What’s new?#

Current development version#

Changelog#

0.4.1 Patch notes#

  • Version 0.4.1 is a bug-fixing patch release for version 0.4. This includes changes to importing of BatchSimulate due to previously-undetected install/import issues (#1034), configuration of packaging metadata format (same PR), and elimination of a discrepancy in our method of cleaning local compiled files that led to architecture-specific files being included in the Pypi 0.4 release, which caused simulations on some platforms to fail (#1035). The public Pypi version has already been updated to 0.4.1.

0.4 Release Notes#

v0.4 represents a major milestone in development of hnn_core and the HNN ecosystem as a whole. v0.4 includes over two years of active development work by many people (>800 commits!), and brings with it many new and exciting features, including significant improvements to robustness, testing, and bug-fixing.

New Features#

  • hnn_core now includes a fully-tested and robust GUI of its own. The hnn_core GUI was present as a prototype in v0.3, but it is now ready for production. New features and visual improvements will still be coming to it in the future, such as the ability to use optimization. See our new Install page for ways to install it, and we have already begun incorporating it into a new, fresh series of tutorials for our upcoming revamp of the HNN website. If you have installed it, you can start the GUI using hnn-gui in your terminal/command prompt window.

  • The BatchSimulate class: Thanks to Abdul Samad Siddiqui and Google Summer of Code 2024, there is now the capability to run “batches” of simulations across multiple parameter sets, enabling easy analysis and simulation of behavior across parameter sweeps. See our example for more details. Note that currently, only its loky backend is supported, and the "hnn-core[parallel]" dependencies must be installed for it to be used.

  • Significant improvements to the API, documentation, and pedagogical examples especially for Optimization, among others.

  • Calcium concentration can now be recorded: recorded calcium concentration from either the soma, or all sections, are enabled by setting record_ca to soma or all in simulate_dipole(). Recordings are accessed through ca.

  • There is now a new class NetworkPlotter which can be used to visualize an entire network in 3D, including firing animations; see our example of how to use it here.

  • There is now a new function plot_drive_strength() for illustrating the absolute or relative amount of strength that a particular drive provides to different cell types.

  • A very large amount of polishing, bug fixes, general improvements, etc.

Deprecations#

  • The new Python 3.13 is not supported by hnn_core at this time, due to NEURON’s current lack of support for it. This will change in the near future. We still support 3.8 through 3.12 (inclusively).

Upcoming Deprecations#

  • Both plot_laminar_lfp() and plot_dipole() will have their tmin and tmax arguments removed in the future. Please set the x-axis limits using methods called directly on the existing matplotlib objects, or using matplotlib.pyplot.xlim.

  • Network’s argument of legacy_mode for importing old param files will be removed in the future.

  • add_tonic_bias()’s argument of cell_type, along with setting the argument amplitude to a single float, will be removed in the future. Instead, set the amplitude argument to a dictionary as described in the docstring.

  • simulate_dipole()’s argument of postproc for post-processing will be removed in the future. Instead, use explicit smoothing and scaling via Dipole methods.

API Changes#

  • New argument to Network initialization: you can now set mesh_shape to easily make a grid of different sizes of Networks.

  • Cell initialization argument topology has had both its name changed to cell_tree and its data type significantly changed; see the API docs of Cell for details.

  • jones_2009_model() and other built-in Network Models including law_2021_model() and calcium_model() all accept the aforementioned mesh_shape argument like Network.

  • The API for optimization has changed significantly. Instead of running the function optimize_evoked obtained using from hnn_core.optimization import optimize_evoked, you should use the new Optimizer class and its methods; see our example of evoked-response optimization here.

  • plot_spikes_hist() now accepts more arguments, including invert_spike_types, color, and any **kwargs_hist which can be applied to matplotlib.axes.Axes.hist. See the docstring for details.

  • plot_spikes_raster() now accepts many more arguments, including cell_types, colors, show_legend, marker_size, dpl, and overlay_dipoles. See the docstring for details.

