() (hnn_core.cell method)": [[21, "hnn_core.Cell.build"]], "copy() (hnn_core.cell method)": [[21, "hnn_core.Cell.copy"]], "create_tonic_bias() (hnn_core.cell method)": [[21, "hnn_core.Cell.create_tonic_bias"]], "define_shape() (hnn_core.cell method)": [[21, "hnn_core.Cell.define_shape"]], "distance_section() (hnn_core.cell method)": [[21, "hnn_core.Cell.distance_section"]], "modify_section() (hnn_core.cell method)": [[21, "hnn_core.Cell.modify_section"]], "parconnect_from_src() (hnn_core.cell method)": [[21, "hnn_core.Cell.parconnect_from_src"]], "plot_morphology() (hnn_core.cell method)": [[21, "hnn_core.Cell.plot_morphology"]], "record() (hnn_core.cell method)": [[21, "hnn_core.Cell.record"]], "setup_source_netcon() (hnn_core.cell method)": [[21, "hnn_core.Cell.setup_source_netcon"]], "syn_create() (hnn_core.cell method)": [[21, "hnn_core.Cell.syn_create"]], "to_dict() (hnn_core.cell method)": [[21, "hnn_core.Cell.to_dict"]], "cellresponse (class in hnn_core)": [[22, "hnn_core.CellResponse"]], "__getitem__() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.__getitem__"]], "__repr__() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.__repr__"]], "mean_rates() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.mean_rates"]], "plot_spikes_hist() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.plot_spikes_hist"]], "plot_spikes_raster() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.plot_spikes_raster"]], "to_dict() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.to_dict"]], "update_types() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.update_types"]], "write() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.write"]], "network (class in hnn_core)": [[23, "hnn_core.Network"]], "__repr__() (hnn_core.network method)": [[23, "hnn_core.Network.__repr__"]], "add_bursty_drive() (hnn_core.network method)": [[23, "hnn_core.Network.add_bursty_drive"]], "add_connection() (hnn_core.network method)": [[23, "hnn_core.Network.add_connection"]], "add_electrode_array() (hnn_core.network method)": [[23, "hnn_core.Network.add_electrode_array"]], "add_evoked_drive() (hnn_core.network method)": [[23, "hnn_core.Network.add_evoked_drive"]], "add_poisson_drive() (hnn_core.network method)": [[23, "hnn_core.Network.add_poisson_drive"]], "add_tonic_bias() (hnn_core.network method)": [[23, "hnn_core.Network.add_tonic_bias"]], "clear_connectivity() (hnn_core.network method)": [[23, "hnn_core.Network.clear_connectivity"]], "clear_drives() (hnn_core.network method)": [[23, "hnn_core.Network.clear_drives"]], "copy() (hnn_core.network method)": [[23, "hnn_core.Network.copy"]], "gid_to_type() (hnn_core.network method)": [[23, "hnn_core.Network.gid_to_type"]], "plot_cells() (hnn_core.network method)": [[23, "hnn_core.Network.plot_cells"]], "set_cell_positions() (hnn_core.network method)": [[23, "hnn_core.Network.set_cell_positions"]], "write_configuration() (hnn_core.network method)": [[23, "hnn_core.Network.write_configuration"]], "calcium_model() (in module hnn_core)": [[24, "hnn_core.calcium_model"]], "dipole (class in hnn_core.dipole)": [[25, "hnn_core.dipole.Dipole"]], "copy() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.copy"]], "plot() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.plot"]], "plot_psd() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.plot_psd"]], "plot_tfr_morlet() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.plot_tfr_morlet"]], "savgol_filter() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.savgol_filter"]], "scale() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.scale"]], "smooth() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.smooth"]], "write() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.write"]], "average_dipoles() (in module hnn_core.dipole)": [[26, "hnn_core.dipole.average_dipoles"]], "extracellulararray (class in hnn_core.extracellular)": [[27, "hnn_core.extracellular.ExtracellularArray"]], "__repr__() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.__repr__"]], "copy() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.copy"]], "plot_csd() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.plot_csd"]], "plot_lfp() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.plot_lfp"]], "sfreq (hnn_core.extracellular.extracellulararray property)": [[27, "hnn_core.extracellular.ExtracellularArray.sfreq"]], "smooth() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.smooth"]], "to_dict() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.to_dict"]], "hnngui (class in hnn_core.gui)": [[28, "hnn_core.gui.HNNGUI"]], "analysis_config (hnn_core.gui.hnngui property)": [[28, "hnn_core.gui.HNNGUI.analysis_config"]], "capture() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.capture"]], "compose() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.compose"]], "data (hnn_core.gui.hnngui property)": [[28, "hnn_core.gui.HNNGUI.data"]], "get_cell_parameters_dict() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.get_cell_parameters_dict"]], "load_parameters() (hnn_core.gui.hnngui static method)": [[28, "hnn_core.gui.HNNGUI.load_parameters"]], "run_notebook_cells() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.run_notebook_cells"]], "jones_2009_model() (in module hnn_core)": [[29, "hnn_core.jones_2009_model"]], "law_2021_model() (in module hnn_core)": [[30, "hnn_core.law_2021_model"]], "optimizer (class in hnn_core.optimization)": [[31, "hnn_core.optimization.Optimizer"]], "__repr__() (hnn_core.optimization.optimizer method)": [[31, "hnn_core.optimization.Optimizer.__repr__"]], "fit() (hnn_core.optimization.optimizer method)": [[31, "hnn_core.optimization.Optimizer.fit"]], "plot_convergence() (hnn_core.optimization.optimizer method)": [[31, "hnn_core.optimization.Optimizer.plot_convergence"]], "joblibbackend (class in hnn_core.parallel_backends)": [[32, "hnn_core.parallel_backends.JoblibBackend"]], "simulate() (hnn_core.parallel_backends.joblibbackend method)": [[32, "hnn_core.parallel_backends.JoblibBackend.simulate"]], "mpibackend (class in hnn_core.parallel_backends)": [[33, "hnn_core.parallel_backends.MPIBackend"]], "simulate() (hnn_core.parallel_backends.mpibackend method)": [[33, "hnn_core.parallel_backends.MPIBackend.simulate"]], "terminate() (hnn_core.parallel_backends.mpibackend method)": [[33, "hnn_core.parallel_backends.MPIBackend.terminate"]], "pick_connection() (in module hnn_core)": [[34, "hnn_core.pick_connection"]], "read_dipole() (in module hnn_core)": [[35, "hnn_core.read_dipole"]], "read_params() (in module hnn_core)": [[36, "hnn_core.read_params"]], "read_spikes() (in module hnn_core)": [[37, "hnn_core.read_spikes"]], "simulate_dipole() (in module hnn_core)": [[38, "hnn_core.simulate_dipole"]], "networkplotter (class in hnn_core.viz)": [[39, "hnn_core.viz.NetworkPlotter"]], "export_movie() (hnn_core.viz.networkplotter method)": [[39, "hnn_core.viz.NetworkPlotter.export_movie"]], "plot_cell_connectivity() (in module hnn_core.viz)": [[40, "hnn_core.viz.plot_cell_connectivity"]], "plot_cell_morphology() (in module hnn_core.viz)": [[41, "hnn_core.viz.plot_cell_morphology"]], "plot_cells() (in module hnn_core.viz)": [[42, "hnn_core.viz.plot_cells"]], "plot_connectivity_matrix() (in module hnn_core.viz)": [[43, "hnn_core.viz.plot_connectivity_matrix"]], "plot_dipole() (in module hnn_core.viz)": [[44, "hnn_core.viz.plot_dipole"]], "plot_laminar_csd() (in module hnn_core.viz)": [[45, "hnn_core.viz.plot_laminar_csd"]], "plot_laminar_lfp() (in module hnn_core.viz)": [[46, "hnn_core.viz.plot_laminar_lfp"]], "plot_psd() (in module hnn_core.viz)": [[47, "hnn_core.viz.plot_psd"]], "plot_spikes_hist() (in module hnn_core.viz)": [[48, "hnn_core.viz.plot_spikes_hist"]], "plot_spikes_raster() (in module hnn_core.viz)": [[49, "hnn_core.viz.plot_spikes_raster"]], "plot_tfr_morlet() (in module hnn_core.viz)": [[50, "hnn_core.viz.plot_tfr_morlet"]], "distal": [[51, "term-distal"]], "drive": [[51, "term-drive"]], "gid": [[51, "term-gid"]], "proximal": [[51, "term-proximal"]]}})
\ No newline at end of file
+Search.setIndex({"docnames": ["api", "auto_examples/howto/index", "auto_examples/howto/optimize_evoked", "auto_examples/howto/optimize_rhythmic", "auto_examples/howto/plot_batch_simulate", "auto_examples/howto/plot_connectivity", "auto_examples/howto/plot_firing_pattern", "auto_examples/howto/plot_hnn_animation", "auto_examples/howto/plot_record_extracellular_potentials", "auto_examples/howto/plot_simulate_mpi_backend", "auto_examples/howto/sg_execution_times", "auto_examples/index", "auto_examples/sg_execution_times", "auto_examples/workflows/index", "auto_examples/workflows/plot_simulate_alpha", "auto_examples/workflows/plot_simulate_beta", "auto_examples/workflows/plot_simulate_evoked", "auto_examples/workflows/plot_simulate_gamma", "auto_examples/workflows/plot_simulate_somato", "auto_examples/workflows/sg_execution_times", "contributing", "generated/hnn_core.Cell", "generated/hnn_core.CellResponse", "generated/hnn_core.Network", "generated/hnn_core.calcium_model", "generated/hnn_core.dipole.Dipole", "generated/hnn_core.dipole.average_dipoles", "generated/hnn_core.extracellular.ExtracellularArray", "generated/hnn_core.gui.HNNGUI", "generated/hnn_core.jones_2009_model", "generated/hnn_core.law_2021_model", "generated/hnn_core.optimization.Optimizer", "generated/hnn_core.parallel_backends.JoblibBackend", "generated/hnn_core.parallel_backends.MPIBackend", "generated/hnn_core.pick_connection", "generated/hnn_core.read_dipole", "generated/hnn_core.read_params", "generated/hnn_core.read_spikes", "generated/hnn_core.simulate_dipole", "generated/hnn_core.viz.NetworkPlotter", "generated/hnn_core.viz.plot_cell_connectivity", "generated/hnn_core.viz.plot_cell_morphology", "generated/hnn_core.viz.plot_cells", "generated/hnn_core.viz.plot_connectivity_matrix", "generated/hnn_core.viz.plot_dipole", "generated/hnn_core.viz.plot_laminar_csd", "generated/hnn_core.viz.plot_laminar_lfp", "generated/hnn_core.viz.plot_psd", "generated/hnn_core.viz.plot_spikes_hist", "generated/hnn_core.viz.plot_spikes_raster", "generated/hnn_core.viz.plot_tfr_morlet", "glossary", "governance", "index", "network_file_desc", "parallel", "roadmap", "sg_execution_times", "whats_new"], "filenames": ["api.rst", "auto_examples/howto/index.rst", "auto_examples/howto/optimize_evoked.rst", "auto_examples/howto/optimize_rhythmic.rst", "auto_examples/howto/plot_batch_simulate.rst", "auto_examples/howto/plot_connectivity.rst", "auto_examples/howto/plot_firing_pattern.rst", "auto_examples/howto/plot_hnn_animation.rst", "auto_examples/howto/plot_record_extracellular_potentials.rst", "auto_examples/howto/plot_simulate_mpi_backend.rst", "auto_examples/howto/sg_execution_times.rst", "auto_examples/index.rst", "auto_examples/sg_execution_times.rst", "auto_examples/workflows/index.rst", "auto_examples/workflows/plot_simulate_alpha.rst", "auto_examples/workflows/plot_simulate_beta.rst", "auto_examples/workflows/plot_simulate_evoked.rst", "auto_examples/workflows/plot_simulate_gamma.rst", "auto_examples/workflows/plot_simulate_somato.rst", "auto_examples/workflows/sg_execution_times.rst", "contributing.rst", "generated/hnn_core.Cell.rst", "generated/hnn_core.CellResponse.rst", "generated/hnn_core.Network.rst", "generated/hnn_core.calcium_model.rst", "generated/hnn_core.dipole.Dipole.rst", "generated/hnn_core.dipole.average_dipoles.rst", "generated/hnn_core.extracellular.ExtracellularArray.rst", "generated/hnn_core.gui.HNNGUI.rst", "generated/hnn_core.jones_2009_model.rst", "generated/hnn_core.law_2021_model.rst", "generated/hnn_core.optimization.Optimizer.rst", "generated/hnn_core.parallel_backends.JoblibBackend.rst", "generated/hnn_core.parallel_backends.MPIBackend.rst", "generated/hnn_core.pick_connection.rst", "generated/hnn_core.read_dipole.rst", "generated/hnn_core.read_params.rst", "generated/hnn_core.read_spikes.rst", "generated/hnn_core.simulate_dipole.rst", "generated/hnn_core.viz.NetworkPlotter.rst", "generated/hnn_core.viz.plot_cell_connectivity.rst", "generated/hnn_core.viz.plot_cell_morphology.rst", "generated/hnn_core.viz.plot_cells.rst", "generated/hnn_core.viz.plot_connectivity_matrix.rst", "generated/hnn_core.viz.plot_dipole.rst", "generated/hnn_core.viz.plot_laminar_csd.rst", "generated/hnn_core.viz.plot_laminar_lfp.rst", "generated/hnn_core.viz.plot_psd.rst", "generated/hnn_core.viz.plot_spikes_hist.rst", "generated/hnn_core.viz.plot_spikes_raster.rst", "generated/hnn_core.viz.plot_tfr_morlet.rst", "glossary.rst", "governance.rst", "index.rst", "network_file_desc.rst", "parallel.rst", "roadmap.rst", "sg_execution_times.rst", "whats_new.rst"], "titles": ["API Documentation", "How to", "05. Optimize simulated evoked response parameters", "08. Optimize simulated rhythmic responses", "07. Batch Simulation", "03. Modifying local connectivity", "01. Plot firing pattern", "06. Animating HNN simulations", "02. Record extracellular potentials", "04. Use MPI backend for parallelization", "Computation times", "Tutorials", "Computation times", "Tutorials", "02. Simulate Alpha and Beta Rhythms", "05. Simulate beta modulated ERP", "01. Simulate Event Related Potentials (ERPs)", "03. Simulate Gamma Rhythms", "04. From MEG sensor-space data to HNN simulation", "Computation times", "Contributions", "hnn_core.Cell", "hnn_core.CellResponse", "hnn_core.Network", "hnn_core.calcium_model", "hnn_core.dipole.Dipole", "hnn_core.dipole.average_dipoles", "hnn_core.extracellular.ExtracellularArray", "hnn_core.gui.HNNGUI", "hnn_core.jones_2009_model", "hnn_core.law_2021_model", "hnn_core.optimization.Optimizer", "hnn_core.parallel_backends.JoblibBackend", "hnn_core.parallel_backends.MPIBackend", "hnn_core.pick_connection", "hnn_core.read_dipole", "hnn_core.read_params", "hnn_core.read_spikes", "hnn_core.simulate_dipole", "hnn_core.viz.NetworkPlotter", "hnn_core.viz.plot_cell_connectivity", "hnn_core.viz.plot_cell_morphology", "hnn_core.viz.plot_cells", "hnn_core.viz.plot_connectivity_matrix", "hnn_core.viz.plot_dipole", "hnn_core.viz.plot_laminar_csd", "hnn_core.viz.plot_laminar_lfp", "hnn_core.viz.plot_psd", "hnn_core.viz.plot_spikes_hist", "hnn_core.viz.plot_spikes_raster", "hnn_core.viz.plot_tfr_morlet", "Glossary", "Project Governance", "hnn-core", "Network File Content", "Parallel backends", "The HNN Roadmap", "Computation times", "What\u2019s new?"], "terms": {"These": [1, 