What’s new?

0.2

Notable Changes

• Local field potentials can now be recorded during simulations [Example]

• Ability to optimize parameters to reproduce event related potentials from real data [Example]

• Published models using HNN were added and can be loaded via dedicated functions

• Several improvements enabling easy modification of connectivity and cell properties [Example]

• Improved visualization including spectral analysis, connectivity, and cell morphology

Changelog

• Store all connectivity information under connectivity before building the network, by Nick Tolley in #276

• Add new function plot_cell_morphology() to visualize cell morphology, by Mainak Jas in #319

• Compute dipole component in z-direction automatically from cell morphology instead of hard coding, by Mainak Jas in #327

• Store Cell instances in Network’s cells attribute by Ryan Thorpe in #321

• Add probability argument to add_connection(). Connectivity patterns can also be visualized with plot_connectivity_matrix(), by Nick Tolley in #318

• Add function to visualize connections originating from individual cells plot_cell_connectivity(), by Nick Tolley in #339

• Add method for calculating extracellular potentials using electrode arrays add_electrode_array() that are stored under net.rec_array as a dictionary of ExtracellularArray containers, by Mainak Jas, Nick Tolley and Christopher Bailey in #329

• Add function to visualize extracellular potentials from laminar array simulations, by Christopher Bailey in #329

• Previously published models can now be loaded via law_2021_model() and jones_2009_model(), by Nick Tolley in #348

• Add ability to interactivity explore connections in plot_cell_connectivity() by Mainak Jas in #376

• Add calcium_model() with a distance dependent calcium channel conductivity, by Nick Tolley and Sarah Pugliese in #348

• Each drive spike train sampled through an independent process corresponds to a single artificial drive cell, the number of which users can set when adding drives with n_drive_cells and cell_specific, by Ryan Thorpe in #383

• Add pick_connection() to query the indices of specific connections in connectivity, by Nick Tolley in #367

• Drives in external_drives no longer contain a ‘conn’ key and the connectivity list contains more items when adding drives from a param file or when in legacy mode, by Ryan Thorpe, Mainak Jas, and Nick Tolley in #369

• Add optimize_evoked() to optimize the timing and weights of driving inputs for simulating evoked responses, by Blake Caldwell and Mainak Jas in #77

• Add method for setting in-plane cell distances and layer separation in the network set_cell_positions(), by Christopher Bailey in #370

• External drives API now accepts probability argument for targetting subsets of cells, by Nick Tolley in #416

Bug

• Remove rounding error caused by repositioning of NEURON cell sections, by Mainak Jas and Ryan Thorpe in #314

• Fix issue where common drives use the same parameters for all cell types, by Nick Tolley in #350

• Fix bug where depth of L5 and L2 cells were swapped, by Christopher Bailey in #352

• Fix bug where average_dipoles() failed when there were less than two dipoles in the input dipole list, by Kenneth Loi in #368

• Fix bug where read_spikes() wasn’t returning a CellResponse instance with updated spike types, by Ryan Thorpe in #382

• Dipole.times and Cell_response.times now reflect the actual integration points instead of the intended times, by Mainak Jas in #397

• Fix overlapping non-cell-specific drive gid assignment over different ranks in MPIBackend, by Ryan Thorpe and Mainak Jas in #399

• Allow read_dipoles() to read dipole from a file with only two columns (times and data), by Mainak Jas in #421

API

• New API for defining cell-cell connections. Custom connections can be added with add_connection(), by Nick Tolley in #276

• Remove L2Pyr, L5Pyr, L2Basket, and L5Basket classes in favor of instantation through functions and a more consistent Cell class by Mainak Jas in #322

• Remove parameter distribution in add_bursty_drive(). The distribution is now Gaussian by default, by Mainak Jas in #330

• New API for accessing and modifying Cell attributes (e.g., synapse and biophysics parameters) as cells are now instantiated from template cells specified in a Network instance’s cell_types attribute by Ryan Thorpe in #321

• New API for network creation. The default network is now created with net = jones_2009_model(params), by Nick Tolley in #318

• Replace parameter T with tstop in add_tonic_bias() and create_tonic_bias() to be more consistent with other functions and improve readability, by Kenneth Loi in #354

• Deprecated postproc argument in simulate_dipole(), whereby user should explicitly smooth and scale resulting dipoles, by Christopher Bailey in #372

• Number of drive cells and their connectivity can now be specified through the n_drive_cells and cell_specific arguments in Network.add_xxx_drive() methods, replacing use of repeats and sync_within_trial, by Ryan Thorpe in #383

• Simulation end time and integration time have to be specified now with tstop and dt in simulate_dipole(), by Mainak Jas in #397