  • plot_cell_morphology() now accepts more arguments, including color and several arguments related to its position and viewing window, including pos, xlim, ylim, and zlim. See the docstring for details.

  • plot_laminar_csd() now accepts more arguments, including vmin, vmax, sink, and interpolation. See the docstring for details.

  • MPIBackend now accepts many more arguments, including use_hwthreading_if_found, sensible_default_cores, override_hwthreading_option, and override_oversubscribe_option. See the docstring for details; the ability to customize it has been greatly increased.

  • read_params() now accepts a new argument file_contents which lets you pass in network configuration contents using a string.

People who contributed to this release (in alphabetical order of family name):#

PRs merged (API)#

PRs merged (Bug fixes and corrections)#

PRs merged (GUI changes)#

  • Add RMSE calculation and plotting to GUI, by Huzi Cheng in #636

  • Update GUI to use ipywidgets v8.0.0+ API, by George Dang in #696

  • Add GUI visualization testing, by Abdul Samad Siddiqui in #726

  • Add pre defined plot sets for simulated data in GUI, by Camilo Diaz in #746

  • Add GUI widget to enable/disable synchronous input in simulations, by Camilo Diaz in #750

  • Add GUI widgets to save simulation as csv and updated the file upload to support csv data, by Camilo Diaz in #753

  • Refactor GUI tests, by George Dang in #765

  • Refactor GUI import of _read_dipole_text function, by George Dang in #771

  • Add GUI feature to include Tonic input drives in simulations, by Camilo Diaz #773

  • Add GUI feature to read and modify cell parameters, by Camilo Diaz in #806

  • Refactor GUI read_network_configuration, by George Dang in #833

  • Change the configuration/parameter file format support of the GUI. Loading of connectivity and drives use a new multi-level json structure that mirrors the structure of the Network object. Flat parameter and json configuration files are no longer supported by the GUI, by George Dang in #837

  • GUI load confirmation message, by George Dang in #846

  • Differentiate L5/L2 Pyr geomtetry options in GUI, by Nick Tolley in #848

  • Updated the GUI load drive widget to be able to load tonic biases from a network configuration file. George Dang in #852

  • Update GUI initialization of network, by George Dang in #853

  • Update GUI color, by Nick Tolley in #855

  • Added “No. Drive Cells” input widget to the GUI and changed the “Synchronous Input” checkbox to “Cell-Specific” to align with the API George Dang in #861

  • Add GUI export of configurations, George Dang in #862

  • Add screenshot of GUI to README, George Dang in #865 and #866

  • Add button to delete a single drive on GUI drive windows, by George Dang in #890

  • Add post-processing for GUI figures, by George Dang in #893

  • Add minimum spectral frequency widget to GUI for adjusting spectrogram frequency axis, by George Dang in #894

  • Update GUI to display “L2/3”, by Austin E. Soplata in #904

  • Update PSD plot in GUI to use plot config provided frequencies instead of hard-coded values, by Dylan Daniels in #914

  • Flip drives in input histogram based on position in GUI by Dylan Daniels in #923

  • Add GUI widget to adjust default smoothing value, by Dylan Daniels in #924

  • Change Morlet cycles divisor for better alpha spectral plotting by Austin E. Soplata in #928

  • Add GUI log error message if spectral arguments are invalid by Austin E. Soplata in #944

  • Move GUI log messages to bottom of output by George Dang in #946

  • Add GUI frequency default visualization parameters and many other smaller visual changes by Dylan Daniels in #952

  • Capture printed messages to logger in GUI by Dylan Daniels in #956

  • Correctly set layer-specific dipole axes limits in GUI, by Dylan Daniels in #1022

  • Improve spike raster plot by overlaying dipoles, by Dylan Daniels in #1026

PRs merged (Other)#

0.3#

Changelog#

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 as 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):#

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#

Bug#

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 instantiation 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):#

0.1#

Changelog#

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):#