11, 15, 20, 25, 27, 29, 44, 46, 50, 55, 56], "ar": [1, 3, 4, 5, 6, 8, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 29, 32, 33, 34, 36, 38, 44, 46, 47, 48, 50, 52, 53, 54, 55, 56, 58], "short": [1, 11, 25, 47, 51], "exampl": [1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 34, 48, 54, 55, 56, 57, 58], "show": [1, 2, 3, 4, 5, 6, 8, 11, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 28, 31, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "us": [1, 4, 5, 6, 7, 8, 10, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 30, 33, 39, 42, 44, 45, 46, 48, 50, 52, 53, 54, 55, 56, 57, 58], "hnn": [1, 2, 4, 6, 8, 9, 10, 11, 13, 14, 16, 17, 19, 23, 28, 29, 32, 33, 39, 51, 52, 57, 58], "core": [1, 2, 3, 4, 9, 11, 13, 14, 16, 17, 18, 28, 33, 51, 52, 55, 56, 58], "api": [1, 5, 11, 13, 20, 39, 52, 53], "accomplish": [1, 11], "specif": [1, 5, 11, 15, 20, 21, 23, 24, 25, 44, 51, 52, 54, 56, 58], "task": [1, 4, 11, 18], "01": [1, 2, 10, 11, 13, 15, 17, 18, 19, 57], "plot": [1, 2, 3, 5, 7, 8, 9, 10, 11, 14, 16, 17, 18, 21, 22, 23, 25, 27, 28, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 56, 57, 58], "fire": [1, 5, 10, 11, 17, 22, 23, 54, 57, 58], "pattern": [1, 5, 10, 11, 17, 23, 29, 34, 40, 57, 58], "02": [1, 10, 11, 13, 15, 17, 18, 19, 57], "record": [1, 5, 6, 7, 10, 11, 16, 18, 21, 22, 23, 27, 38, 53, 54, 56, 57, 58], "extracellular": [1, 10, 11, 23, 38, 46, 57, 58], "potenti": [1, 7, 10, 11, 13, 15, 18, 19, 21, 23, 27, 51, 53, 56, 57, 58], "03": [1, 6, 7, 8, 9, 10, 11, 13, 14, 15, 16, 18, 19, 57], "modifi": [1, 2, 3, 4, 10, 11, 15, 16, 20, 21, 25, 27, 30, 57, 58], "local": [1, 6, 8, 10, 11, 18, 27, 53, 56, 57, 58], "connect": [1, 6, 10, 11, 14, 15, 17, 21, 23, 28, 29, 30, 32, 33, 34, 38, 40, 43, 51, 56, 57, 58], "04": [1, 10, 11, 13, 15, 19, 57], "mpi": [1, 8, 10, 11, 20, 28, 33, 53, 56, 57, 58], "backend": [1, 4, 10, 11, 16, 18, 20, 28, 53, 57, 58], "parallel": [1, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 17, 18, 20, 21, 32, 33, 56, 57, 58], "05": [1, 10, 11, 13, 18, 19, 29, 31, 35, 38, 57], "optim": [1, 10, 11, 29, 35, 38, 47, 56, 57, 58], "simul": [1, 5, 6, 8, 9, 10, 11, 13, 19, 23, 25, 27, 28, 29, 31, 32, 33, 35, 38, 39, 47, 50, 51, 53, 55, 57, 58], "evok": [1, 4, 5, 6, 7, 8, 10, 11, 14, 15, 16, 18, 22, 23, 24, 29, 31, 35, 38, 48, 54, 57, 58], "respons": [1, 5, 6, 8, 10, 11, 14, 15, 16, 18, 22, 24, 29, 31, 35, 38, 47, 54, 57, 58], "paramet": [1, 3, 4, 5, 7, 10, 11, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 54, 57, 58], "06": [1, 10, 11, 18, 55, 57], "anim": [1, 10, 11, 39, 56, 57, 58], "07": [1, 10, 11, 18, 57], "batch": [1, 10, 11, 56, 57, 58], "go": [2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 56], "end": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 23, 25, 47, 50, 52, 54, 55, 56, 58], "download": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 53], "full": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 25, 35, 36, 39, 56], "code": [2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 52, 53, 58], "run": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 28, 31, 33, 52, 53, 54, 55, 56, 58], "thi": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 30, 33, 38, 40, 48, 52, 53, 54, 55, 56], "your": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53], "browser": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "via": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 22, 52, 55, 56, 58], "binder": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "demonstr": [2, 3, 5, 6, 7, 9, 14, 15, 16, 17, 18], "how": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 32, 33, 38, 40, 52, 54, 55, 56], "model": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 22, 24, 29, 30, 32, 33, 39, 53, 58], "match": [2, 5, 18, 23, 29, 34, 53, 55, 58], "an": [2, 4, 5, 6, 8, 15, 16, 17, 18, 20, 21, 22, 23, 24, 25, 27, 28, 29, 34, 36, 37, 39, 40, 42, 46, 48, 49, 51, 52, 53, 54, 56, 58], "experiment": [2, 25, 31], "dipol": [2, 3, 4, 5, 8, 9, 14, 16, 17, 18, 21, 23, 27, 31, 32, 33, 35, 38, 44, 46, 47, 50, 53, 54, 55, 56, 58], "waveform": [2, 6, 8, 14, 16, 17, 18, 25, 27, 38], "author": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 52], "carolina": [2, 3, 58], "fernandez": [2, 3, 58], "cxf418": [2, 3], "miami": [2, 3], "edu": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 55, 56], "nick": [2, 4, 5, 6, 7, 8, 14, 15, 58], "tollei": [2, 4, 5, 6, 7, 8, 14, 15, 58], "nicholas_tollei": [2, 4, 5, 6, 7, 8, 14, 15], "brown": [2, 4, 5, 6, 7, 8, 9, 14, 15, 16, 18, 53, 56], "ryan": [2, 4, 18, 58], "thorp": [2, 4, 18, 58], "ryan_thorp": [2, 4, 18], "mainak": [2, 4, 6, 8, 9, 14, 16, 17, 18, 58], "ja": [2, 4, 6, 8, 9, 14, 16, 17, 18, 53, 58], "mja": [2, 4, 6, 9, 14, 17], "mgh": [2, 4, 6, 9, 14, 16, 17], "harvard": [2, 4, 6, 9, 14, 16, 17], "import": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 55, 56], "o": [2, 5, 6, 7, 9, 14, 16, 17, 18], "path": [2, 5, 6, 7, 9, 14, 16, 17, 18, 21, 22, 23, 25, 29, 35, 36, 37], "op": [2, 5, 6, 7, 9, 14, 16, 17, 18], "matplotlib": [2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 53, 58], "pyplot": [2, 3, 4, 5, 6, 8, 14, 15, 16, 17, 18], "plt": [2, 3, 4, 5, 6, 7, 8, 14, 15, 16, 17, 18, 25, 27, 31, 44, 46], "let": [2, 3, 4, 5, 6, 9, 14, 16, 17, 18, 55], "u": [2, 3, 4, 5, 6, 9, 14, 16, 17, 18, 20, 23, 54], "hnn_core": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 55], "from": [2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 19, 20, 21, 22, 23, 25, 27, 28, 29, 30, 32, 33, 35, 36, 37, 38, 39, 40, 42, 43, 45, 47, 48, 49, 51, 52, 53, 55, 56, 57, 58], "mpibackend": [2, 3, 9, 28, 55, 58], "jones_2009_model": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 24, 30, 58], "simulate_dipol": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 33, 54, 55, 58], "read_dipol": [2, 58], "hnn_core_root": [2, 17, 18], "join": [2, 6, 17, 18, 52], "dirnam": [2, 17, 18], "__file__": [2, 17, 18], "The": [2, 3, 4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 34, 35, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 58], "number": [2, 3, 4, 7, 9, 14, 16, 18, 20, 23, 25, 27, 28, 32, 33, 38, 50, 54, 55, 58], "mai": [2, 3, 4, 8, 16, 20, 23, 27, 46, 52], "need": [2, 3, 4, 6, 7, 9, 18, 20, 23, 28, 52, 53, 55, 56], "depend": [2, 3, 4, 15, 18, 24, 52, 55, 56, 58], "current": [2, 3, 4, 5, 6, 8, 16, 17, 18, 21, 22, 23, 27, 28, 38, 45, 52, 53, 54, 56], "machin": [2, 3, 4, 56], "n_proc": [2, 3, 9, 33, 55], "10": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 24, 27, 29, 30, 39, 53, 56], "first": [2, 3, 5, 6, 7, 11, 13, 14, 15, 16, 17, 18, 21, 23, 25, 39, 40, 53, 54, 55, 56, 58], "we": [2, 3, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 52, 53, 56], "load": [2, 5, 6, 9, 16, 18, 29, 33, 58], "data": [2, 4, 5, 6, 8, 11, 13, 14, 16, 19, 21, 22, 23, 25, 26, 27, 28, 31, 33, 45, 46, 47, 53, 55, 57, 58], "object": [2, 3, 5, 6, 7, 8, 14, 16, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 37, 38, 39, 40, 41, 42, 43, 44, 47, 48, 49, 50, 52, 53, 54, 55, 58], "i": [2, 3, 4, 5, 6, 8, 9, 14, 15, 16, 17, 18, 20, 21, 22, 23, 25, 27, 28, 29, 31, 33, 34, 36, 38, 39, 40, 42, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 55, 56, 58], "differ": [2, 4, 5, 6, 14, 15, 16, 17, 20, 22, 23, 30, 37, 40, 55, 58], "experi": [2, 38, 53], "than": [2, 14, 16, 18, 20, 23, 52, 53, 55, 58], "one": [2, 6, 14, 15, 18, 20, 23, 25, 27, 33, 34, 44, 46, 47, 50, 52, 53, 56], "which": [2, 5, 6, 7, 8, 9, 11, 13, 15, 16, 17, 18, 20, 23, 25, 27, 28, 44, 46, 47, 50, 51, 53, 55, 56, 58], "base": [2, 11, 13, 15, 16, 18, 20, 21, 52, 53, 56, 58], "were": [2, 3, 25, 27, 46, 53, 58], "tune": [2, 53], "so": [2, 3, 9, 16, 18, 20, 25, 52, 53, 58], "initi": [2, 14, 23, 54, 56], "rmse": [2, 58], "larg": [2, 8, 56], "give": [2, 20, 52, 53], "procedur": [2, 56], "lot": [2, 5, 20], "work": [2, 20, 52, 53, 55, 56], "urllib": 2, "request": [2, 33, 51, 52], "urlretriev": 2, "data_url": 2, "http": [2, 15, 18, 20, 27, 39, 53, 55, 56], "raw": [2, 18, 25, 27, 44, 46, 50], "githubusercont": 2, "com": [2, 4, 8, 14, 16, 17, 18, 20, 53, 56], "jonescompneurolab": [2, 20, 53, 56], "master": [2, 20, 53], "meg_detection_data": 2, "s1_suprat": 2, "txt": [2, 6, 22, 25, 35, 37], "exp_dpl": 2, "": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 37, 50, 52, 54, 55, 56], "some": [2, 5, 8, 17, 18, 53, 56], "tstop": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 31, 32, 33, 38, 54, 58], "time": [2, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 28, 30, 32, 33, 38, 39, 45, 46, 47, 50, 52, 54, 55, 58], "1": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 24, 25, 27, 29, 30, 32, 33, 52, 54, 55, 56], "scale_factor": [2, 3, 31], "3000": [2, 3, 5, 14, 16], "smooth_window_len": [2, 3, 31], "30": [2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 28, 39], "net_init": 2, "proxim": [2, 3, 4, 6, 14, 15, 16, 17, 18, 21, 23, 28, 34, 51, 54], "weights_ampa_p1": [2, 6, 15, 16], "l2_basket": [2, 4, 5, 6, 15, 16, 18, 23, 30, 34], "0": [2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 21, 22, 23, 25, 27, 29, 38, 39, 41, 47, 50, 55, 56, 57], "2913": 2, "l2_pyramid": [2, 3, 4, 6, 9, 14, 15, 16, 17, 18, 22, 23, 34], "9337": 2, "l5_basket": [2, 4, 5, 6, 15, 16, 18, 22, 23, 30, 34], "1951": 2, "l5_pyramid": [2, 3, 4, 5, 6, 9, 14, 15, 16, 17, 18, 22, 23, 30, 34], "3602": 2, "weights_nmda_p1": 2, "9240": 2, "0845": 2, "5849": 2, "65105": 2, "synaptic_delays_p": [2, 18], "add_evoked_dr": [2, 4, 6, 15, 16, 18, 23, 58], "evprox1": [2, 6, 15, 16, 18, 22, 37], "mu": [2, 4, 6, 8, 14, 15, 16, 18, 23, 29, 54], "5": [2, 3, 4, 5, 6, 8, 9, 14, 15, 17, 18, 19, 21, 23, 27, 30], "6813": 2, "sigma": [2, 4, 6, 15, 16, 18, 23, 54, 58], "20": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 39, 55], "3969": 2, "numspik": [2, 3, 4, 6, 9, 14, 15, 16, 18, 23], "locat": [2, 3, 4, 5, 6, 9, 14, 15, 16, 17, 18, 21, 23, 28, 34, 51, 54], "weights_ampa": [2, 3, 4, 6, 9, 14, 15, 16, 17, 18, 23, 54], "weights_nmda": [2, 6, 15, 16, 18, 23, 54], "synaptic_delai": [2, 3, 4, 6, 14, 15, 16, 17, 18, 23, 54], "distal": [2, 3, 5, 6, 9, 14, 15, 16, 18, 21, 23, 28, 30, 34, 51, 54], "weights_ampa_d1": [2, 6, 15, 16], "8037": 2, "5738": 2, "3626": 2, "weights_nmda_d1": [2, 6, 15, 16], "2492": 2, "6183": 2, "1121": 2, "synaptic_delays_d1": [2, 6, 16], "evdist1": [2, 6, 15, 16, 18, 22, 23, 37], "58": [2, 6, 18], "6539": 2, "5810": 2, "2": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 30, 52, 54, 55], "weights_ampa_p2": [2, 6, 15, 16], "weights_nmda_p2": 2, "evprox2": [2, 6, 15, 16, 18], "80": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 58], "mpi_cmd": [2, 3, 9, 33, 55], "mpiexec": [2, 3, 9, 33, 55], "init_dpl": 2, "n_trial": [2, 3, 5, 9, 14, 16, 17, 18, 22, 23, 27, 32, 33, 38, 55], "scale": [2, 3, 5, 14, 16, 17, 18, 25, 27, 31, 38, 46, 56, 58], "smooth": [2, 3, 5, 8, 14, 15, 16, 18, 25, 27, 31, 38, 45, 52, 58], "now": [2, 3, 6, 8, 14, 15, 16, 17, 18, 20, 58], "start": [2, 5, 9, 11, 13, 14, 20, 21, 22, 23, 25, 32, 33, 47, 50, 53, 54, 55, 56, 58], "defin": [2, 3, 4, 5, 6, 8, 16, 18, 21, 22, 23, 27, 29, 41, 46, 48, 55, 56, 58], "function": [2, 3, 4, 14, 15, 20, 23, 25, 27, 28, 44, 46, 50, 54, 56, 58], "tell": [2, 3], "routin": [2, 3, 31, 56], "network": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 24, 27, 28, 29, 30, 32, 33, 34, 38, 39, 40, 42, 43, 51, 55, 56, 58], "drive": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 28, 29, 40, 51, 56, 58], "take": [2, 3, 17, 28, 52], "attach": [2, 3, 8, 21, 23], "dictionari": [2, 3, 4, 5, 6, 8, 21, 22, 23, 27, 28, 36, 37, 48, 54, 56, 58], "wish": [2, 3, 23], "def": [2, 3, 4, 5, 15], "set_param": [2, 3, 4, 31], "net": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 24, 27, 28, 29, 30, 32, 33, 34, 38, 39, 40, 42, 43, 48, 49, 54, 55, 58], "param": [2, 3, 17, 18, 23, 24, 28, 29, 30, 36, 38, 56, 58], "evprox2_ampa_l2_basket": 2, "evprox2_ampa_l2_pyramid": 2, "evprox2_ampa_l5_basket": 2, "evprox2_ampa_l5_pyramid": 2, "evprox2_nmda_l2_basket": 2, "evprox2_nmda_l2_pyramid": 2, "evprox2_nmda_l5_basket": 2, "evprox2_nmda_l5_pyramid": 2, "evprox2_mu": 2, "evprox2_sigma": 2, "Then": [2, 3, 8, 16, 18], "constraint": [2, 3, 31], "must": [2, 3, 9, 21, 22, 23, 25, 27, 34, 37, 38, 40, 41, 48, 52, 53, 54], "tupl": [2, 3, 21, 23, 25, 27, 29, 31, 39, 41, 44, 47, 54, 58], "where": [2, 3, 5, 15, 18, 21, 23, 27, 52, 55, 56, 58], "valu": [2, 3, 4, 8, 11, 13, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 34, 35, 36, 38, 43, 44, 46, 50, 54, 58], "each": [2, 3, 4, 5, 6, 8, 9, 11, 13, 14, 15, 16, 21, 22, 23, 25, 26, 27, 31, 32, 33, 37, 38, 46, 48, 50, 51, 53, 54, 55, 58], "lower": [2, 3, 14, 17, 18, 27, 31, 39, 45], "bound": [2, 3, 27, 45], "second": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 25, 39], "upper": [2, 3, 18, 27, 39, 45], "correspond": [2, 3, 14, 15, 17, 18, 22, 23, 27, 34, 40, 56, 58], "follow": [2, 3, 9, 11, 13, 15, 16, 18, 20, 23, 28, 52, 53, 56], "synapt": [2, 3, 21, 23, 34, 38, 40, 43, 54, 56, 58], "weight": [2, 3, 5, 6, 15, 16, 18, 23, 28, 30, 31, 40, 43, 54, 58], "rang": [2, 3, 6, 8, 14, 17, 18, 22, 23, 25, 34, 37, 50, 58], "unit": [2, 3, 23, 25, 27, 46, 53, 56, 58], "micro": [2, 3, 21, 54], "siemen": [2, 3], "chosen": [2, 3], "keep": [2, 3, 52], "physiolog": [2, 3, 18], "realist": [2, 3, 8, 14, 15, 29], "regim": [2, 3], "dict": [2, 3, 4, 18, 21, 22, 23, 25, 28, 29, 37, 41, 48, 54], "100": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 23, 28, 39, 41], "120": [2, 5, 6, 7, 8, 9, 14, 15, 16, 17], "fit": [2, 3, 18, 25, 31], "max_it": 31, "40": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "final": [2, 3, 5, 6, 7, 8, 9, 15, 16, 17, 18, 20, 52, 53, 55], "can": [2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 20, 21, 23, 25, 27, 28, 29, 39, 41, 44, 46, 47, 50, 52, 53, 54, 55, 56, 58], "alongsid": 2, "post": [2, 18, 56], "well": [2, 5, 17, 18, 23, 25, 51, 53, 55, 56, 58], "converg": [2, 3, 31, 58], "opt_dpl": [2, 3], "net_": [2, 3], "fig": [2, 3, 5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 25, 27, 31, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50], "ax": [2, 3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58], "subplot": [2, 3, 5, 6, 8, 14, 15, 16, 17, 18, 40], "sharex": [2, 5, 6, 8, 15, 16, 17, 18], "true": [2, 4, 5, 6, 8, 14, 15, 16, 17, 18, 21, 22, 23, 25, 27, 28, 29, 31, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 58], "figsiz": [2, 3, 4, 5, 6, 