• CellResponse.reset() method is not supported any more, by Mainak Jas in #397

• Target cell types and their connections are created for each drive according to the synaptic weight and delay dictionaries assigned in Network.add_xxx_drive(), by Ryan Thorpe in #369

• Cell objects can no longer be accessed from Network as the cells attribute has been removed, by Ryan Thorpe in #436

People who contributed to this release (in alphabetical order):

• Alex Rockhill

• Blake Caldwell

• Christopher Bailey

• Dylan Daniels

• Kenneth Loi

• Mainak Jas

• Nick Tolley

• Ryan Thorpe

• Sarah Pugliese

• Stephanie R. Jones

0.1

Changelog

• Add ability to simulate multiple trials in parallel using joblibs, by Mainak Jas in #44

• Rhythmic inputs can now be turned off by setting their conductance weights to 0 instead of setting their start times to exceed the simulation stop time, by Ryan Thorpe in #105

• Reader for parameter files, by Blake Caldwell in #80

• Add plotting of voltage at soma to inspect firing pattern of cells, by Mainak Jas in #86

• Add ability to simulate a single trial in parallel across cores using MPI, by Blake Caldwell in #79

• Modify plot_dipole() to accept both lists and individual instances of Dipole object, by Nick Tolley in #145

• Update plot_hist_input to plot_spikes_hist() which can plot histogram of spikes for any cell type, by Nick Tolley in #157

• Add function to compute mean spike rates with user specified calculation type, by Nick Tolley and Mainak Jas in #155

• Add ability to record somatic voltages from all cells, by Nick Tolley in #190

• Add ability to instantiate external feed event times of a network prior to building it, by Christopher Bailey in #191

• Add ability to record somatic currents from all cells, by Nick Tolley in #199

• Add option to turn off dipole postprocessing, by Carmen Kohl in #188

• Add ability to add tonic inputs to cell types with add_tonic_bias(), by Mainak Jas in #209

• Modify plot_spikes_raster() to display individual cells, by Nick Tolley in #231

• Add copy() method for cloning a Network instance, by Christopher Bailey in #221

• Add methods for creating input drives and biases to network: add_evoked_drive(), add_poisson_drive(), add_bursty_drive() and add_tonic_bias(), by Christopher Bailey in #221

• Add functions for plotting power spectral density (plot_psd()) and Morlet time-frequency representations (plot_tfr_morlet()), by Christopher Bailey in #264

• Add y-label units (nAm) to all visualisation functions involving dipole moments, by Christopher Bailey in #264

• Add Savitzky-Golay filtering method savgol_filter() to Dipole; copied from mne-python savgol_filter(), by Christopher Bailey in #264

Bug

• Fix missing autapses in network construction, by Mainak Jas in #50

• Fix rhythmic input feed, by Ryan Thorpe in #98

• Fix bug introduced into rhythmic input feed and add test, by Christopher Bailey in #102

• Fix bug in amplitude of delay (for connection between L2 Basket and Gaussian feed) being passed incorrectly, by Mainak Jas in #146

• Connections now cannot be removed by setting the weights to 0., by Mainak Jas and Ryan Thorpe in #162

• MPI and Joblib backends now apply jitter across multiple trials identically, by Ryan Thorpe in #171

• Fix bug in Poisson input where the first spike was being missed after the start time, by Mainak Jas in #204

• Fix bug in network to add empty spike when empty file is read in, by Samika Kanekar and Ryan Thorpe in #207

API

• Make a context manager for Network class, by Mainak Jas and Blake Caldwell in #86

• Create Spikes class, add write methods and read functions for Spikes and Dipole classes, by Ryan Thorpe in #96

• Only specify n_jobs when instantiating the JoblibBackend, by Blake Caldwell in #79

• Make a context manager for parallel backends (JoblibBackend, MPIBackend), by Blake Caldwell in #79

• Add average_dipoles() function, by Blake Caldwell in #156

• New API for defining external drives and biases to network. By default, a Network is created without drives, which are added using class methods. The argument add_drives_from_params controls this behaviour, by Christopher Bailey in #221

• Examples apply random state seeds that reproduce the output of HNN GUI documentation, by Christopher Bailey in #221

• Force conversion to nAm (from fAm) for output of simulate_dipole() regardless of postproc-argument, which now only controls parameter file-based smoothing and scaling, by Christopher Bailey in #264

People who contributed to this release (in alphabetical order):

• Blake Caldwell

• Christopher Bailey

• Carmen Kohl

• Mainak Jas

• Nick Tolley

• Ryan Thorpe

• Samika Kanekar

• Stephanie R. Jones