What’s new?

0.3

Changelog

• Add option to select drives using argument ‘which_drives’ in optimize_evoked(), by Mohamed A. Sherif in #478.

• Changed conn_seed default to None (from 3) in add_connection(), by Mattan Pelah in #492.

• Add interface to modify attributes of sections in modify_section(), by Nick Tolley in #481

• Add ability to target specific sections when adding drives or connections, by Nick Tolley in #419

• Runtime output messages now specify the trial with which each simulation time checkpoint belongs too, by Ryan Thorpe in #546.

• Add warning if network drives are not loaded, by Orsolya Beatrix Kolozsvari in #516

• Add ability to record voltages and synaptic currents from all sections in CellResponse, by Nick Tolley in #502.

• Add ability to return unweighted RMSE for each optimization iteration in optimize_evoked(), by Kaisu Lankinen in #610.

Bug

• Fix bugs in drives API to enable: rate constant argument as float; evoked drive with connection probability, by Nick Tolley in #458

• Allow regular strings as filenames in write() by Mainak Jas in #456.

• Fix to make network output independent of the order in which drives are added to the network by making the seed of the random process generating spike times in drives use the offset of the gid with respect to the first gid in the population by Mainak Jas in #462.

• Negative event_seed is no longer allowed by Mainak Jas in #462.

• Evoked drive optimization no longer assigns a default timing sigma value to a drive if it is not already specified, by Ryan Thorpe in #446.

• Subsets of trials can be indexed when using plot_spikes_raster() and plot_spikes_hist(), by Nick Tolley in #472.

• Add option to plot the averaged dipole in plot_dipole when dpl is a list of dipoles, by Huzi Cheng in #475.

• Fix bug where plot_morphology() did not accurately reflect the shape of the cell being simulated, by Nick Tolley in #481

• Fix bug where pick_connection() did not return an empty list when searching non existing connections, by Nick Tolley in #515

• Fix bug in MPIBackend that caused an MPI runtime error (RuntimeError: MPI simulation failed. Return code: 143), when running a simulation with an oversubscribed MPI session on a reduced network, by Ryan Thorpe in #545.

• Fix bug where pick_connection() failed when searching for connections with a list of cell types, by Nick Tolley in #559

• Fix bug where add_evoked_drive() failed when adding a drive with just NMDA weights, by Nick Tolley in #611

• Fix bug where read_params() failed to create a network when legacy mode is False, by Nick Tolley in #614

• Fix bug where plot_dipole() failed to check the instance type of Dipole, by Rajat Partani in #606

API

• Optimization of the evoked drives can be conducted on any Network template model by passing a Network instance directly into optimize_evoked(). Simulations run during optimization can now consist of multiple trials over which the simulated dipole is averaged, by Ryan Thorpe in #446.

• plot_dipole now supports separate visualizations of different layers, by Huzi Cheng in #479.

• Current source density (CSD) can now be calculated with calculate_csd2d() and plotted with plot_csd(). The method for plotting local field potential (LFP) is now found at plot_lfp(), by Steven Brandt and Ryan Thorpe in #517.

• Recorded voltages/currents from the soma, as well all sections, are enabled by setting either record_vsec or record_isec to ‘all’ or ‘soma’ in simulate_dipole(). Recordings are now accessed through vsec and isec, by Nick Tolley in #502.

• legacy_mode is now set to False by default in all for all Network objects, by Nick Tolley and Ryan Thorpe in #619.

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

• Christopher Bailey

• Huzi Cheng

• Kaisu Lankinen

• Mainak Jas

• Mattan Pelah

• Mohamed A. Sherif

• Mostafa Khalil

• Nick Tolley

• Orsolya Beatrix Kolozsvari

• Rajat Partani

• Ryan Thorpe

• Stephanie R. Jones

• Steven Brandt

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