8, 15, 16, 17, 18], "6": [2, 3, 4, 5, 6, 8, 15, 16, 17, 18, 20, 30], "origin": [2, 11, 13, 15, 18, 20, 23, 51, 53, 54, 56, 58], "layer": [2, 3, 5, 8, 15, 16, 17, 18, 23, 25, 29, 44, 47, 50, 54, 56, 58], "agg": [2, 3, 4, 5, 15, 16, 25, 26, 44, 47, 50], "fals": [2, 3, 4, 5, 8, 14, 15, 16, 17, 18, 21, 23, 24, 25, 28, 29, 30, 32, 33, 38, 43, 44, 50, 54, 58], "color": [2, 3, 6, 14, 15, 18, 21, 22, 25, 27, 28, 39, 41, 43, 44, 45, 46, 47, 48, 50, 58], "tab": [2, 3], "blue": [2, 27, 45], "orang": 2, "green": [2, 3, 18], "legend": [2, 3, 4, 5, 15, 18], "cell_respons": [2, 5, 6, 8, 14, 15, 16, 17, 18, 23, 37, 48, 49, 54, 58], "plot_spikes_hist": [2, 5, 6, 14, 15, 16, 18, 22, 58], "fig1": [2, 3], "plot_converg": [2, 3, 31], "jupyt": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 28, 56], "notebook": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 28, 56], "optimize_evok": [2, 10, 57, 58], "ipynb": [2, 3, 4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "python": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 20, 53, 55, 56, 58], "sourc": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54, 56, 58], "py": [2, 3, 4, 5, 6, 7, 8, 9, 10, 14, 15, 16, 17, 18, 19, 20, 53, 55, 56, 57, 58], "zip": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18], "galleri": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 57], "gener": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 20, 23, 51, 52, 53, 54, 56, 58], "sphinx": [2, 3, 4, 5, 6, 7, 8, 9, 11, 14, 15, 16, 17, 18, 20], "do": [4, 6, 14, 18, 20, 52, 53, 56], "allow": [4, 5, 7, 8, 9, 16, 18, 23, 52, 54, 58], "user": [4, 8, 11, 13, 18, 33, 52, 53, 56, 58], "effici": [4, 56], "multipl": [4, 16, 23, 27, 34, 55, 56, 58], "comprehens": 4, "analysi": [4, 8, 14, 15, 17, 29, 56, 58], "abdul": [4, 58], "samad": [4, 58], "siddiqui": [4, 58], "abdulsamadsid1": 4, "gmail": [4, 8, 14, 16, 17, 18], "numpi": [4, 15, 17, 20, 22, 45, 46, 53, 58], "np": [4, 15, 17, 55, 58], "batch_simul": 4, "batchsimul": [4, 58], "n_job": [4, 16, 18, 32, 55, 58], "param_valu": 4, "none": [4, 6, 15, 16, 18, 21, 22, 23, 24, 25, 27, 28, 29, 30, 31, 32, 33, 34, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 58], "set": [4, 5, 8, 11, 13, 16, 17, 18, 21, 23, 27, 29, 38, 43, 45, 52, 53, 55, 56, 58], "instanc": [4, 21, 22, 23, 24, 25, 26, 27, 29, 30, 31, 34, 35, 36, 37, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54, 58], "option": [4, 16, 18, 21, 23, 25, 27, 31, 33, 38, 44, 45, 46, 50, 54, 55, 58], "If": [4, 16, 20, 21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 51, 52, 53, 54], "new": [4, 5, 15, 18, 20, 22, 23, 26, 27, 39, 42, 48, 49, 51, 55], "creat": [4, 5, 15, 16, 17, 18, 20, 21, 22, 23, 27, 29, 35, 38, 39, 42, 48, 49, 51, 56, 58], "specifi": [4, 5, 6, 8, 9, 20, 21, 22, 23, 28, 32, 33, 38, 41, 48, 55, 58], "type": [4, 6, 16, 17, 20, 21, 22, 23, 28, 34, 37, 48, 49, 55, 56, 58], "weight_basket": 4, "weight_pyr": 4, "add": [4, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 23, 27, 28, 29, 51, 54, 55, 58], "evprox": [4, 5, 16, 18, 22, 48], "grid": [4, 8, 21, 23, 29], "param_grid": 4, "logspac": 4, "4": [3, 4, 5, 6, 8, 15, 17, 18, 29, 30], "calcul": [4, 6, 8, 18, 22, 23, 25, 27, 50, 56, 58], "summari": 4, "statist": [4, 56], "summary_func": 4, "min": 4, "max": [4, 18], "peak": [4, 15], "list": [4, 5, 8, 14, 16, 21, 22, 23, 25, 26, 27, 28, 31, 32, 33, 34, 37, 38, 40, 41, 44, 45, 46, 47, 48, 49, 50, 52, 54, 58], "contain": [4, 11, 13, 15, 21, 22, 23, 25, 26, 27, 36, 37, 54, 56, 58], "return": [4, 5, 15, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 52, 55, 58], "summary_stat": 4, "dpl_data": 4, "dpl": [4, 5, 6, 7, 8, 9, 14, 16, 17, 18, 25, 26, 28, 32, 33, 35, 38, 44, 47, 50, 55, 58], "min_peak": 4, "max_peak": 4, "append": [4, 22, 23], "collect": [4, 22, 37, 54], "comment": [4, 52], "off": [4, 53, 58], "dask": 4, "distribut": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 23, 24, 53, 54, 55, 56, 58], "packag": [4, 7, 9, 16, 18, 20, 53], "instal": [4, 9, 18, 25, 55], "client": 4, "threads_per_work": 4, "n_worker": 4, "process": [4, 9, 18, 20, 23, 33, 55, 56, 58], "simulation_result": 4, "combin": [4, 16, 17, 18], "multiprocess": 4, "print": [4, 5, 6, 8, 15, 16, 17, 55], "multiprocessingbackend": 4, "concurr": 4, "worker": 4, "done": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 25, 55], "elaps": [4, 18], "29": [4, 6, 10, 18], "9": [3, 4, 6, 18, 25], "001242556683917088": 4, "004900589999999999": 4, "03665290820701789": 4, "02352069470140582": 4, "038695414756536456": 4, "022995093327209466": 4, "03373821891133495": 4, "03047248131934011": 4, "re": [4, 17, 23, 52, 56], "figur": [4, 5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 22, 23, 25, 27, 31, 39, 40, 42, 43, 44, 45, 46, 47, 48, 49, 50, 58], "label": [4, 18, 25, 44, 45, 46, 47, 58], "xlabel": [4, 6, 18], "index": [4, 6, 14, 21, 22, 23, 39, 40, 43, 48, 49, 54, 56, 58], "ylabel": [4, 6, 18], "magnitud": 4, "titl": [4, 6, 20], "across": [4, 6, 9, 16, 18, 22, 23, 25, 34, 44, 47, 48, 51, 55, 56, 58], "tight_layout": [4, 7, 8, 14], "total": [4, 5, 6, 7, 8, 9, 10, 12, 14, 15, 16, 17, 18, 19, 25, 57], "script": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 53, 56], "minut": [4, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "612": [4, 10], "plot_batch_simul": [4, 10, 57], "sphinx_gallery_thumbnail_numb": [5, 8, 16, 17, 18], "To": [5, 6, 7, 8, 14, 15, 16, 17, 18, 20, 23, 25, 27, 28, 44, 46, 50, 53, 55, 56], "explor": [5, 40, 58], "chang": [5, 7, 8, 14, 15, 20, 21, 23, 24, 40, 56], "instanti": [5, 7, 15, 18, 23, 24, 29, 30, 56, 58], "note": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 20, 21, 23, 24, 25, 27, 29, 30, 34, 38, 40, 47, 53, 55, 56], "add_drives_from_param": [5, 23, 24, 29, 30, 58], "predefin": 5, "without": [5, 9, 14, 15, 16, 18, 20, 23, 27, 32, 56, 58], "shown": [5, 20, 40, 52, 53], "previous": [5, 20, 58], "net_erp": [5, 15], "come": 5, "reflect": [5, 15, 25, 52, 58], "canon": 5, "neocort": [5, 15, 17, 18, 24, 52, 53], "microcircuit": 5, "detail": [5, 6, 7, 8, 11, 13, 14, 16, 17, 18, 20, 24, 52, 53, 56], "everi": [5, 21, 23, 41, 55], "cell": [5, 6, 7, 8, 14, 15, 16, 17, 18, 22, 23, 24, 25, 27, 28, 29, 30, 32, 33, 34, 37, 38, 40, 41, 42, 48, 49, 51, 53, 56, 58], "visual": [5, 7, 8, 11, 13, 14, 16, 18, 28, 39, 40, 43, 58], "plot_connectivity_weight": 5, "plot_cell_connect": [5, 58], "search": [5, 21, 34, 58], "pick_connect": [5, 58], "indic": [5, 21, 23, 34, 41, 58], "provid": [5, 11, 13, 15, 16, 22, 23, 25, 27, 28, 34, 36, 44, 46, 48, 50, 51, 52, 53, 56, 58], "viz": [3, 5, 7, 14, 15, 16, 17, 18, 28], "plot_connectivity_matrix": [5, 58], "len": 5, "conn_indic": [5, 34], "src_gid": [5, 23, 34, 40, 54, 58], "target_gid": [5, 23, 34, 54, 58], "loc": [5, 15, 21, 23, 34, 54], "soma": [5, 6, 8, 15, 21, 23, 24, 34, 38, 41, 51, 58], "receptor": [5, 15, 16, 21, 23, 34, 54], "gabaa": [5, 15, 17, 23, 30, 34], "conn_idx": [5, 40, 43], "here": [5, 6, 14, 18], "pop": 5, "method": [5, 7, 8, 14, 16, 18, 21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 38, 39, 45, 47, 54, 56, 58], "sampl": [5, 8, 18, 22, 23, 25, 27, 45, 46, 54, 58], "random": [5, 9, 14, 23, 54, 58], "element": [5, 21, 22, 23, 27, 28, 40, 41, 48, 52], "copi": [5, 14, 15, 16, 20, 21, 23, 25, 27, 58], "38": [5, 6, 18], "count": [5, 15], "35": [5, 6, 15, 24], "src": [5, 15, 18, 23, 54], "target": [2, 5, 15, 21, 23, 31, 34, 40, 54, 58], "probabl": [5, 15, 23, 28, 54, 58], "025": [5, 15, 38], "delai": [5, 15, 23, 39, 54, 58], "lamtha": [5, 15, 21, 23, 54], "70": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "dure": [5, 8, 15, 23, 55, 56, 58], "store": [5, 6, 8, 21, 23, 24, 29, 30, 54, 58], "under": [5, 8, 23, 52, 58], "spike": [5, 6, 8, 9, 14, 15, 16, 17, 18, 21, 22, 23, 37, 48, 49, 53, 54, 58], "activ": [5, 6, 8, 14, 15, 17, 18, 22, 23, 27, 37, 39, 48, 49, 52, 55, 56, 58], "after": [5, 8, 11, 13, 15, 17, 18, 20, 27, 29, 53, 55, 58], "plot_spikes_rast": [5, 6, 8, 15, 17, 18, 22, 58], "dpl_erp": 5, "170": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "joblib": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 53, 56, 58], "trial": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 22, 23, 25, 27, 28, 32, 33, 37, 38, 39, 48, 49, 50, 53, 55, 58], "over": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 22, 23, 25, 26, 33, 47, 52, 56, 58], "job": [5, 6, 7, 8, 14, 15, 16, 17, 18, 32], "build": [5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 21, 24, 56, 58], "neuron": [5, 6, 7, 8, 9, 14, 15, 16, 17, 21, 22, 23, 24, 27, 34, 53, 54, 55, 56, 58], "m": [5, 6, 7, 8, 9, 11, 13, 14, 15, 16, 17, 18, 20, 21, 23, 25, 27, 32, 33, 38, 45, 46, 47, 52, 54], "50": [3, 5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 27, 28, 39, 46, 58], "60": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18, 28], "90": [5, 6, 7, 8, 9, 14, 15, 16, 17, 18], "110": [5, 6, 7, 8, 9, 14, 15, 16, 17], "130": [5, 6, 7, 8, 9, 14, 15, 16, 17], "140": [5, 6, 7, 8, 9, 14, 15, 16, 17], "150": [5, 6, 7, 8, 9, 14, 15, 16, 17, 21, 28, 41], "160": [5, 6, 7, 8, 9, 14, 15, 16, 17], "size": [5, 6, 7, 8, 9, 15, 16, 17, 18, 21, 23, 28], "640x480": [5, 6, 7, 8, 9, 16, 17], "also": [5, 6, 7, 20, 22, 23, 27, 46, 48, 52, 53, 55, 56, 58], "our": [5, 11, 13, 14, 15, 16, 17, 18, 20, 52, 53, 56], "own": [5, 8, 20], "test": [5, 28, 52, 53, 55, 56, 58], "effect": [5, 14, 15, 17, 18, 23], "clear_connect": [5, 23], "clear": [5, 17, 23, 28, 56], "all": [5, 6, 7, 11, 13, 14, 15, 16, 17, 20, 21, 22, 23, 28, 29, 33, 34, 38, 40, 43, 44, 48, 49, 52, 53, 54, 55, 56, 57, 58], "By": [5, 8, 15, 17, 24, 25, 44, 58], "default": [5, 6, 7, 8, 15, 16, 17, 18, 21, 22, 23, 25, 27, 29, 30, 31, 33, 38, 39, 40, 41, 43, 44, 45, 46, 47, 48, 50, 53, 54, 55, 58], "retain": [5, 23], "remov": [5, 6, 15, 23, 30, 52, 53, 58], "clear_driv": [5, 23, 58], "add_connect": [5, 23, 58], "custom": [5, 9, 16, 58], "between": [5, 8, 15, 17, 20, 21, 23, 27, 29, 30, 33, 39, 52, 54, 55, 56, 58], "l5": [5, 8, 14, 15, 16, 17, 24, 25, 26, 29, 30, 44, 47, 50, 58], "pyramid": [5, 6, 8, 14, 15, 17, 21, 23, 24, 25, 29, 30, 34, 56], "l2": [5, 8, 14, 15, 16, 25, 26, 29, 30, 34, 44, 47, 50, 58], "basket": [5, 15, 17, 29, 58], "either": [5, 55, 58], "name": [5, 18, 20, 21, 22, 23, 25, 27, 33, 40, 43, 48, 50, 54, 56], "id": [5, 6, 18, 21, 22, 37, 40, 51], "gid": [5, 6, 21, 22, 23, 34, 51, 58], "directli": [5, 53, 56, 58], "get_network": 5, "ampa": [5, 6, 14, 15, 16, 23, 34, 54], "conn_se": [5, 23, 54, 58], "3": [5, 6, 7, 8, 14, 15, 16, 17, 18, 21, 23, 27, 29, 30, 41, 53, 54], "net_al": 5, "dpl_all": 5, "addition": [5, 6, 56], "argument": [5, 22, 23, 34, 48, 58], "spars": 5, "instead": [5, 16, 20, 25, 38, 58], "try": [5, 16, 17, 18], "same": [5, 6, 8, 17, 18, 22, 23, 26, 28, 48, 55, 58], "chanc": 5, "other": [5, 6, 20, 23, 51, 52, 53, 55, 56, 58], "net_spars": 5, "dpl_spars": 5, "With": 5, "previou": [5, 15, 23, 27], "appear": [5, 40], "synchron": [5, 16, 17, 18, 23, 58], "rhythmic": [1, 5, 11, 23, 29, 31, 38, 47, 57, 58], "period": [5, 14, 17, 52], "visibl": 5, "vertic": 5, "line": [5, 23, 25, 27, 47, 52, 53, 55, 56], "sever": [5, 15, 18, 30, 56, 58], "simultan": [5, 14, 15, 53, 56], "produc": [5, 6, 7, 14, 21, 23, 25, 52], "more": [5, 6, 7, 11, 13, 17, 18, 20, 24, 52, 53, 55, 56, 58], "popul": [5, 17, 23, 55, 58], "sparsiti": 5, "addit": [5, 8, 15, 20, 22, 30, 48, 52, 56], "decai": [5, 17, 21], "distanc": [5, 8, 21, 23, 24, 27, 58], "In": [5, 8, 18, 20, 52, 55, 56], "still": [5, 56], "smaller": [5, 14, 18, 40, 56], "As": [5, 23, 52, 56], "step": [5, 8, 14, 15, 17, 18, 20, 28, 32, 33, 38, 56], "see": [5, 7, 8, 15, 16, 18, 20, 21, 22, 23, 24, 25, 27, 48, 53, 54, 55, 56], "impact": [5, 56], "aggreg": [5, 8, 16, 18, 22, 25, 49], "plot_dipol": [5, 14, 15, 16, 58], "constrained_layout": [5, 6, 14, 15, 16, 17, 18], "window_len": [5, 8, 14, 16, 25, 27], "scaling_factor": [5, 16, 17], "spike_typ": [5, 6, 16, 18, 22, 48], "evdist": [5, 16, 18, 22, 48], "600x600": [5, 16, 17, 18], "24": [5, 6, 10, 18], "217": [5, 6, 10], "plot_connect": [5, 10, 57], "inspect": [6, 14, 15, 58], "tempfil": [6, 16], "read_spik": [6, 58], "have": [6, 8, 20, 21, 34, 41, 52, 53, 54, 56, 58], "doe": [6, 23, 53], "ani": [6, 22, 23, 34, 48, 52, 53, 54, 55, 58], "input": [6, 15, 16, 18, 21, 22, 23, 26, 35, 37, 48, 52, 54, 58], "onli": [6, 14, 15, 16, 17, 18, 23, 25, 34, 38, 53, 55, 56, 58], "ahead": 6, "nmda": [6, 15, 16, 23, 30, 34, 54, 58], "normal": [6, 9, 14, 18, 20], "certain": [6, 20], "mean": [6, 15, 22, 23, 58], "standard": [6, 9, 14, 18, 23, 27, 46], "deviat": [6, 9, 14, 23], "006562": [6, 16], "7e": 6, "142300": [6, 16], "019482": [6, 16], "004317": [6, 16], "080074": [6, 16], "63": [6, 16, 18], "53": [6, 15, 16, 18], "85": [6, 16, 18, 21], "event_se": [6, 9, 14, 15, 16, 17, 18, 23, 54, 58], "274": [6, 15, 16], "reason": 6, "call": [6, 20, 25, 33, 58], "resembl": [6, 18, 25, 47], "two": [6, 8, 15, 16, 21, 29, 46, 52, 55, 58], "up": [6, 7, 8, 18, 25, 47, 55, 56, 58], "dendrit": [6, 8, 14, 15, 21, 23, 24, 27, 30, 34, 51], "down": [6, 8, 54], "neg": [6, 18, 58], "deflect": [6, 18], "08831": [6, 16], "01525": [6, 16], "19934": [6, 16], "00865": [6, 16], "synaptic_delays_prox": [6, 16], "zero": [6, 15, 16, 18, 23, 25, 50], "pass": [6, 15, 16, 18, 22, 23, 25, 33, 34, 45, 46, 47, 48, 55, 58], "explicitli": [6, 15, 16, 18, 22, 58], "26": [6, 16], "61": [6, 16, 18], "47": [6, 16, 18, 19], "544": [6, 15, 16], "dynam": [6, 8, 15, 16, 18, 20, 23, 24, 53, 54, 56], "somat": [6, 30, 38, 58], "voltag": [6, 7, 21, 22, 23, 27, 38, 39, 46, 54, 58], "enabl": [6, 20, 21, 23, 29, 44, 53, 54, 56, 58], "000003": [6, 16], "438840": [6, 16], "008958": [6, 16], "684013": [6, 16], "omit": [6, 15, 16, 17, 18, 23], "137": [6, 16], "12": [6, 16, 17, 18], "8": [3, 6, 7, 8, 9, 16, 18, 20, 53, 58], "33": [6, 16, 18], "814": [6, 15, 16, 58], "record_vsec": [6, 7, 21, 38, 54, 58], "explain": [6, 18], "about": [6, 20, 52, 54], "structur": [6, 7, 18, 21, 23, 56], "thei": [6, 20, 52, 53], "better": [6, 7, 18, 53], "interpret": [6, 18, 53, 56], "uniqu": [6, 9, 14, 21, 22, 23, 27, 51, 53, 54, 56, 58], "gid_rang": [6, 22, 23, 37, 54], "ordereddict": 6, "135": [6, 8, 15], "270": [6, 9, 14, 15, 23], "505": 6, "775": 6, "1045": 6, "section": [6, 7, 15, 21, 22, 23, 38, 41, 52, 53, 58], "cellrespons": [6, 23, 37, 48, 49, 55, 58], "individu": [6, 21, 22, 41, 48, 52, 56, 58], "includ": [6, 11, 13, 14, 16, 22, 25, 30, 33, 34, 39, 40, 43, 45, 47, 48, 50, 