diff --git a/examples/plot_connectivity.py b/examples/plot_connectivity.py index 48c22cc08..ef7c40409 100644 --- a/examples/plot_connectivity.py +++ b/examples/plot_connectivity.py @@ -1,6 +1,6 @@ """ ===================== -07. Plot Connectivity +06. Plot Connectivity ===================== This example demonstrates how to modify the network connectivity. @@ -8,7 +8,7 @@ # Author: Nick Tolley -# sphinx_gallery_thumbnail_number = 4 +# sphinx_gallery_thumbnail_number = 5 from hnn_core.network import Network import os.path as op @@ -68,7 +68,7 @@ location, receptor = 'distal', 'ampa' weight, delay, lamtha = 1.0, 1.0, 70 src = 'L5_pyramidal' -for target in ['L5_pyramidal', 'L5_pyramidal']: +for target in ['L5_pyramidal', 'L2_basket']: net_all.add_connection(src, target, location, receptor, delay, weight, lamtha) @@ -76,7 +76,7 @@ location, receptor = 'soma', 'gabaa' weight, delay, lamtha = 1.0, 1.0, 70 src = 'L2_basket' -for target in ['L2_basket', 'L5_pyramidal']: +for target in ['L5_pyramidal', 'L2_basket']: net_all.add_connection(src, target, location, receptor, delay, weight, lamtha) @@ -84,11 +84,14 @@ net_all.cell_response.plot_spikes_raster() ############################################################################### -# That's a lot of spiking! We can additionally use the ``probability``. -# argument to create a sparse connectivity pattern instead of all-to-all. Let's -# try creating the same network with a 10% change of cells connecting -# to each other. The resulting connectivity pattern can also be visualized -# with ``net.connectivity[idx].plot()`` +# With the previous connection pattern there appears to be synchronous rhythmic +# firing of the L5 pyramidal cells with a period of 10 ms. The synchronous +# activity is visible as vertical lines where several cells fire simultaneously +# We can additionally use the ``probability``. argument to create a sparse +# connectivity pattern instead of all-to-all. Let's try creating the same +# network with a 10% chance of cells connecting to each other. The resulting +# connectivity pattern can also be visualized with +# ``net.connectivity[idx].plot()`` probability = 0.1 net_sparse = Network(params, add_drives_from_params=True) @@ -104,7 +107,7 @@ location, receptor = 'soma', 'gabaa' weight, delay, lamtha = 1.0, 1.0, 70 src = 'L2_basket' -for target in ['L2_basket', 'L5_pyramidal']: +for target in ['L5_pyramidal', 'L2_basket']: net_sparse.add_connection(src, target, location, receptor, delay, weight, lamtha, probability) @@ -114,10 +117,9 @@ net_sparse.connectivity[-1].plot() ############################################################################### -# Using the sparse connectivity pattern led produced a lot more spiking in -# the L5 pyramidal cells. While there are less excitatory connections overall, -# there was also a decrease in the inhibtory connections. This shift in -# activity is often referred to as the excitatory/inhibitory (E/I) balance. +# Using the sparse connectivity pattern produced a lot more spiking in +# the L5 pyramidal cells. Nevertheless there appears to be some rhythmicity +# where the cells are firing synchronously with a smaller period of 4-5 ms. # As a final step, we can see how this change in spiking activity impacts # the aggregate current dipole. import matplotlib.pyplot as plt diff --git a/examples/plot_simulate_mpi_backend.py b/examples/plot_simulate_mpi_backend.py index 2623a341c..005a88995 100644 --- a/examples/plot_simulate_mpi_backend.py +++ b/examples/plot_simulate_mpi_backend.py @@ -1,6 +1,6 @@ """ ======================================= -06. Use MPI backend for parallelization +07. Use MPI backend for parallelization ======================================= This example demonstrates how to use the MPI backend for