52, 55, 56, 58], "trial_idx": [6, 8, 9, 14, 16, 17, 22, 39, 48, 49], "vsec": [6, 21, 22, 54, 58], "kei": [6, 15, 20, 21, 22, 23, 25, 37, 40, 41, 48, 52, 54, 58], "dict_kei": [6, 15], "7": [6, 10, 15, 16, 17, 18, 25, 50, 53, 55], "11": [3, 6, 18], "13": [6, 17, 18, 25, 27, 44, 46, 50, 57], "14": [6, 18], "15": [3, 6, 14, 15], "16": [6, 15, 18], "17": [6, 18], "18": [6, 18], "19": [3, 6, 18, 19, 24], "21": [3, 6, 9, 10, 18], "22": [6, 18], "23": 6, "25": [6, 8, 14, 15, 18], "27": [6, 16, 18], "28": [6, 18], "31": [6, 18], "32": [6, 18, 30], "34": [6, 14, 18, 19], "36": [6, 18], "37": 6, "39": [6, 18, 21], "41": [6, 8, 10, 18], "42": [6, 18], "43": 6, "44": [6, 18, 58], "45": [3, 6, 7, 15, 18], "46": 6, "48": [6, 18], "49": [6, 18], "51": [6, 18], "52": [6, 18], "54": 6, "55": [3, 6, 18], "56": [6, 18], "57": [6, 15, 19], "59": [6, 16, 18, 19], "62": [6, 18], "64": [6, 18], "65": [6, 17, 18], "66": [6, 18], "67": [6, 18], "68": [6, 18], "69": [6, 18], "71": [6, 18], "72": [6, 8, 18], "73": [6, 18], "74": [6, 18], "75": [6, 15, 18], "76": [6, 18], "77": [6, 18, 58], "78": [6, 18], "79": [6, 18, 58], "81": [6, 18], "82": [6, 18], "83": [6, 14, 18], "84": [6, 18], "86": [6, 18, 58], "87": [6, 18], "88": [6, 18], "89": [6, 18], "91": [6, 18], "92": [6, 18, 53], "93": [6, 18], "94": [6, 18], "95": [6, 18], "96": [6, 18, 28, 58], "97": [6, 18], "98": [6, 18, 58], "99": [6, 18], "101": 6, "102": [6, 8, 14, 15, 29, 58], "103": [6, 8], "104": [6, 56], "105": [6, 58], "106": 6, "107": 6, "108": 6, "109": 6, "111": [6, 18, 56], "112": [6, 18], "113": 6, "114": 6, "115": 6, "116": 6, "117": 6, "118": [6, 14], "119": 6, "121": 6, "122": 6, "123": 6, "124": [6, 56], "125": [6, 15], "126": 6, "127": 6, "128": 6, "129": [6, 56], "131": 6, "132": 6, "133": 6, "134": [6, 18], "136": 6, "138": 6, "139": 6, "141": 6, "142": 6, "143": [6, 58], "144": 6, "145": [6, 58], "146": [6, 58], "147": 6, "148": 6, "149": 6, "151": 6, "152": 6, "153": [6, 14, 19], "154": 6, "155": [6, 58], "156": [6, 58], "157": [6, 58], "158": 6, "159": 6, "161": [6, 17, 18, 19], "162": [6, 58], "163": 6, "164": 6, "165": 6, "166": 6, "167": 6, "168": 6, "169": 6, "171": [6, 58], "172": 6, "173": 6, "174": 6, "175": 6, "176": 6, "177": 6, "178": 6, "179": 6, "180": [6, 9, 14, 15, 17], "181": 6, "182": 6, "183": 6, "184": 6, "185": 6, "186": 6, "187": 6, "188": [6, 58], "189": [6, 18], "190": [6, 9, 14, 15, 17, 19, 58], "191": [6, 58], "192": 6, "193": 6, "194": 6, "195": 6, "196": 6, "197": 6, "198": 6, "199": [6, 58], "200": [6, 9, 14, 15, 17, 21, 27, 28, 31, 39, 46], "201": 6, "202": 6, "203": 6, "204": [6, 18, 58], "205": 6, "206": 6, "207": [6, 58], "208": 6, "209": [6, 58], "210": [6, 9, 14, 15, 17], "211": 6, "212": [6, 8, 10], "213": 6, "214": 6, "215": 6, "216": 6, "218": 6, "219": 6, "220": [6, 9, 14, 15, 17], "221": [6, 58], "222": 6, "223": 6, "224": 6, "225": [6, 7], "226": 6, "227": 6, "228": 6, "229": 6, "230": [6, 9, 14, 15, 17], "231": [6, 58], "232": 6, "233": 6, "234": 6, "235": [6, 16, 19], "236": 6, "237": 6, "238": 6, "239": 6, "240": [6, 9, 14, 15, 17], "241": 6, "242": [6, 18], "243": 6, "244": 6, "245": 6, "246": [6, 18, 19], "247": 6, "248": 6, "249": 6, "250": [6, 9, 14, 15, 17, 21, 41], "251": 6, "252": 6, "253": 6, "254": 6, "255": 6, "256": 6, "257": 6, "258": 6, "259": 6, "260": [6, 9, 14, 15], "261": 6, "262": 6, "263": 6, "264": [6, 58], "265": 6, "266": [6, 18], "267": 6, "268": 6, "269": 6, "d": [6, 15, 18, 20, 22, 55], "gid_to_typ": [6, 23], "mv": [6, 21, 39], "write": [6, 22, 23, 25, 55, 58], "them": [6, 16, 20, 23, 33, 52, 56], "text": [6, 15], "file": [6, 9, 10, 12, 16, 17, 18, 19, 20, 22, 23, 25, 28, 29, 35, 36, 37, 38, 56, 57, 58], "format": [6, 18, 22, 23, 54, 58], "syntax": 6, "filenam": [6, 39, 58], "written": [6, 55], "spk_1": 6, "spk_2": 6, "read": [6, 16, 17, 18, 20, 23, 28, 35, 36, 37, 38, 53, 55, 58], "back": [6, 17, 20, 55], "wildcard": [6, 37], "express": [6, 37], "temporarydirectori": 6, "tmp_dir_nam": 6, "spk_": [6, 22, 37], "home": [6, 7, 8, 9, 14, 16, 18], "circleci": [6, 7, 8, 9, 14, 16, 18, 20], "project": [6, 8, 14, 15, 18, 55], "howto": [6, 8, 10, 57], "plot_firing_pattern": [6, 10, 57], "deprecationwarn": 6, "deprec": [6, 23, 29, 56, 58], "futur": [6, 23, 29, 52, 56], "version": [6, 18, 20, 53, 55, 56, 58], "pleas": [6, 20, 51, 53], "save": [6, 23, 54, 58], "along": [6, 8, 24, 27, 53, 56], "tmp": 6, "tmph4ypzpfi": 6, "spk_0": 6, "rate": [6, 8, 22, 23, 27, 58], "class": [6, 7, 9, 21, 22, 23, 25, 27, 28, 31, 32, 33, 35, 39, 56, 58], "window": [6, 8, 14, 18, 21, 25, 27, 28, 31, 39, 41, 47, 53, 56], "tstart": [3, 6, 9, 14, 15, 22, 23], "all_rat": 6, "mean_rat": [6, 22], "mean_typ": [6, 22], "trial_rat": 6, "243697478991596": 6, "705882352941176": 6, "126050420168063": 6, "176470588235297": 6, "raster": [6, 8, 15, 16], "histogram": [6, 15, 16, 18, 22, 48, 58], "idx": [6, 23], "per": [6, 22, 25, 39, 50], "g": [6, 15, 16, 17, 20, 21, 22, 23, 25, 27, 30, 37, 46, 48, 50, 54, 56, 58], "r": [6, 8, 14, 15, 16, 17, 18, 21, 22, 27, 29, 41, 45, 48, 58], "500x700": 6, "868": [6, 10], "ll": [7, 8, 14, 17, 20], "necessari": [7, 15, 20, 52], "modul": [7, 8, 11, 13, 14, 19, 20, 23, 29, 30, 56, 57], "would": [7, 18, 52, 55], "like": [7, 15, 20, 22, 25, 27, 45, 46, 56], "read_param": [7, 17, 58], "network_model": [7, 8], "add_erp_drives_to_jones_model": [7, 8], "begin": [7, 15, 20, 21, 23, 55, 56], "For": [7, 8, 9, 18, 20, 23, 24, 25, 34, 52, 53, 54, 55], "reduc": [7, 15, 18, 55, 58], "speed": [7, 8, 20], "mesh_shap": [7, 23, 24, 29, 30], "move": 7, "further": [7, 51, 52, 53, 56], "apart": [7, 8, 9, 14], "inplane_dist": [7, 8, 21, 23], "\u00b5m": 7, "set_cell_posit": [7, 8, 23, 29, 58], "300": [3, 7, 9, 14, 15, 39], "networkplott": [7, 58], "3d": [7, 18, 21, 39, 40, 41, 43], "net_plot": 7, "miniconda": [7, 9, 16], "env": [7, 9, 16], "testenv": [7, 9, 16], "lib": [7, 9, 16, 55], "python3": [7, 9, 16], "site": [7, 9, 16], "959": 7, "userwarn": [7, 8, 14, 55], "layout": [7, 8, 14, 28], "ha": [7, 8, 14, 15, 20, 21, 23, 25, 54, 55, 56, 58], "tight": [7, 8, 14], "anoth": [7, 15, 33], "angl": 7, "adjust": [7, 18, 20, 25, 29, 39, 40, 43, 45, 50, 58], "azimuth": [7, 39], "elev": [7, 39], "azim": [7, 39], "next": [7, 14, 15, 20, 23, 27], "event": [7, 8, 11, 13, 14, 15, 18, 19, 23, 30, 52, 53, 54, 57, 58], "relat": [7, 8, 9, 11, 13, 15, 19, 28, 52, 53, 56, 57, 58], "erp": [7, 8, 11, 13, 18, 19, 30, 53, 56, 57], "membran": [7, 8, 21, 23, 27, 54, 56], "turn": [7, 58], "reiniti": 7, "plotter": 7, "export_movi": [7, 39], "xyz": 7, "limit": [7, 18, 21, 23, 25, 27, 31, 39, 41, 50, 52, 56], "xlim": [7, 18, 21, 39, 41], "400": [7, 15], "1600": 7, "ylim": [7, 21, 39, 41], "zlim": [7, 21, 39, 41], "500": [7, 39], "animation_demo": 7, "gif": 7, "dpi": [7, 28, 39], "fp": [7, 39], "interv": [7, 39], "funcanim": 7, "0x7f7fef2fdb80": 7, "965": [7, 10], "plot_hnn_anim": [7, 10, 57], "main": [8, 56], "output": [8, 18, 22, 23, 25, 28, 29, 55, 58], "e": [8, 14, 16, 17, 18, 20, 21, 22, 23, 25, 27, 37, 46, 50, 52, 54, 56, 58], "intracellular": 8, "flow": [8, 18], "apic": [8, 15, 21], "At": [8, 18, 55], "eeg": [8, 11, 13, 18, 52, 53, 56], "sensor": [8, 11, 13, 19, 56, 57], "primari": [8, 18, 53, 56], "contributor": [8, 20, 53, 55], "measur": [8, 23, 27, 53, 56], "field": [8, 18, 27, 53, 56, 58], "close": [8, 53], "lfp": [8, 45, 53, 58], "result": [8, 14, 17, 23, 30, 32, 33, 52, 53, 58], "leak": 8, "medium": 8, "through": [8, 11, 13, 22, 48, 52, 56, 58], "passiv": 8, "channel": [8, 15, 18, 24, 30, 45, 52, 58], "simplifi": 8, "assumpt": 8, "approxim": [8, 14, 18, 23, 25, 27, 54], "virtual": [8, 52, 53], "electrod": [8, 23, 27, 46, 54, 58], "place": [8, 14, 16, 17, 20, 25, 27, 58], "around": 8, "christoph": [8, 14, 16, 17, 58], "bailei": [8, 14, 16, 17, 58], "cjb": [8, 16], "cfin": [8, 16], "au": [8, 16], "dk": [8, 16], "mainakja": [8, 18], "jone": [8, 14, 15, 16, 17, 18, 24, 29, 30, 58], "et": [8, 14, 15, 16, 24, 29, 30, 53, 56], "al": [8, 14, 15, 16, 24, 29, 30, 53, 56], "2009": [8, 14, 15, 24, 29, 30], "consist": [8, 9, 14, 15, 20, 33, 54, 58], "squar": [8, 21, 23, 29, 40], "plane": [8, 21, 23, 29, 58], "influenc": [8, 15, 17], "moment": [8, 16, 17, 18, 23, 25, 58], "space": [8, 9, 11, 13, 14, 19, 21, 23, 41, 56, 57], "um": [8, 21, 23, 27, 29, 54], "three": [8, 15, 20, 56], "requir": [8, 16, 17, 18, 20, 23, 53, 55, 56], "posit": [8, 15, 18, 21, 23, 27, 41, 54], "It": [8, 15, 21, 40, 55], "decid": [8, 52], "placement": 8, "plot_cel": [8, 16, 23, 58], "within": [8, 14, 18, 23, 56], "arrang": [8, 23, 29], "regular": [8, 17, 18, 52, 58], "align": [8, 21], "z": [8, 21, 23, 27, 39, 41, 54, 58], "axi": [8, 21, 22, 23, 25, 27, 31, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "linear": [8, 20, 56], "multielectrod": 8, "arrai": [8, 22, 23, 25, 27, 45, 46, 50, 52, 58], "intercontact": 8, "x": [8, 21, 23, 25, 27, 39, 41, 45, 54], "y": [8, 21, 23, 27, 39, 41, 54, 55, 58], "coordin": [8, 18, 21, 23, 27, 54], "triplet": 8, "extend": [8, 23, 27, 56], "2000": 8, "resid": 8, "1300": [8, 28], "2300": 8, "center": [8, 23, 27], "constant": [8, 15, 17, 23, 30, 43, 58], "conduct": [8, 15, 23, 24, 27, 54, 58], "point": [8, 18, 22, 23, 27, 29, 39, 54, 55, 58], "add_electrode_arrai": [8, 23, 27, 58], "depth": [8, 18, 58], "325": 8, "2150": 8, "electrode_po": [8, 23], "dep": 8, "shank1": 8, "rec_arrai": [8, 23, 27, 54, 58], "electrodearrai": 8, "comput": [8, 16, 17, 18, 20, 26, 51, 53, 56, 58], "resourc": [8, 56], "thu": [8, 18, 25, 53], "slightli": 8, "slow": 8, "consider": 8, "extracellulararrai": [8, 23, 58], "psa": [8, 23, 27], "yet": [8, 21, 54], "both": [8, 16, 20, 56, 58], "trace": [8, 14, 18, 25, 27, 44, 46, 50], "decim": [8, 25, 27, 39, 44, 46, 50], "factor": [8, 14, 18, 23, 25, 27, 31, 39, 44, 46, 50], "khz": 8, "appli": [8, 14, 17, 18, 23, 25, 27, 29, 32, 33, 38, 44, 45, 46, 47, 50, 54, 56, 58], "significantli": 8, "40k": 8, "8k": 8, "2k": 8, "gridspec_kw": 8, "height_ratio": 8, "seri": [8, 18, 27, 46], "its": [8, 17, 18, 23, 52, 53, 56], "comparison": [8, 14, 15, 16], "plot_lfp": [8, 27, 58], "major": [8, 15, 52, 56], "set_xlabel": 8, "csd": [8, 27, 45, 53, 58], "bottom": 8, "plot_csd": [8, 27, 58], "plot_record_extracellular_potenti": [8, 10, 57], "quantit": [8, 14, 15, 29], "biophys": [8, 14, 15, 16, 18, 29, 52, 53, 56, 58], "neural": [8, 14, 15, 16, 18, 24, 29, 53, 56], "meg": [8, 11, 13, 14, 15, 19, 29, 52, 53, 56, 57], "rhythm": [8, 11, 13, 15, 19, 29, 53, 56, 57], "rhythmogenesi": [8, 14, 15, 29], "sensori": [8, 14, 15, 29, 56], "j": [8, 14, 15, 16, 18, 29], "neurophysiol": [8, 14], "3554": [8, 14, 15, 29], "3572": [8, 14, 15, 29], "kajikawa": 8, "schroeder": 8, "c": [8, 15, 18, 20, 53, 55], "847": 8, "858": 8, "2011": 8, "even": [9, 51, 53], "singl": [9, 14, 17, 18, 28, 34, 52, 53, 56, 58], "you": [9, 11, 13, 14, 16, 17, 18, 20, 23, 25, 27, 51, 53, 55], "softwar": [9, 18, 52, 53, 56], "want": [9, 16, 18, 20, 52, 53], "configur": [9, 17, 18, 23, 28, 58], "blake": [9, 16, 58], "caldwel": [9, 16, 18, 58], "blake_caldwel": [9, 16], "alpha": [3, 9, 11, 13, 17, 18, 19, 53, 57], "hz": [3, 9, 14, 15, 17, 18, 22, 23, 25, 47], "bursti": [9, 14, 23, 40, 54], "continu": [9, 14, 22, 52, 53, 55, 56], "burst": [9, 14, 23], "pair": [9, 14, 23, 54], "occurr": [9, 14, 23], "jitter": [9, 14, 23, 58], "amount": [9, 14, 27, 46], "repeat": [9, 14, 20, 58], "train": [9, 14, 23, 54, 58], "4e": [3, 9, 14], "add_bursty_dr": [3, 9, 14, 15, 16, 23, 58], "burst_rat": [3, 9, 14, 15, 23], "burst_std": [3, 9, 14, 15, 23], "spike_isi": [3, 9, 14, 15, 23], "n_drive_cel": [3, 9, 14, 15, 16, 18, 23, 54, 58], "278": 9, "processor": [9, 55], "launcher": [9, 33], "openmpi": [9, 33, 53, 55], "system": [9, 11, 13, 53, 55], "310": [9, 14, 15], "sequenti": [9, 28, 53, 56], "numproc": [9, 55], "mechan": [9, 15, 16, 17, 20, 21, 24, 30, 54, 56], "mod": [9, 16, 20, 21, 54], "x86_64": [9, 16], "libnrnmech": [9, 16], "280": [9, 14, 15], "290": [9, 14, 15], "527": [9, 10], "plot_simulate_mpi_backend": [9, 10, 57], "401": 10, "execut": [10, 12, 19, 33, 53, 55, 57], "auto_exampl": [10, 12, 19, 56], "mem": [10, 12, 19, 57], "mb": [10, 12, 18, 19, 57], "00": [10, 12, 18, 19, 57], "000": [10, 12, 18, 57], "workflow": [11, 13, 14, 16, 17, 18, 19, 20, 56, 57, 58], "commonli": [11, 13, 53, 56], "studi": [11, 13, 16, 18, 30, 53, 56], "signal": [3, 11, 13, 14, 17, 18, 52, 53, 55, 56], "low": [11, 13, 17, 52, 53, 56], "frequenc": [3, 11, 13, 14, 15, 17, 18, 25, 31, 47, 50, 53, 56, 58], "beta": [3, 11, 13, 17, 19, 30, 53, 57], "gamma": [11, 13, 19, 53, 57], "band": [3, 11, 13, 18, 31], "gui": [11, 13, 14, 16, 17, 23, 29, 58], "websit": [11, 13, 52, 56], "reproduc": [11, 13, 15, 18, 30, 56, 58], "subset": [11, 13, 23, 58], "elabor": [11, 13], "strongli": [11, 13], "recommend": [11, 13, 14, 16, 17, 18, 20, 23, 25, 27, 44, 46, 50, 52, 53], "background": [11, 13, 18, 39, 52], "inform": [11, 13, 15, 20, 23, 53, 54, 58], "instruct": [11, 13, 20, 53], "clearer": [11, 13], "prior": [11, 13, 14, 18, 56, 58], "public": [11, 13, 15, 18, 53], "investig": [11, 13, 56], "brain": [11, 13, 18, 24, 53, 56], "somatosensori": [11, 13, 18], "help": [11, 13, 15, 18, 20, 53, 56], "get": [11, 13, 16, 18, 23, 53, 54, 55], "auto_examples_python": 11, "auto_examples_jupyt": 11, "n": [12, 15, 18], "A": [12, 15, 21, 23, 25, 26, 27, 28, 31, 33, 46, 51, 52, 53, 55, 56, 58], "complex": [14, 56], "si": 14, "tutori": [14, 16, 17, 18], "review": [14, 16, 17, 20, 52], "below": [14, 16, 17, 20, 54, 55], "recreat": [14, 16, 17], "similar": [14, 15, 17, 20, 23, 56], "albeit": [14, 16], "spectrogram": 14, "sam": [14, 16, 17], "neymotin": [14, 15, 16, 17, 18], "samnemo": [14, 16, 17], "cj": [14, 17], "excit": [14, 17], "synaps": [14, 15, 17, 21, 23, 34, 54, 58], "weights_ampa_p": [3, 14, 18], "syn_delays_p": [3, 14], "alpha_prox": [3, 14], "284": 14, "automat": [14, 22, 27, 45, 53, 58], "choos": [14, 56], "emul": 14, "larger": [14, 18, 52], "patch": [14, 18], "cortex": [14, 15, 18, 27, 30], "simpl": [14, 25, 44, 53, 55], "0x7f7ff43d7df0": 14, "oper": [14, 16, 18, 25, 27, 28, 34, 52], "alter": [14, 15, 25, 27], "insid": [14, 16, 25, 50], "summat": 14, "greater": [14, 23, 52], "volum": [14, 23, 27], "confirm": [14, 17], "what": [14, 15, 16, 33], "inde": 14, "power": [3, 14, 25, 47, 50, 58], "spectral": [3, 14, 25, 47, 58], "densiti": [3, 14, 25, 27, 45, 47, 53, 56, 58], "psd": [3, 14, 25, 47], "plot_psd": [3, 14, 17, 25, 58], "tmin": [14, 15, 17, 18, 25, 27, 44, 46, 47, 50, 58], "tmax": [14, 18, 25, 27, 44, 46, 47, 50, 58], "exclud": 14, "burn": 14, "make": [14, 16, 53, 55, 56, 58], "befor": [14, 16, 17, 20, 23, 38, 52, 53, 55, 56, 58], "order": [14, 18, 25, 55], "compar": [14, 15, 17, 20, 53, 55, 56], "convolv": [14, 25, 27], "long": [14, 15, 56], "ham": [14, 18, 25, 27, 47], "dpl_smooth": 14, "overlai": 14, "onc": [14, 20, 21, 52, 53, 55, 56], "b": [14, 15, 18, 21, 22, 27, 41, 45, 48], "set_xlim": 14, "399": [14, 58], "fmin": [14, 17, 25, 47], "fmax": [3, 14, 17, 25, 47], "1e3": [14, 18], "set_xscal": 14, "log": [14, 20, 28], "plot_simulate_alpha": [14, 19, 57], "spread": [14, 33], "arriv": [14, 15, 52], "opposit": 14, "tend": 14, "known": 14, "weights_ampa_d": [3, 14, 18], "syn_delays_d": [3, 14], "alpha_dist": [3, 14], "296": 14, "verifi": [14, 55], "wa": [14, 15, 18, 33, 56, 58], "most": [14, 15, 18, 25, 47, 53, 56], "recent": [14, 56], "domin": [14, 17], "shift": 14, "abov": [14, 15, 17, 52, 53], "lead": [14, 15, 17, 18, 22, 23, 48], "absolut": 14, "again": [14, 52], "smooth_dpl": 14, "plot_": 14, "avail": [14, 18, 23, 55, 56], "prestimulu": 15, "law": [15, 30], "2021": [15, 30, 56], "modif": [15, 58], "transient": [15, 30], "neocortex": 15, "suppress": 15, "percept": [15, 30], "incom": 15, "law_2021_model": [15, 58], "describ": [15, 23, 29, 30, 53, 54], "One": [15, 27], "signific": [3, 15], "substanti": [15, 52, 56], "increas": [15, 17, 20, 30], "rise": [15, 21], "fall": 15, "gabab": [15, 23, 30, 34], "calcium": [15, 21, 22, 24, 30, 38, 56, 58], "basal": [15, 30], "properti": [15, 27, 28, 54, 58], "cell_typ": [15, 16, 17, 23, 54, 58], "attribut": [15, 21, 22, 23, 25, 27, 28, 32, 33, 39, 41, 54, 58], "geometri": 15, "net_jon": 15, "jones_ris": 15, "tau1": [15, 21, 54], "law_ris": 15, "f": [15, 55], "jones_fal": 15, "tau2": [15, 17, 21, 54], "law_fal": 15, "apical_1": 15, "mech": [15, 54], "nbasal": 15, "ca": [15, 21, 22, 58], "miss": [15, 51, 58], "basal_1": 15, "hh2": 15, "cad": 15, "kca": 15, "km": 15, "cat": 15, "martinotti": 15, "recurr": 15, "tuft": 15, "inhibit": [15, 30], "remain": [15, 18, 52], "replac": [15, 30, 58], "nconnect": 15, "0002": 15, "001": [15, 18], "depress": 15, "consid": [15, 18, 20, 25, 27, 51, 52], "case": [15, 20, 52, 56, 58], "tactil": [15, 16, 18, 30], "stimulu": [15, 18], "deliv": 15, "later": [15, 23, 54], "cortic": [15, 16, 18, 51], "column": [15, 23, 25, 37, 51, 54, 56, 58], "direct": [15, 16, 24, 51, 52, 58], "thalam": [15, 51, 56], "nuclei": [15, 51], "repres": [15, 18, 23, 25, 26, 54, 56], "indirect": [15, 51], "late": [15, 18], "due": [15, 17, 23, 58], "add_erp_dr": 15, "stimulus_start": 15, "0005": [15, 18], "004": [15, 18], "syn_delays_d1": 15, "002": [15, 18], "0011": 15, "syn_delays_prox": 15, "nb": [15, 16, 23, 25, 29], "005": 15, "induc": 15, "just": [15, 21, 38, 58], "strong": [15, 17], "enough": 15, "caus": [15, 55, 58], "mediat": 15, "ultim": [15, 56], "detect": [15, 16, 18, 21, 33], "add_beta_dr": 15, "beta_start": 15, "00032": 15, "00008": 15, "00004": 15, "beta_dist": 15, "tstart_std": [15, 23], "00002": 15, "syn_delays_p1": 15, "beta_prox": 15, "distinct": 15, "net_beta": 15, "net_beta_erp": 15, "And": 15, "been": [15, 20, 25, 56, 58], "observ": [15, 16, 17, 18], "cours": [15, 17, 18, 20, 25, 47, 50], "dpls_beta": 15, "dpls_erp": 15, "dpls_beta_erp": 15, "320": 15, "330": [15, 58], "340": 15, "350": [15, 58], "360": 15, "370": [15, 58], "380": 15, "390": 15, "occur": [15, 18, 22, 23], "exclus": [15, 58], "gaussian": [15, 23, 54, 58], "sustain": 15, "pyrmaid": 15, "asymmetr": 15, "tail": 15, "set_titl": 15, "fix": [15, 17, 20, 23, 25, 50, 52, 58], "tile": [15, 17], "freq": [15, 17, 25, 50], "arang": [15, 17], "plot_tfr_morlet": [15, 17, 25, 58], "n_cycl": [15, 17, 25, 50], "700x700": 15, "happen": [15, 16], "when": [15, 16, 20, 23, 28, 29, 33, 44, 52, 53, 56, 58], "hand": 15, "roughli": 15, "understand": [15, 18], "stimuli": 15, "associ": [15, 18, 23, 45, 46, 56, 58], "amplitud": [15, 16, 17, 18, 21, 23, 54, 58], "puglies": [15, 58], "shin": 15, "h": [15, 21, 32, 33, 38, 54, 55], "sliva": 15, "lee": [15, 17], "moor": [15, 18], "thalamocort": [15, 30, 53], "regul": [15, 30], "relationship": [15, 30], "human": [15, 17, 18, 24, 30, 52, 53, 56], "biorxiv": 15, "440210": 15, "doi": [15, 18, 27, 53, 56], "org": [15, 18, 27, 39, 53, 56], "1101": 15, "pritchett": [15, 18], "l": [15, 18, 21, 54], "sikora": 15, "stufflebeam": [15, 18], "h\u00e4m\u00e4l\u00e4inen": [15, 18], "journal": [15, 16, 29, 53], "neurophysiologi": [15, 29, 53], "1152": [15, 27], "jn": [15, 27], "00535": 15, "silberberg": 15, "markram": 15, "2007": [15, 16, 18], "disynapt": 15, "735": 15, "746": [15, 58], "1016": 15, "012": 15, "394": [15, 19], "plot_simulate_beta": [15, 19, 57], "threshold": [16, 17, 21, 23, 54], "level": [16, 52, 53, 56], "neurosci": [16, 17, 18, 51], "mmja": 16, "plot_morphologi": [16, 21, 58], "axes3d": [16, 21, 23, 39, 40, 41, 42, 43], "extern": [16, 23, 56, 58], "prescrib": 16, "separ": [16, 23, 25, 29, 50, 55, 56, 58], "possibl": [16, 23, 25, 38, 50, 52], "click": [16, 40], "link": [16, 17, 20], "document": [16, 52, 56, 58], "add_poisson_dr": [16, 17, 23, 58], "000007": 16, "could": [16, 28, 33, 56], "equal": [16, 27, 56], "joblibbackend": [16, 18, 33, 55, 58], "rather": [16, 18, 56], "explicit": [16, 18, 20], "analyz": 16, "contribut": [16, 18, 23, 52, 54, 56], "featur": [16, 20, 52, 53, 56, 58], "averag": [16, 18, 22, 25, 26, 44, 47, 50, 58], "exogen": [16, 17, 18, 51, 54, 56], "achiev": [16, 25, 27, 44, 46, 50], "cell_specif": [16, 18, 23, 54, 58], "ad": [16, 20, 23, 27, 28, 29, 58], "net_sync": 16, "interrog": [16, 53], "external_dr": [16, 23, 54, 58], "dpls_sync": 16, "alwai": 16, "look": [16, 17, 20, 55], "conjunct": 16, "avoid": [16, 20, 23, 27, 55], "misinterpret": 16, "seed": [16, 23, 54, 58], "draw": 16, "conclus": 16, "stephani": [16, 29, 58], "correl": [16, 18], "magnetoencephalographi": [16, 18, 53], "10751": [16, 18], "10764": [16, 18], "plot_simulate_evok": [16, 19, 53, 57], "establish": 17, "interneuron": 17, "weak": 17, "params_fnam": [17, 18, 28, 36], "gamma_l5weak_l2weak": 17, "json": [17, 18, 23, 29, 36, 58], "gbar_l": 17, "gbar_l2basket_l2basket": 17, "gbar_l2basket_l2pyr_gabaa": 17, "007": 17, "gbar_l2basket_l2pyr_gabab": 17, "gbar_l2basket_l5pyr": 17, "gbar_l2pyr_l2basket": 17, "0012": 17, "gbar_l2pyr_l2pyr_ampa": 17, "gbar_l2pyr_l2pyr_nmda": 17, "gbar_l2pyr_l5basket": 17, "gbar_l2pyr_l5pyr": 17, "gbar_l5basket_l5basket": 17, "0075": 17, "gbar_l5basket_l5pyr_gabaa": 17, "08": [1, 11, 17, 18, 19, 29, 31, 38, 47, 57], "gbar_l5basket_l5pyr_gabab": 17, "gbar_l5pyr_l5basket": 17, "00091": 17, "gbar_l5pyr_l5pyr_ampa": 17, "gbar_l5pyr_l5pyr_nmda": 17, "tonic": [17, 21, 22, 23, 48, 54, 58], "poisson": [17, 22, 23, 40, 48, 58], "0008": 17, "rate_const": [17, 23, 58], "1349": 17, "30000": 17, "respond": 17, "while": [17, 20, 52, 53], "rel": [17, 23], "displai": [17, 25, 28, 58], "vari": [17, 53], "fraction": 17, "reach": [17, 52], "oscil": 17, "represent": [17, 18, 21, 25, 50, 54, 58], "togeth": [17, 55], "steadi": 17, "state": [17, 21, 58], "henc": [17, 18, 20], "pick": [17, 18], "bia": [17, 21, 23, 58], "notic": 17, "less": [17, 58], "nois": [17, 18], "fact": [17, 51], "depolar": 17, "entir": [17, 20, 21, 25, 39, 41, 47, 50, 53], "durat": [17, 25, 47], "add_tonic_bia": [17, 23, 58], "nearli": 17, "inhibitori": [17, 29, 34, 56], "latenc": 17, "ipsp": 17, "onto": 17, "bring": 17, "ping": 17, "sometim": 17, "although": 17, "mechanist": [17, 53], "decreas": [17, 24, 30], "shorten": 17, "refactori": 17, "distinguish": [17, 52], "laminar": [17, 27, 45, 46, 56, 58], "frontier": 17, "2013": 17, "plot_simulate_gamma": [17, 19, 57], "invers": [18, 23, 56], "solut": 18, "median": [18, 56], "nerv": [18, 56], "s1": 18, "mne": [18, 25, 55, 56, 58], "dataset": [18, 56], "expound": 18, "came": 18, "sequenc": [18, 55, 56], "implement": [18, 20], "those": [18, 23, 52, 56], "who": [18, 52, 56], "articul": 18, "present": [18, 22, 23, 27, 29, 33, 34, 48], "part": [18, 55], "motiv": 18, "nibabel": 18, "pip": [18, 20, 53, 55, 56], "somato": 18, "minimum_norm": 18, "apply_invers": 18, "make_inverse_oper": 18, "subject": [18, 52, 56], "data_path": 18, "raw_fnam": 18, "sub": [18, 52, 58], "_task": 18, "_meg": 18, "fif": 18, "fwd_fname": 18, "deriv": 18, "fwd": 18, "subjects_dir": 18, "freesurf": 18, "mne_data": 18, "tar": 18, "gz": 18, "osf": 18, "io": [18, 56], "tp4sg": 18, "611m": 18, "08m": 18, "8mb": 18, "6m": 18, "9mb": 18, "8m": 18, "3mb": 18, "2m": 18, "4mb": 18, "5m": 18, "5mb": 18, "6mb": 18, "0m": 18, "3m": 18, "0mb": 18, "7mb": 18, "106m": 18, "115m": 18, "125m": 18, "134m": 18, "1mb": 18, "144m": 18, "153m": 18, "163m": 18, "172m": 18, "182m": 18, "191m": 18, "201m": 18, "210m": 18, "220m": 18, "229m": 18, "239m": 18, "248m": 18, "258m": 18, "267m": 18, "277m": 18, "286m": 18, "296m": 18, "305m": 18, "315m": 18, "324m": 18, "334m": 18, "2mb": 18, "343m": 18, "352m": 18, "359m": 18, "367m": 18, "373m": 18, "379m": 18, "388m": 18, "396m": 18, "405m": 18, "412m": 18, "420m": 18, "429m": 18, "437m": 18, "445m": 18, "453m": 18, "459m": 18, "466m": 18, "473m": 18, "481m": 18, "491m": 18, "500m": 18, "510m": 18, "519m": 18, "528m": 18, "537m": 18, "546m": 18, "554m": 18, "563m": 18, "572m": 18, "581m": 18, "590m": 18, "599m": 18, "607m": 18, "78tb": 18, "untar": 18, "content": [18, 20], "attempt": [18, 33], "complet": [18, 20, 55, 56], "582": 18, "estim": [18, 27, 45], "filter": [18, 25, 27, 58], "read_raw_fif": 18, "preload": 18, "l_freq": 18, "h_freq": [18, 25], "identifi": [18, 21, 23, 34, 54, 56], "find_ev": 18, "stim_channel": 18, "sti": 18, "014": 18, "epoch": 18, "event_id": 18, "baselin": [18, 56], "reject": 18, "grad": 18, "4000e": 18, "eog": 18, "350e": 18, "read_forward_solut": 18, "cov": 18, "compute_covari": 18, "inv": 18, "info": [18, 54], "open": [18, 20, 51, 52, 53, 55, 56], "01_task": 18, "somato_meg": 18, "237600": 18, "506999": 18, "791": 18, "1688": 18, "sec": 18, "readi": [18, 20, 55], "269399": 18, "897": 18, "077": 18, "contigu": 18, "segment": [18, 21, 23, 27], "fir": [18, 25], "design": [18, 52, 53, 56], "phase": 18, "non": [18, 23, 53, 55, 56, 58], "causal": 18, "bandpass": 18, "domain": [18, 56], "firwin": 18, "0194": 18, "passband": 18, "rippl": 18, "db": 18, "stopband": 18, "attenu": 18, "edg": 18, "transit": 18, "bandwidth": 18, "cutoff": [18, 25], "length": [18, 21, 25, 27, 31, 54, 55], "993": 18, "307": 18, "287": 18, "found": [18, 20, 39, 58], "stim": 18, "Not": [18, 23], "metadata": 18, "No": 18, "correct": [18, 52, 53], "item": [18, 34, 58], "bad": 18, "drop": 18, "forward": 18, "desir": 18, "matrix": [18, 43], "kind": 18, "3523": 18, "8155": 18, "306": 18, "free": [18, 20], "orient": [18, 53], "transform": [18, 56], "frame": [18, 39], "rank": [18, 55, 58], "toler": 18, "5e": 18, "2e": 18, "ep": 18, "dim": 18, "singular": 18, "mag": 18, "projector": 18, "plot_simulate_somato": [18, 19, 57], "runtimewarn": 18, "someth": 18, "went": 18, "wrong": 18, "driven": 18, "exce": [18, 58], "theoret": 18, "auto": 18, "integ": [18, 21, 25, 27, 44, 46, 50], "covari": 18, "empir": [18, 56], "12432": 18, "convert": [18, 20, 21, 27, 56, 58], "surfac": 18, "emploi": [18, 56], "rotat": 18, "out": [18, 55], "select": [18, 20, 28, 40, 58], "planar": 18, "7615": 18, "004172": 18, "17919e": 18, "exp": [18, 23], "loos": 18, "whiten": 18, "small": 18, "eigenvalu": 18, "pca": 18, "svd": 18, "largest": 18, "42284": 18, "86104e": 18, "nchan": 18, "nzero": 18, "There": [18, 33, 53, 56], "reconstruct": 18, "wherea": 18, "offer": 18, "techniqu": 18, "best": [18, 20, 56], "howev": [18, 20, 25, 47], "assum": [18, 23, 27], "pick_ori": 18, "appropri": [18, 52], "snr": 18, "lambda2": 18, "stc": 18, "return_residu": 18, "verbos": 18, "prepar": 18, "nave": [18, 25], "invert": 18, "vector": [18, 25], "eigenlead": 18, "residu": 18, "varianc": 18, "extract": [18, 55], "postcentr": 18, "gyru": 18, "hemi": 18, "rh": 18, "label_tag": 18, "g_postcentr": 18, "label_s1": 18, "read_labels_from_annot": 18, "parc": 18, "aparc": 18, "a2009": 18, "regexp": 18, "parcel": 18, "annot": [18, 58], "geometr": 18, "mri": 18, "framework": [18, 20, 56], "upward": 18, "deep": 18, "superfici": 18, "downward": 18, "respect": [18, 58], "uncom": 18, "interact": [18, 40, 52, 53, 56, 58], "render": [18, 20, 28, 44], "pyvista": 18, "librari": 18, "should": [18, 20, 21, 23, 27, 52, 53, 55, 58], "central": 18, "040": 18, "imag": [18, 25, 50, 53], "get_brain_class": 18, "brain_label": 18, "white": 18, "add_label": 18, "stc_label": 18, "in_label": 18, "view_layout": 18, "horizont": 18, "initial_tim": 18, "nbrain": 18, "nbrain_label": 18, "nstc_label": 18, "region": [18, 51], "mode": [18, 58], "pca_flip": 18, "promin": 18, "compon": [3, 18, 26, 56, 58], "posterior": 18, "wall": 18, "sulcu": 18, "sinc": [18, 25], "dipolar": 18, "travel": 18, "flip_data": 18, "extract_label_time_cours": 18, "dipole_tc": 18, "1e9": 18, "ro": 18, "nam": [18, 25, 58], "axhlin": 18, "k": [18, 25, 44], "n20": 18, "average_dipol": [18, 58], "implic": 18, "earli": 18, "0036": 18, "0039": 18, "0019": 18, "0020": 18, "weights_nmda_p": 18, "0029": 18, "0030": 18, "276": [18, 58], "003": 18, "0043": 18, "0032": 18, "0009": 18, "weights_nmda_d": 18, "0051": 18, "0010": 18, "synaptic_delays_d": 18, "277": 18, "0041": 18, "0018": 18, "0017": 18, "evdist2": 18, "275": 18, "noisier": 18, "accur": [18, 24, 58], "macroscop": 18, "dpl_smooth_win": 18, "dpl_scalefctr": 18, "_nolegend_": 18, "set_ylabel": 18, "sa": 18, "daniel": [18, 58], "mcdougal": 18, "ra": [18, 21, 54], "carneval": 18, "nt": 18, "ci": [18, 55, 58], "hine": 18, "ml": 18, "sr": 18, "neurosolv": [18, 24, 52, 53], "tool": [18, 52, 53, 56], "cellular": [18, 20, 52, 53, 56], "elif": [18, 56], "e51214": 18, "2020": [18, 56], "7554": [18, 56], "51214": 18, "guid": [20, 52, 53], "until": [20, 54], "welcom": [20, 53], "form": [20, 21, 23, 27, 52], "piec": 20, "bug": [20, 52], "properli": [20, 28], "doc": 20, "incorpor": 20, "branch": 20, "few": [20, 53], "book": 20, "page": [20, 52, 53], "typic": [20, 55], "made": [20, 23, 34, 52, 56], "fork": 20, "repositori": [20, 52, 53, 56], "usual": [20, 27, 46], "clone": [20, 58], "person": 20, "push": 20, "github": [20, 52, 53, 56], "share": [20, 52], "upstream": 20, "codebas": [20, 52], "offici": 20, "remot": 20, "url": 20, "usernam": 20, "account": [20, 53, 56], "button": [20, 28], "top": [20, 27, 46], "right": [20, 40, 52], "corner": [20, 27, 46], "On": 20, "termin": [20, 33, 55], "cd": [20, 55], "check": [20, 33, 53, 58], "correctli": 20, "v": [20, 53], "fetch": 20, "exist": [20, 23, 28, 58], "cool_featur": 20, "checkout": 20, "relev": [20, 23, 34, 52, 56], "commit": [20, 52], "stage": 20, "area": [20, 56], "ensur": [20, 52, 55, 56], "statu": [20, 28, 52], "messag": [20, 53, 55, 58], "tip": 20, "merg": [20, 52], "prefix": 20, "mrg": 20, "flag": 20, "dev": [20, 55], "setup": [20, 58], "build_mod": 20, "extra": [20, 28], "access": [20, 28, 56, 58], "perform": [20, 56], "last": [20, 25, 28, 39], "compil": 20, "rebuilt": 20, "command": [20, 28, 33, 53, 55, 56], "pytest": [20, 55], "simpli": [20, 53], "skip": [20, 55], "mpi4pi": [20, 33, 53, 55], "highli": 20, "encourag": [20, 52], "suit": 20, "whether": [20, 23, 54], "html": [20, 39, 56], "given": [20, 23, 25, 38, 50, 53], "rst": 20, "whats_new": 20, "credit": [20, 55], "releas": [20, 23, 29, 56], "conflict": 20, "built": [20, 52, 56], "noplot": 20, "view": [20, 39, 56], "histori": 20, "therefor": [20, 54], "resolv": [20, 52], "articl": 20, "delet": 20, "easiest": 20, "approach": [20, 52, 56], "editor": [20, 53], "frequent": 20, "awar": 20, "being": [20, 55, 56, 58], "face": 20, "difficult": 20, "easier": 20, "squash": 20, "action": [20, 21, 51], "circl": 20, "autom": 20, "cach": 20, "don": 20, "t": [20, 55, 58], "worri": 20, "But": 20, "rebuild": 20, "build_cach": 20, "md5": 20, "monoton": 20, "v2": 20, "v3": 20, "po": [21, 41, 54], "sect_loc": [21, 23, 54], "cell_tre": [21, 54], "str": [21, 22, 23, 25, 27, 28, 29, 33, 34, 35, 36, 37, 39, 40, 41, 43, 44, 45, 46, 47, 48, 50, 54], "int": [21, 22, 23, 25, 27, 28, 29, 32, 33, 34, 38, 39, 40, 41, 43, 44, 46, 48, 49, 50, 54, 58], "global": [21, 51], "n_cell": [21, 23, 54], "cannot": [21, 52, 58], "tree": [21, 54, 56], "root": 21, "node": 21, "sec_nam": 21, "node_po": 21, "adjac": 21, "parent": 21, "children": 21, "section_soma": 21, "diam": [21, 54], "cm": [21, 27, 54], "end_pt": [21, 54], "nest": 21, "parametr": 21, "morphologi": [21, 39, 41, 58], "insert": [21, 54], "dipole_pp": [21, 54], "record_vsoma": [21, 54], "isec": [21, 22, 54, 58], "soma_gabaa": [21, 54], "soma_gabab": [21, 54], "etc": [21, 22, 23, 27, 37, 38, 40, 52, 54, 55, 56], "record_isec": [21, 38, 54, 58], "record_isoma": [21, 54], "speicifc": 21, "concentr": [21, 22, 38], "record_ca": [21, 38, 58], "tonic_bias": [21, 54], "iclamp": [21, 54], "clamp": [21, 23, 54], "bias": [21, 23, 54, 58], "assign": [21, 23, 51, 54, 58], "__repr__": [21, 22, 23, 27, 31], "repr": [21, 22, 23, 27, 31], "self": [21, 22, 23, 27, 31], "sec_name_ap": 21, "applic": [21, 56], "belong": [21, 58], "create_tonic_bia": [21, 58], "t0": [21, 23, 54], "float": [21, 22, 23, 25, 27, 31, 32, 33, 38, 39, 41, 44, 45, 46, 47, 50, 54, 58], "define_shap": 21, "redefin": 21, "accord": [21, 22, 23, 49, 54, 58], "subtre": 21, "distance_sect": 21, "target_sec_nam": 21, "curr_nod": 21, "find": 21, "string": [21, 22, 27, 36, 46, 48, 55, 58], "mid": 21, "modify_sect": [21, 58], "micron": [21, 54], "diamet": [21, 23, 27, 54], "capacit": [21, 54], "farad": [21, 54], "axial": [21, 54], "resist": [21, 54], "ohm": [21, 54], "leav": 21, "parconnect_from_src": 21, "gid_presyn": 21, "nc_dict": [21, 54], "postsyn": 21, "centric": 21, "presyn": 21, "TO": 21, "presynapt": 21, "pos_src": 21, "a_weight": 21, "a_delai": 21, "exp2syn": 21, "postsynapt": 21, "nc": 21, "netcon": 21, "1200": [21, 41], "ex": [21, 22, 40, 41, 48], "apical_trunk": [21, 41], "bool": [21, 22, 23, 25, 27, 28, 29, 31, 32, 33, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50, 54], "handl": [21, 22, 23, 25, 27, 31, 33, 40, 41, 42, 43, 44, 45, 46, 47, 48, 50], "setup_source_netcon": 21, "_pc": 21, "syn_creat": 21, "secloc": 21, "nrn": 21, "revers": [21, 23], "syn": [21, 54], "kinet": 21, "scheme": 21, "to_dict": [21, 22, 23, 27], "spike_tim": 22, "spike_gid": 22, "cell_type_nam": 22, "n_spike": 22, "shape": [22, 23, 25, 27, 29, 45, 46, 58], "outer": 22, "inner": 22, "stamp": 22, "vsoma": 22, "isoma": 22, "n_time": [22, 25, 27, 45, 46], "reset": [22, 58], "empti": [22, 58], "update_typ": 22, "updat": [3, 22, 25, 52, 56, 58], "fname": [22, 23, 25, 35, 37, 39], "__getitem__": [], "gid_item": [], "slice": 27, "stop": [22, 28, 32, 33, 38, 54, 58], "spike_r": 22, "kwargs_hist": [22, 48], "valid": [22, 23, 33, 34, 40, 48, 58], "group": [22, 23, 48, 58], "otherwis": [22, 23, 48], "charact": [22, 48], "ev": [22, 48], "equival": [22, 23, 34, 48], "cycl": [22, 23, 25, 48, 50, 58], "keyword": [22, 23, 48], "hist": [22, 48], "legacy_mod": [23, 24, 29, 30, 58], "construct": [23, 28, 29, 56, 58], "mainli": [23, 29], "backward": [23, 29], "compat": [23, 29, 56], "suitabl": [23, 29], "Will": [23, 27, 28, 29, 33, 45], "n_x": [23, 29], "n_y": [23, 29], "ignor": 23, "real": [23, 58], "templat": [23, 58], "artifici": [23, 51, 54, 58], "categori": 23, "272": 23, "542": 23, "pos_dict": [23, 42, 54], "external_bias": [23, 54], "somata": 23, "space_const": [23, 54], "apical_tuft": 23, "cyclic": 23, "doublet": 23, "isi": 23, "independ": [23, 54, 58], "denot": 23, "dispers": [23, 54], "map": [23, 58], "physic": [23, 52], "xy": 23, "randomli": 23, "allow_autaps": [23, 54], "itself": [23, 54], "gid_pair": [23, 40, 54], "min_dist": [23, 27], "infinit": [23, 27], "homogen": [23, 27], "conductor": [23, 27], "treat": [23, 27], "junction": [23, 27], "lsa": [23, 27], "flank": [23, 27], "numer": [23, 27], "error": [23, 27, 53, 55, 58], "minimum": [23, 25, 27, 47, 58], "contact": [23, 27, 45, 46], "act": [23, 27], "behavior": 23, "increment": [23, 55], "exact": [23, 25], "lambda": 23, "renew": 23, "suppli": 23, "intrins": 23, "iter": [23, 58], "net_copi": 23, "lookup": 23, "layer_separ": 23, "impli": 23, "affect": [23, 38], "write_configur": 23, "overwrit": [23, 25], "hierarch": 23, "hdf5": [23, 25, 35, 54, 58], "boolean": 23, "throw": [23, 53], "alreadi": [23, 53, 58], "yield": 23, "improv": [24, 56, 58], "kohl": [24, 58], "topragr": 24, "2022": [24, 30], "biolog": [24, 52], "introduc": [24, 58], "maximum": [24, 25, 47], "gbar": 24, "linearli": 24, "refer": [24, 25, 29, 30, 51, 53, 58], "carmen": [24, 58], "underli": [24, 53, 56], "auditori": 24, "reveal": 24, "topographi": 24, "timecours": 25, "1e": 25, "amper": [25, 53, 56], "meter": [25, 53, 56], "n_layer": 25, "dipl": 25, "sfreq": [25, 27], "scale_appli": 25, "dpl_copi": 25, "rgba": [25, 27, 44, 46], "black": [25, 39, 40, 44], "periodogram": [25, 47], "scipi": [25, 27, 44, 46, 47, 50, 53], "welch": [25, 47], "nyquist": [25, 47], "pad": [25, 50], "colormap": [25, 39, 40, 43, 46, 50, 58], "inferno": [25, 50], "colorbar": [25, 27, 39, 40, 43, 45, 50], "colorbar_insid": [25, 50], "morlet": [25, 50, 58], "tfr_array_morlet": 25, "interest": [25, 50, 52], "millisecond": [25, 50], "higher": [25, 27, 31, 44, 46, 50], "success": [25, 27, 44, 46, 50], "beyond": [25, 50], "mirror": [25, 50], "viridi": [25, 39, 40, 50], "put": [25, 28, 50], "heatmap": [25, 50], "savgol_filt": [25, 58], "savitzki": [25, 58], "golai": [25, 58], "prefer": [25, 27, 38], "high": [25, 56], "polynomi": 25, "iir": 25, "determin": [25, 40, 52], "5th": 25, "multipli": 25, "convolut": [25, 27], "member": [26, 52], "precomput": 27, "n_electrod": 27, "tabl": [27, 52], "00122": 27, "2010": 27, "rat": 27, "array_copi": 27, "vmin": [27, 39, 45], "vmax": [27, 39, 45], "interpol": [27, 45, 58], "spline": [27, 45], "sink": [27, 45, 58], "red": [27, 40, 45], "smoothen": [27, 45, 58], "trial_no": 27, "contact_no": 27, "cividi": [27, 46], "voltage_offset": [27, 46], "voltage_scalebar": [27, 46], "overlaid": 27, "offset": [27, 46, 58], "listedcolormap": [27, 46], "quadruplet": [27, 46], "height": [27, 28, 46], "uv": [27, 46], "bar": [27, 28, 43, 46], "left": [27, 28, 40, 46], "extracellular_copi": 27, "theme_color": 28, "8a2be2": 28, "total_height": 28, "800": 28, "total_width": 28, "header_height": 28, "button_height": 28, "operation_box_height": 28, "drive_widget_width": 28, "left_sidebar_width": 28, "576": 28, "log_window_height": 28, "status_height": 28, "theme": 28, "whole": [28, 55], "dashboard": 28, "pixel": 28, "width": 28, "header": 28, "box": 28, "sidebad": 28, "screen": 28, "style": 28, "simulation_data": 28, "widget_tstop": 28, "widget": [28, 58], "widget_dt": 28, "widget_ntri": 28, "control": [28, 58], "widget_backend_select": 28, "widget_viz_layout_select": 28, "widget_mpi_cmd": 28, "widget_n_job": 28, "multi": [28, 56], "widget_drive_type_select": 28, "widget_location_select": 28, "add_drive_button": 28, "clickabl": 28, "run_button": 28, "trigger": 28, "load_button": 28, "receiv": [28, 33, 55], "upload": [28, 58], "delete_drive_button": 28, "plot_outputs_dict": 28, "panel": 28, "plot_dropdown_types_dict": 28, "dropdown": 28, "menu": 28, "drive_widget": 28, "drive_box": 28, "connectivity_textfield": 28, "add_logging_window_logg": 28, "analysis_config": 28, "everyth": [28, 53], "except": 28, "captur": 28, "extra_margin": 28, "screenshot": 28, "ifram": 28, "snapshot": 28, "margin": 28, "compos": [28, 29, 52], "return_layout": 28, "ipython": [28, 53], "easi": [28, 53, 58], "get_cell_parameters_dict": 28, "cell_parameters_dict": 28, "purpos": [28, 52], "static": 28, "load_paramet": 28, "run_notebook_cel": 28, "penultim": 28, "init": 28, "hit": 28, "twice": 28, "neurophi": 29, "1307": 29, "ratio": [3, 29], "expans": 30, "cereb": 30, "robert": 30, "cerebr": 30, "668": 30, "688": 30, "initial_net": 31, "solver": [31, 58], "cobyla": [], "obj_fun": [3, 31], "dipole_rms": 31, "dt": [32, 33, 38, 58], "postproc": [32, 33, 38, 58], "integr": [32, 33, 38, 56, 58], "cvode": [32, 33, 38], "postprocess": [32, 33, 58], "hyperthread": 33, "actual": [33, 58], "proc": [33, 55], "popen": [33, 55], "expected_data_length": 33, "sent": [33, 55], "proc_queu": 33, "thread": 33, "queue": [33, 55], "hold": 33, "safe": 33, "wai": [33, 38, 52, 53, 55], "\u00e5simul": 33, "logic": [34, 58], "OR": 34, "AND": 34, "file_cont": 36, "pars": 36, "pathnam": 37, "3rd": 37, "dipole_smooth_win": 38, "dipole_scalefctr": 38, "bg_color": 39, "voltage_colormap": 39, "3100": 39, "2200": 39, "time_idx": 39, "helper": 39, "viewpoint": [39, 52], "frame_start": 39, "frame_stop": 39, "writer": 39, "pillow": 39, "export": [39, 55], "movi": 39, "dot": 39, "inch": 39, "altern": [39, 55, 56], "stabl": [39, 56], "animation_api": 39, "cross": 40, "show_weight": 43, "grei": 43, "gradient": 43, "contact_label": [45, 46], "n_channel": 45, "set_yticklabel": [45, 46], "dimension": [46, 56], "n_contact": 46, "jetblu": 46, "definit": 51, "vocabulari": 51, "concept": 51, "think": 51, "term": 51, "issu": [51, 52, 53, 58], "pull": [51, 52], "anatom": [51, 53], "awai": 51, "extrins": 51, "often": 51, "excitatori": 51, "perturb": 51, "split": [51, 55], "closer": 51, "formal": [52, 53], "clarifi": 52, "variou": [52, 54], "commun": [52, 55, 56], "goal": 52, "hypothesi": 52, "research": [52, 53], "upon": 52, "principl": 52, "circuit": [52, 53, 56], "bridg": 52, "macroscal": [52, 56], "magneto": 52, "electro": 52, "encephalographi": 52, "foundat": [52, 56], "transpar": 52, "institut": 52, "neutral": 52, "aim": 52, "support": [52, 58], "collabor": 52, "acknowledg": 52, "divers": 52, "skill": 52, "scientif": [52, 53], "neuro": 52, "mind": 52, "advanc": [52, 56], "invit": 52, "anyon": 52, "particip": [52, 56], "philosophi": [52, 56], "pathwai": 52, "becom": 52, "deeper": 52, "engag": [52, 56], "talent": 52, "team": [52, 56], "toward": 52, "involv": [52, 58], "propos": 52, "onlin": 52, "discuss": [52, 53, 56], "among": [52, 56], "steer": 52, "outlin": [52, 55, 56], "concret": 52, "mani": 52, "submit": 52, "weekli": 52, "meet": 52, "email": 52, "hackathon": 52, "behalf": 52, "strive": 52, "barrier": 52, "dedic": [52, 58], "ongo": 52, "Being": 52, "easili": 52, "expect": [52, 55], "approv": 52, "host": 52, "qualiti": 52, "quantiti": 52, "elig": 52, "elect": 52, "consensu": 52, "extenu": 52, "circumst": 52, "revok": 52, "inact": 52, "year": 52, "reinstat": 52, "resum": 52, "membership": 52, "nomin": 52, "least": 52, "vote": 52, "third": 52, "strateg": 52, "plan": 52, "overal": 52, "basi": 52, "aspect": 52, "expertis": [52, 53], "effort": [52, 56], "attend": 52, "deem": 52, "scope": [52, 56], "vision": 52, "organ": [52, 56], "technic": 52, "servic": 52, "manag": [52, 58], "benefit": 52, "polici": 52, "inquir": 52, "grant": 52, "grace": 52, "former": 52, "retir": 52, "li": 52, "sole": 52, "seek": 52, "purview": 52, "minor": 52, "typo": 52, "sentenc": 52, "confid": 52, "agre": 52, "resolut": 52, "amongst": 52, "held": 52, "facilit": [52, 56], "guidanc": 52, "rais": 52, "taken": 52, "opportun": 52, "address": [52, 58], "logist": 52, "matter": 52, "yearli": 52, "revisit": 52, "draft": 52, "suggest": 52, "leaner": 53, "cleaner": 53, "clinician": 53, "conveni": 53, "modular": 53, "evalu": 53, "hypothes": [53, 56], "electroencephalographi": 53, "intracrani": 53, "electrocorticographi": 53, "ecog": 53, "electr": 53, "nano": 53, "precis": 53, "characterist": 53, "multimod": 53, "flexibl": [53, 56], "serv": 53, "visit": 53, "veri": 53, "ipywidget": [53, 56, 58], "voila": 53, "ipympl": 53, "ipykernel": 53, "scikit": 53, "learn": [53, 56], "platform": [53, 56], "psutil": [53, 55], "anaconda": 53, "tradit": 53, "unset": [53, 55], "pythonpath": 53, "pythonhom": 53, "becaus": 53, "environ": [53, 55], "ones": 53, "conda": [53, 55], "track": 53, "latest": 53, "develop": 53, "nightli": 53, "upgrad": 53, "repo": 53, "zipbal": 53, "fine": 53, "bayesian": [31, 53], "opt": 53, "tweak": 53, "zsh": 53, "maco": [53, 55], "usag": [53, 55], "cpu": [53, 55], "precompil": 53, "sure": 53, "encount": 53, "forum": 53, "block": [53, 55], "magic": 53, "manner": 53, "spyder": 53, "tracker": 53, "question": 53, "joss": 53, "2023": 53, "5848": 53, "21105": 53, "05848": 53, "broken": 54, "object_typ": 54, "n_pyr_x": 54, "nr": 54, "n_pyr_i": 54, "celsiu": 54, "temperatur": 54, "degre": 54, "co": 54, "ordint": 54, "cell_nam": 54, "tempor": 54, "whose": [3, 54], "target_typ": 54, "num_target": 54, "src_type": 54, "num_src": 54, "runtim": [55, 58], "embarrassingli": 55, "interfac": [55, 56, 58], "linux": 55, "sudo": 55, "apt": 55, "libopenmpi": 55, "bin": 55, "dyld_fallback_library_path": 55, "conda_prefix": 55, "shell": 55, "mkdir": 55, "p": 55, "deactiv": 55, "echo": 55, "old_dyld_fallback_library_path": 55, "env_var": 55, "sh": 55, "nrniv": 55, "hello": 55, "comm_world": 55, "get_rank": 55, "quit": 55, "2b7985ba": 55, "2019": 55, "duke": 55, "yale": 55, "bluebrain": 55, "copyright": 55, "1984": 55, "2018": 55, "launch": 55, "binari": 55, "subprocess": 55, "child": 55, "mpisimul": 55, "carri": 55, "stdin": 55, "base64": 55, "encod": 55, "pickl": 55, "mark": 55, "unpickl": 55, "stdout": 55, "stderr": 55, "consol": 55, "progress": 55, "warn": [55, 58], "send": 55, "byte": 55, "know": 55, "doesn": 55, "proccess": 55, "wait": 55, "exit": 55, "successfulli": 55, "decod": 55, "caller": 55, "flush": 55, "whenev": 55, "immedi": 55, "side": 55, "util": 55, "special": 55, "decor": 55, "conftest": 55, "failur": 55, "subsequ": 55, "fail": [55, 58], "generaliz": 56, "circuitri": 56, "am": 56, "friendli": 56, "teach": 56, "graphic": 56, "essenti": 56, "intuit": 56, "gain": 56, "chose": 56, "dive": 56, "utili": 56, "priorit": 56, "practic": 56, "interoper": 56, "netpyn": 56, "entail": 56, "reorgan": 56, "creation": [56, 58], "march": 56, "adopt": 56, "abil": [56, 58], "web": 56, "cli": 56, "extens": 56, "clean": [56, 58], "minim": 56, "pertain": 56, "spectra": 56, "lanalysi": 56, "feb": 56, "sep": 56, "gh": [56, 58], "expand": 56, "renam": 56, "predict": 56, "invas": 56, "fundament": 56, "profil": 56, "inher": 56, "difficulti": 56, "focuss": 56, "snpe": 56, "gon\u00e7alv": 56, "56261": 56, "adapt": 56, "sweep": 56, "architectur": 56, "hhn": 56, "amng": 56, "challeng": 56, "development": 56, "begun": 56, "bed": 56, "hnn2": 56, "multicompart": 56, "seamlessli": 56, "beamform": 56, "dual": 56, "metacel": 56, "ui": 56, "convers": [56, 58], "elimin": 56, "enhanc": 56, "advantag": 56, "meaning": 56, "rigor": 56, "quickli": 56, "motor": 56, "stimul": 56, "footnot": 56, "claim": 56, "understood": 56, "knowledg": 56, "591": [], "thrown": 58, "dylan": 58, "818": 58, "646": 58, "manual": 58, "640": 58, "678": 58, "v8": 58, "georg": 58, "dang": 58, "696": 58, "703": 58, "705": 58, "overlap": 58, "camilo": 58, "diaz": 58, "741": 58, "739": 58, "invalid": 58, "744": 58, "kwarg": 58, "732": 58, "pre": 58, "disabl": 58, "750": 58, "csv": 58, "753": 58, "rajat": 58, "partani": 58, "757": 58, "649": 58, "773": 58, "katharina": 58, "duecker": 58, "769": 58, "convert_to_json": 58, "legaci": 58, "772": 58, "capabl": 58, "782": 58, "754": 58, "806": 58, "815": 58, "inconsist": 58, "642": 58, "scalar": 58, "670": 58, "695": 58, "overwritten": 58, "795": 58, "isin": 58, "in1d": 58, "799": 58, "810": 58, "812": 58, "644": 58, "648": 58, "constrain": 58, "pujol": 58, "_": 58, "652": 58, "766": 58, "which_driv": 58, "moham": 58, "sherif": 58, "478": 58, "mattan": 58, "pelah": 58, "492": 58, "481": 58, "419": 58, "checkpoint": 58, "too": 58, "546": 58, "orsolya": 58, "beatrix": 58, "kolozsvari": 58, "516": 58, "502": 58, "unweight": 58, "kaisu": 58, "lankinen": 58, "610": 58, "458": 58, "456": 58, "462": 58, "longer": 58, "446": 58, "472": 58, "huzi": 58, "cheng": 58, "475": 58, "did": 58, "515": 58, "runtimeerror": 58, "oversubscrib": 58, "session": 58, "545": 58, "559": 58, "611": 58, "614": 58, "606": 58, "479": 58, "calculate_csd2d": 58, "steven": 58, "brandt": 58, "517": 58, "619": 58, "conncetr": 58, "804": 58, "mostafa": 58, "khalil": 58, "publish": 58, "plot_cell_morphologi": 58, "319": 58, "hard": 58, "327": 58, "321": 58, "318": 58, "339": 58, "329": 58, "348": 58, "376": 58, "calcium_model": 58, "sarah": 58, "383": 58, "queri": 58, "367": 58, "conn": 58, "369": 58, "accept": 58, "416": 58, "round": 58, "reposit": 58, "314": 58, "common": 58, "swap": 58, "352": 58, "kenneth": 58, "loi": 58, "368": 58, "wasn": 58, "382": 58, "intend": 58, "397": 58, "421": 58, "l2pyr": 58, "l5pyr": 58, "l2basket": 58, "l5basket": 58, "favor": 58, "322": 58, "readabl": 58, "354": 58, "wherebi": 58, "372": 58, "add_xxx_driv": 58, "sync_within_tri": 58, "436": 58, "alex": 58, "rockhil": 58, "reader": 58, "plot_hist_input": 58, "feed": 58, "visualis": 58, "autaps": 58, "incorrectli": 58, "ident": 58, "samika": 58, "kanekar": 58, "context": 58, "behaviour": 58, "forc": 58, "fam": 58, "regardless": 58, "alpha_prox_weight": 3, "alpha_prox_tstart": 3, "alpha_prox_burst_r": 3, "alpha_prox_burst_std": 3, "alpha_dist_weight": 3, "alpha_dist_tstart": 3, "alpha_dist_burst_r": 3, "alpha_dist_burst_std": 3, "maximize_psd": [3, 31], "maxim": 3, "f_band": [3, 31], "relative_bandpow": [3, 31], "optimize_rhythm": [3, 57], "obj_fun_kwarg": 31, "673": 58, "intern": 58, "647": 58}, "objects": {"hnn_core": [[21, 0, 1, "", "Cell"], [22, 0, 1, "", "CellResponse"], [23, 0, 1, "", "Network"], [24, 2, 1, "", "calcium_model"], [29, 2, 1, "", "jones_2009_model"], [30, 2, 1, "", "law_2021_model"], [34, 2, 1, "", "pick_connection"], [35, 2, 1, "", "read_dipole"], [36, 2, 1, "", "read_params"], [37, 2, 1, "", "read_spikes"], [38, 2, 1, "", "simulate_dipole"]], "hnn_core.Cell": [[21, 1, 1, "", "__repr__"], [21, 1, 1, "", "build"], [21, 1, 1, "", "copy"], [21, 1, 1, "", "create_tonic_bias"], [21, 1, 1, "", "define_shape"], [21, 1, 1, "", "distance_section"], [21, 1, 1, "", "modify_section"], [21, 1, 1, "", "parconnect_from_src"], [21, 1, 1, "", "plot_morphology"], [21, 1, 1, "", "record"], [21, 1, 1, "", "setup_source_netcon"], [21, 1, 1, "", "syn_create"], [21, 1, 1, "", "to_dict"]], "hnn_core.CellResponse": [[22, 1, 1, "", "__repr__"], [22, 1, 1, "", "mean_rates"], [22, 1, 1, "", "plot_spikes_hist"], [22, 1, 1, "", "plot_spikes_raster"], [22, 1, 1, "", "to_dict"], [22, 1, 1, "", "update_types"], [22, 1, 1, "", "write"]], "hnn_core.Network": [[23, 1, 1, "", "__repr__"], [23, 1, 1, "", "add_bursty_drive"], [23, 1, 1, "", "add_connection"], [23, 1, 1, "", "add_electrode_array"], [23, 1, 1, "", "add_evoked_drive"], [23, 1, 1, "", "add_poisson_drive"], [23, 1, 1, "", "add_tonic_bias"], [23, 1, 1, "", "clear_connectivity"], [23, 1, 1, "", "clear_drives"], [23, 1, 1, "", "copy"], [23, 1, 1, "", "gid_to_type"], [23, 1, 1, "", "plot_cells"], [23, 1, 1, "", "set_cell_positions"], [23, 1, 1, "", "write_configuration"]], "hnn_core.dipole": [[25, 0, 1, "", "Dipole"], [26, 2, 1, "", "average_dipoles"]], "hnn_core.dipole.Dipole": [[25, 1, 1, "", "copy"], [25, 1, 1, "", "plot"], [25, 1, 1, "", "plot_psd"], [25, 1, 1, "", "plot_tfr_morlet"], [25, 1, 1, "", "savgol_filter"], [25, 1, 1, "", "scale"], [25, 1, 1, "", "smooth"], [25, 1, 1, "", "write"]], "hnn_core.extracellular": [[27, 0, 1, "", "ExtracellularArray"]], "hnn_core.extracellular.ExtracellularArray": [[27, 1, 1, "", "__repr__"], [27, 1, 1, "", "copy"], [27, 1, 1, "", "plot_csd"], [27, 1, 1, "", "plot_lfp"], [27, 3, 1, "", "sfreq"], [27, 1, 1, "", "smooth"], [27, 1, 1, "", "to_dict"]], "hnn_core.gui": [[28, 0, 1, "", "HNNGUI"]], "hnn_core.gui.HNNGUI": [[28, 3, 1, "", "analysis_config"], [28, 1, 1, "", "capture"], [28, 1, 1, "", "compose"], [28, 3, 1, "", "data"], [28, 1, 1, "", "get_cell_parameters_dict"], [28, 1, 1, "", "load_parameters"], [28, 1, 1, "", "run_notebook_cells"]], "hnn_core.optimization": [[31, 0, 1, "", "Optimizer"]], "hnn_core.optimization.Optimizer": [[31, 1, 1, "", "__repr__"], [31, 1, 1, "", "fit"], [31, 1, 1, "", "plot_convergence"]], "hnn_core.parallel_backends": [[32, 0, 1, "", "JoblibBackend"], [33, 0, 1, "", "MPIBackend"]], "hnn_core.parallel_backends.JoblibBackend": [[32, 1, 1, "", "simulate"]], "hnn_core.parallel_backends.MPIBackend": [[33, 1, 1, "", "simulate"], [33, 1, 1, "", "terminate"]], "hnn_core.viz": [[39, 0, 1, "", "NetworkPlotter"], [40, 2, 1, "", "plot_cell_connectivity"], [41, 2, 1, "", "plot_cell_morphology"], [42, 2, 1, "", "plot_cells"], [43, 2, 1, "", "plot_connectivity_matrix"], [44, 2, 1, "", "plot_dipole"], [45, 2, 1, "", "plot_laminar_csd"], [46, 2, 1, "", "plot_laminar_lfp"], [47, 2, 1, "", "plot_psd"], [48, 2, 1, "", "plot_spikes_hist"], [49, 2, 1, "", "plot_spikes_raster"], [50, 2, 1, "", "plot_tfr_morlet"]], "hnn_core.viz.NetworkPlotter": [[39, 1, 1, "", "export_movie"]]}, "objtypes": {"0": "py:class", "1": "py:method", "2": "py:function", "3": "py:property"}, "objnames": {"0": ["py", "class", "Python class"], "1": ["py", "method", "Python method"], "2": ["py", "function", "Python function"], "3": ["py", "property", "Python property"]}, "titleterms": {"api": [0, 56, 58], "document": [0, 20, 53], "simul": [0, 2, 3, 4, 7, 14, 15, 16, 17, 18, 56], "hnn_core": [0, 21, 22, 23, 24, 25, 26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "network": [0, 23, 54], "model": [0, 52, 56], "optim": [0, 2, 3, 31, 53], "dipol": [0, 25, 26], "extracellulararrai": [0, 27], "extracellular": [0, 8, 27, 54], "visual": [0, 56], "viz": [0, 39, 40, 41, 42, 43, 44, 45, 46, 47, 48, 49, 50], "parallel": [0, 9, 53, 55], "backend": [0, 9, 55], "parallel_backend": [0, 32, 33], "input": 0, "output": 0, "gui": [0, 28, 53, 56], "how": [1, 11, 20], "05": [2, 15], "evok": 2, "respons": [2, 3, 52], "paramet": [2, 56], "07": 4, "batch": 4, "extract": 4, "plot": [4, 6], "result": 4, "03": [5, 17], "modifi": 5, "local": [5, 20], "connect": [5, 54], "01": [6, 16], "fire": 6, "pattern": 6, "06": 7, "anim": 7, "hnn": [7, 18, 20, 53, 56], "02": [8, 14], "record": 8, "potenti": [8, 16], "refer": [8, 14, 15, 16, 17, 18], "04": [9, 18], "us": [9, 29, 31, 35, 38, 47], "mpi": [9, 55], "comput": [10, 12, 19, 57], "time": [10, 12, 19, 57], "tutori": [11, 13, 56], "alpha": 14, "beta": [14, 15], "rhythm": [14, 17], "modul": 15, "erp": [15, 16], "event": 16, "relat": 16, "gamma": 17, "from": 18, "meg": 18, "sensor": 18, "space": 18, "data": [18, 56], "contribut": [20, 53, 58], "set": 20, "up": 20, "your": 20, "develop": [20, 52, 56], "environ": 20, "configur": 20, "git": 20, "make": [20, 52], "first": 20, "pull": 20, "request": 20, "instal": [20, 53, 56], "edit": 20, "core": [20, 53], "run": 20, "test": 20, "updat": 20, "build": 20, "rebas": 20, "continu": 20, "integr": 20, "cell": [21, 54], "cellrespons": 22, "exampl": [29, 31, 35, 38, 47, 53], "calcium_model": 24, "average_dipol": 26, "hnngui": 28, "jones_2009_model": 29, "law_2021_model": 30, "joblibbackend": 32, "mpibackend": 33, "pick_connect": 34, "read_dipol": 35, "read_param": 36, "read_spik": 37, "simulate_dipol": 38, "networkplott": 39, "plot_cell_connect": 40, "plot_cell_morphologi": 41, "plot_cel": 42, "plot_connectivity_matrix": 43, "plot_dipol": 44, "plot_laminar_csd": 45, "plot_laminar_lfp": 46, "plot_psd": 47, "plot_spikes_hist": 48, "plot_spikes_rast": 49, "plot_tfr_morlet": 50, "glossari": 51, "project": [52, 56], "govern": [52, 53], "mission": 52, "role": 52, "contributor": 52, "maintain": 52, "council": 52, "decis": 52, "process": [52, 53], "chang": [52, 58], "about": 53, "depend": 53, "option": 53, "bug": [53, 58], "report": 53, "interest": 53, "structur": 53, "cite": 53, "file": 54, "content": 54, "descript": 54, "type": 54, "section": 54, "gid": 54, "rang": 54, "extern": 54, "drive": 54, "bia": 54, "arrai": 54, "joblib": 55, "The": 56, "roadmap": 56, "vision": 56, "timelin": 56, "overview": 56, "short": 56, "term": 56, "goal": 56, "modular": 56, "code": 56, "simplifi": 56, "mainten": 56, "new": [56, 58], "lfp": 56, "csd": 56, "comparison": 56, "estim": 56, "expans": 56, "differ": 56, "cortic": 56, "templat": 56, "choic": 56, "longer": 56, "what": 58, "": 58, "current": 58, "changelog": 58, "0": 58, "3": 58, "peopl": 58, "who": 58, "thi": 58, "releas": 58, "alphabet": 58, "order": 58, "2": 58, "notabl": 58, "1": 58, "08": 3, "rhythmic": 3}, "envversion": {"sphinx.domains.c": 3, "sphinx.domains.changeset": 1, "sphinx.domains.citation": 1, "sphinx.domains.cpp": 9, "sphinx.domains.index": 1, "sphinx.domains.javascript": 3, "sphinx.domains.math": 2, "sphinx.domains.python": 4, "sphinx.domains.rst": 2, "sphinx.domains.std": 2, "sphinx.ext.viewcode": 1, "sphinx.ext.intersphinx": 1, "sphinx": 58}, "alltitles": {"07. Batch Simulation": [[4, "batch-simulation"]], "Extract and Plot Results": [[4, "extract-and-plot-results"]], "03. Modifying local connectivity": [[5, "modifying-local-connectivity"]], "01. Plot firing pattern": [[6, "plot-firing-pattern"]], "06. Animating HNN simulations": [[7, "animating-hnn-simulations"]], "02. Record extracellular potentials": [[8, "record-extracellular-potentials"]], "References": [[8, "references"], [14, "references"], [15, "references"], [16, "references"], [17, "references"], [18, "references"]], "04. Use MPI backend for parallelization": [[9, "use-mpi-backend-for-parallelization"]], "Computation times": [[10, "computation-times"], [12, "computation-times"], [19, "computation-times"], [57, "computation-times"]], "Tutorials": [[13, "tutorials"], [11, "tutorials"]], "02. Simulate Alpha and Beta Rhythms": [[14, "simulate-alpha-and-beta-rhythms"]], "05. Simulate beta modulated ERP": [[15, "simulate-beta-modulated-erp"]], "01. Simulate Event Related Potentials (ERPs)": [[16, "simulate-event-related-potentials-erps"]], "03. Simulate Gamma Rhythms": [[17, "simulate-gamma-rhythms"]], "04. From MEG sensor-space data to HNN simulation": [[18, "from-meg-sensor-space-data-to-hnn-simulation"]], "API Documentation": [[0, "api-documentation"]], "Simulation (hnn_core):": [[0, "simulation-hnn-core"]], "Network Models (hnn_core):": [[0, "network-models-hnn-core"]], "Optimization (hnn_core.optimization):": [[0, "optimization-hnn-core-optimization"]], "Dipole (hnn_core.dipole):": [[0, "dipole-hnn-core-dipole"]], "ExtracellularArray (hnn_core.extracellular):": [[0, "extracellulararray-hnn-core-extracellular"]], "Visualization (hnn_core.viz):": [[0, "visualization-hnn-core-viz"]], "Parallel backends (hnn_core.parallel_backends):": [[0, "parallel-backends-hnn-core-parallel-backends"]], "Input and Output:": [[0, "input-and-output"]], "GUI (hnn_core.gui):": [[0, "gui-hnn-core-gui"]], "How to": [[1, "how-to"], [11, "how-to"]], "05. Optimize simulated evoked response parameters": [[2, "optimize-simulated-evoked-response-parameters"]], "08. Optimize simulated rhythmic responses": [[3, "optimize-simulated-rhythmic-responses"]], "Contributions": [[20, "contributions"]], "Setting up your local development environment": [[20, "setting-up-your-local-development-environment"]], "Configuring git": [[20, "configuring-git"]], "Making your first pull request": [[20, "making-your-first-pull-request"]], "Installing editable hnn-core": [[20, "installing-editable-hnn-core"]], "Running tests": [[20, "running-tests"]], "Updating documentation": [[20, "updating-documentation"]], "Building the documentation": [[20, "building-the-documentation"]], "How to rebase": [[20, "how-to-rebase"]], "Continuous Integration": [[20, "continuous-integration"]], "hnn_core.Cell": [[21, "hnn-core-cell"]], "hnn_core.CellResponse": [[22, "hnn-core-cellresponse"]], "hnn_core.Network": [[23, "hnn-core-network"]], "hnn_core.calcium_model": [[24, "hnn-core-calcium-model"]], "hnn_core.dipole.Dipole": [[25, "hnn-core-dipole-dipole"]], "hnn_core.dipole.average_dipoles": [[26, "hnn-core-dipole-average-dipoles"]], "hnn_core.extracellular.ExtracellularArray": [[27, "hnn-core-extracellular-extracellulararray"]], "hnn_core.gui.HNNGUI": [[28, "hnn-core-gui-hnngui"]], "hnn_core.jones_2009_model": [[29, "hnn-core-jones-2009-model"]], "Examples using hnn_core.jones_2009_model": [[29, "examples-using-hnn-core-jones-2009-model"]], "hnn_core.law_2021_model": [[30, "hnn-core-law-2021-model"]], "hnn_core.optimization.Optimizer": [[31, "hnn-core-optimization-optimizer"]], "Examples using hnn_core.optimization.Optimizer": [[31, "examples-using-hnn-core-optimization-optimizer"]], "hnn_core.parallel_backends.JoblibBackend": [[32, "hnn-core-parallel-backends-joblibbackend"]], "hnn_core.parallel_backends.MPIBackend": [[33, "hnn-core-parallel-backends-mpibackend"]], "hnn_core.pick_connection": [[34, "hnn-core-pick-connection"]], "hnn_core.read_dipole": [[35, "hnn-core-read-dipole"]], "Examples using hnn_core.read_dipole": [[35, "examples-using-hnn-core-read-dipole"]], "hnn_core.read_params": [[36, "hnn-core-read-params"]], "hnn_core.read_spikes": [[37, "hnn-core-read-spikes"]], "hnn_core.simulate_dipole": [[38, "hnn-core-simulate-dipole"]], "Examples using hnn_core.simulate_dipole": [[38, "examples-using-hnn-core-simulate-dipole"]], "hnn_core.viz.NetworkPlotter": [[39, "hnn-core-viz-networkplotter"]], "hnn_core.viz.plot_cell_connectivity": [[40, "hnn-core-viz-plot-cell-connectivity"]], "hnn_core.viz.plot_cell_morphology": [[41, "hnn-core-viz-plot-cell-morphology"]], "hnn_core.viz.plot_cells": [[42, "hnn-core-viz-plot-cells"]], "hnn_core.viz.plot_connectivity_matrix": [[43, "hnn-core-viz-plot-connectivity-matrix"]], "hnn_core.viz.plot_dipole": [[44, "hnn-core-viz-plot-dipole"]], "hnn_core.viz.plot_laminar_csd": [[45, "hnn-core-viz-plot-laminar-csd"]], "hnn_core.viz.plot_laminar_lfp": [[46, "hnn-core-viz-plot-laminar-lfp"]], "hnn_core.viz.plot_psd": [[47, "hnn-core-viz-plot-psd"]], "Examples using hnn_core.viz.plot_psd": [[47, "examples-using-hnn-core-viz-plot-psd"]], "hnn_core.viz.plot_spikes_hist": [[48, "hnn-core-viz-plot-spikes-hist"]], "hnn_core.viz.plot_spikes_raster": [[49, "hnn-core-viz-plot-spikes-raster"]], "hnn_core.viz.plot_tfr_morlet": [[50, "hnn-core-viz-plot-tfr-morlet"]], "Glossary": [[51, "glossary"]], "Project Governance": [[52, "project-governance"]], "Mission": [[52, "mission"]], "Roles and Responsibilities": [[52, "roles-and-responsibilities"]], "Contributors*": [[52, "contributors"]], "Maintainers**": [[52, "maintainers"]], "Developer Council": [[52, "developer-council"]], "Decision-Making Process": [[52, "decision-making-process"]], "Governance Model Changes": [[52, "governance-model-changes"]], "hnn-core": [[53, "hnn-core"]], "About": [[53, "about"]], "Dependencies": [[53, "dependencies"]], "Optional dependencies": [[53, "optional-dependencies"]], "GUI": [[53, "gui"]], "Optimization": [[53, "optimization"]], "Parallel processing": [[53, "parallel-processing"]], "Installation": [[53, "installation"]], "Documentation and examples": [[53, "documentation-and-examples"]], "Bug reports": [[53, "bug-reports"]], "Interested in Contributing?": [[53, "interested-in-contributing"]], "Governance Structure": [[53, "governance-structure"]], "Citing": [[53, "citing"]], "Network File Content": [[54, "network-file-content"]], "File Content Description": [[54, "file-content-description"]], "Cell Type Description": [[54, "cell-type-description"]], "Section Description": [[54, "section-description"]], "Gid Range Description": [[54, "gid-range-description"]], "External Drive Description": [[54, "external-drive-description"]], "External Bias Description": [[54, "external-bias-description"]], "Connection Description": [[54, "connection-description"]], "Extracellular Array Description": [[54, "extracellular-array-description"]], "Parallel backends": [[55, "parallel-backends"]], "Joblib": [[55, "joblib"]], "MPI": [[55, "mpi"]], "The HNN Roadmap": [[56, "the-hnn-roadmap"]], "Project Vision": [[56, "project-vision"]], "Timeline Overview": [[56, "timeline-overview"]], "Short-Term Goals": [[56, "short-term-goals"]], "Modularize HNN code to simplify installation, development and maintenance": [[56, "modularize-hnn-code-to-simplify-installation-development-and-maintenance"]], "Develop a New HNN GUI": [[56, "develop-a-new-hnn-gui"]], "LFP/CSD Simulation, Visualization and Data Comparison": [[56, "lfp-csd-simulation-visualization-and-data-comparison"]], "Parameter Estimation Expansion": [[56, "parameter-estimation-expansion"]], "Different Cortical Model Template Choices": [[56, "different-cortical-model-template-choices"]], "API and Tutorial development": [[56, "api-and-tutorial-development"]], "Longer-Term Goals": [[56, "longer-term-goals"]], "What\u2019s new?": [[58, "what-s-new"]], "Current": [[58, "current"]], "Changelog": [[58, "changelog"], [58, "id5"], [58, "id10"], [58, "id17"]], "Bug": [[58, "bug"], [58, "id6"], [58, "id12"], [58, "id37"]], "API": [[58, "api"], [58, "id7"], [58, "id13"], [58, "id46"]], "0.3": [[58, "id3"]], "People who contributed to this release (in alphabetical order):": [[58, "people-who-contributed-to-this-release-in-alphabetical-order"], [58, "id14"], [58, "id55"]], "0.2": [[58, "id8"]], "Notable Changes": [[58, "notable-changes"]], "0.1": [[58, "id15"]]}, "indexentries": {"cell (class in hnn_core)": [[21, "hnn_core.Cell"]], "__repr__() (hnn_core.cell method)": [[21, "hnn_core.Cell.__repr__"]], "build() (hnn_core.cell method)": [[21, "hnn_core.Cell.build"]], "copy() (hnn_core.cell method)": [[21, "hnn_core.Cell.copy"]], "create_tonic_bias() (hnn_core.cell method)": [[21, "hnn_core.Cell.create_tonic_bias"]], "define_shape() (hnn_core.cell method)": [[21, "hnn_core.Cell.define_shape"]], "distance_section() (hnn_core.cell method)": [[21, "hnn_core.Cell.distance_section"]], "modify_section() (hnn_core.cell method)": [[21, "hnn_core.Cell.modify_section"]], "parconnect_from_src() (hnn_core.cell method)": [[21, "hnn_core.Cell.parconnect_from_src"]], "plot_morphology() (hnn_core.cell method)": [[21, "hnn_core.Cell.plot_morphology"]], "record() (hnn_core.cell method)": [[21, "hnn_core.Cell.record"]], "setup_source_netcon() (hnn_core.cell method)": [[21, "hnn_core.Cell.setup_source_netcon"]], "syn_create() (hnn_core.cell method)": [[21, "hnn_core.Cell.syn_create"]], "to_dict() (hnn_core.cell method)": [[21, "hnn_core.Cell.to_dict"]], "cellresponse (class in hnn_core)": [[22, "hnn_core.CellResponse"]], "__repr__() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.__repr__"]], "mean_rates() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.mean_rates"]], "plot_spikes_hist() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.plot_spikes_hist"]], "plot_spikes_raster() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.plot_spikes_raster"]], "to_dict() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.to_dict"]], "update_types() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.update_types"]], "write() (hnn_core.cellresponse method)": [[22, "hnn_core.CellResponse.write"]], "network (class in hnn_core)": [[23, "hnn_core.Network"]], "__repr__() (hnn_core.network method)": [[23, "hnn_core.Network.__repr__"]], "add_bursty_drive() (hnn_core.network method)": [[23, "hnn_core.Network.add_bursty_drive"]], "add_connection() (hnn_core.network method)": [[23, "hnn_core.Network.add_connection"]], "add_electrode_array() (hnn_core.network method)": [[23, "hnn_core.Network.add_electrode_array"]], "add_evoked_drive() (hnn_core.network method)": [[23, "hnn_core.Network.add_evoked_drive"]], "add_poisson_drive() (hnn_core.network method)": [[23, "hnn_core.Network.add_poisson_drive"]], "add_tonic_bias() (hnn_core.network method)": [[23, "hnn_core.Network.add_tonic_bias"]], "clear_connectivity() (hnn_core.network method)": [[23, "hnn_core.Network.clear_connectivity"]], "clear_drives() (hnn_core.network method)": [[23, "hnn_core.Network.clear_drives"]], "copy() (hnn_core.network method)": [[23, "hnn_core.Network.copy"]], "gid_to_type() (hnn_core.network method)": [[23, "hnn_core.Network.gid_to_type"]], "plot_cells() (hnn_core.network method)": [[23, "hnn_core.Network.plot_cells"]], "set_cell_positions() (hnn_core.network method)": [[23, "hnn_core.Network.set_cell_positions"]], "write_configuration() (hnn_core.network method)": [[23, "hnn_core.Network.write_configuration"]], "calcium_model() (in module hnn_core)": [[24, "hnn_core.calcium_model"]], "dipole (class in hnn_core.dipole)": [[25, "hnn_core.dipole.Dipole"]], "copy() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.copy"]], "plot() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.plot"]], "plot_psd() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.plot_psd"]], "plot_tfr_morlet() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.plot_tfr_morlet"]], "savgol_filter() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.savgol_filter"]], "scale() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.scale"]], "smooth() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.smooth"]], "write() (hnn_core.dipole.dipole method)": [[25, "hnn_core.dipole.Dipole.write"]], "average_dipoles() (in module hnn_core.dipole)": [[26, "hnn_core.dipole.average_dipoles"]], "extracellulararray (class in hnn_core.extracellular)": [[27, "hnn_core.extracellular.ExtracellularArray"]], "__repr__() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.__repr__"]], "copy() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.copy"]], "plot_csd() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.plot_csd"]], "plot_lfp() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.plot_lfp"]], "sfreq (hnn_core.extracellular.extracellulararray property)": [[27, "hnn_core.extracellular.ExtracellularArray.sfreq"]], "smooth() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.smooth"]], "to_dict() (hnn_core.extracellular.extracellulararray method)": [[27, "hnn_core.extracellular.ExtracellularArray.to_dict"]], "hnngui (class in hnn_core.gui)": [[28, "hnn_core.gui.HNNGUI"]], "analysis_config (hnn_core.gui.hnngui property)": [[28, "hnn_core.gui.HNNGUI.analysis_config"]], "capture() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.capture"]], "compose() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.compose"]], "data (hnn_core.gui.hnngui property)": [[28, "hnn_core.gui.HNNGUI.data"]], "get_cell_parameters_dict() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.get_cell_parameters_dict"]], "load_parameters() (hnn_core.gui.hnngui static method)": [[28, "hnn_core.gui.HNNGUI.load_parameters"]], "run_notebook_cells() (hnn_core.gui.hnngui method)": [[28, "hnn_core.gui.HNNGUI.run_notebook_cells"]], "jones_2009_model() (in module hnn_core)": [[29, "hnn_core.jones_2009_model"]], "law_2021_model() (in module hnn_core)": [[30, "hnn_core.law_2021_model"]], "optimizer (class in hnn_core.optimization)": [[31, "hnn_core.optimization.Optimizer"]], "__repr__() (hnn_core.optimization.optimizer method)": [[31, "hnn_core.optimization.Optimizer.__repr__"]], "fit() (hnn_core.optimization.optimizer method)": [[31, "hnn_core.optimization.Optimizer.fit"]], "plot_convergence() (hnn_core.optimization.optimizer method)": [[31, "hnn_core.optimization.Optimizer.plot_convergence"]], "joblibbackend (class in hnn_core.parallel_backends)": [[32, "hnn_core.parallel_backends.JoblibBackend"]], "simulate() (hnn_core.parallel_backends.joblibbackend method)": [[32, "hnn_core.parallel_backends.JoblibBackend.simulate"]], "mpibackend (class in hnn_core.parallel_backends)": [[33, "hnn_core.parallel_backends.MPIBackend"]], "simulate() (hnn_core.parallel_backends.mpibackend method)": [[33, "hnn_core.parallel_backends.MPIBackend.simulate"]], "terminate() (hnn_core.parallel_backends.mpibackend method)": [[33, "hnn_core.parallel_backends.MPIBackend.terminate"]], "pick_connection() (in module hnn_core)": [[34, "hnn_core.pick_connection"]], "read_dipole() (in module hnn_core)": [[35, "hnn_core.read_dipole"]], "read_params() (in module hnn_core)": [[36, "hnn_core.read_params"]], "read_spikes() (in module hnn_core)": [[37, "hnn_core.read_spikes"]], "simulate_dipole() (in module hnn_core)": [[38, "hnn_core.simulate_dipole"]], "networkplotter (class in hnn_core.viz)": [[39, "hnn_core.viz.NetworkPlotter"]], "export_movie() (hnn_core.viz.networkplotter method)": [[39, "hnn_core.viz.NetworkPlotter.export_movie"]], "plot_cell_connectivity() (in module hnn_core.viz)": [[40, "hnn_core.viz.plot_cell_connectivity"]], "plot_cell_morphology() (in module hnn_core.viz)": [[41, "hnn_core.viz.plot_cell_morphology"]], "plot_cells() (in module hnn_core.viz)": [[42, "hnn_core.viz.plot_cells"]], "plot_connectivity_matrix() (in module hnn_core.viz)": [[43, "hnn_core.viz.plot_connectivity_matrix"]], "plot_dipole() (in module hnn_core.viz)": [[44, "hnn_core.viz.plot_dipole"]], "plot_laminar_csd() (in module hnn_core.viz)": [[45, "hnn_core.viz.plot_laminar_csd"]], "plot_laminar_lfp() (in module hnn_core.viz)": [[46, "hnn_core.viz.plot_laminar_lfp"]], "plot_psd() (in module hnn_core.viz)": [[47, "hnn_core.viz.plot_psd"]], "plot_spikes_hist() (in module hnn_core.viz)": [[48, "hnn_core.viz.plot_spikes_hist"]], "plot_spikes_raster() (in module hnn_core.viz)": [[49, "hnn_core.viz.plot_spikes_raster"]], "plot_tfr_morlet() (in module hnn_core.viz)": [[50, "hnn_core.viz.plot_tfr_morlet"]], "distal": [[51, "term-distal"]], "drive": [[51, "term-drive"]], "gid": [[51, "term-gid"]], "proximal": [[51, "term-proximal"]]}})
\ No newline at end of file
diff --git a/dev/whats_new.html b/dev/whats_new.html
index 90badead3..469b8d7ea 100644
--- a/dev/whats_new.html
+++ b/dev/whats_new.html
@@ -231,6 +231,8 @@ 
            Changelogplot_csd(): to set color of sinks and sources, range of the colormap,
 and interpolation method to smoothen CSD plot,
 by Katharina Duecker in #815
            
+
          • Cleaned up internal logic in CellResponse,
+by Nick Tolley in #647.
            •