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Published March 30, 2022 | Version v0.11.0
Software Open

Elephant 0.11.0

Authors/Creators

  • 1. Institute of Neuroscience and Medicine (INM-6) and Institute for Advanced Simulation (IAS-6) and JARA-Institute Brain Structure-Function Relationships (INM-10), Jülich Research Centre, Jülich, Germany
  • 2. Cognitronics and Sensor Systems, CITEC, Bielefeld University, Bielefeld, Germany

Description

Breaking changes
  • For current source density measures electrode coordinates can no longer be supplied via a RecordingChannelGroup object as it is no longer supported in Neo v0.10.0 (#447)
New functionality and features
  • Redesigned elephant.spike_train_generation module using classes (old API is retained for compatibility) (#416)
  • Added function to calculate the multitaper power spectral density estimate in elephant.spectral (#417)
  • Added a boundary correction for the firing rate estimator elephant.statistics.instantaneous_rate with Gaussian kernels (#414)
  • Function to discretise spiketimes for a given spiketrain in elephant.conversion (#454)
  • Support for the new SpikeTrainList object of Neo (#447)
Bug fixes
  • Issue with unit scaling in BinnedSpikeTrain (#425)
  • Changed BinnedSpikeTrain to support quantities<0.12.4 (#418)
  • Fix FloatingPointError in ICSD (#421)
  • t_start information was lost while transposing LFP for current_source_density module (#432)
  • Fix neo_tools unit tests to work with Neo 0.10.0+ (#446)
  • Fixed various issues with consistency of bin boundaries of instantaneous rates (#453)
Documentation
  • Update tutorials ASSET and UE tutorial and datasets to use nixio >=1.5.0 (#441)
  • Updated spade tutorial to work with viziphant 0.2.0 (#444)
  • Fixed figures in the Granger causality tutorial (#434)
  • Add DOIs to documentation (#456)
  • Fixed random seed selection in some tutorials (#430)
Optimizations
  • Highly optimized run-time of the SPADE analysis (#419)
  • More efficient storage of spike complexities by the elephant.statistics.Complexity class (#412)
  • Updated elephant.signal_processing.zscore function for in-place operations (#440)
Other changes
  • Continuous Integration (CI) was moved to github actions (#451)
  • Change test framework from Nose to pytest (#413)
  • Added DOI with zenodo (#445)
  • Versioning for associated elephant-data repository for example datasets introduced (#463)
Selected dependency changes
  • nixio >= 1.5.0
  • neo >= 0.10.0
  • python >= 3.7

Files

NeuralEnsemble/elephant-v0.11.0.zip

Files (1.7 MB)

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Additional details

Related works

Is documented by
Journal article: 10.12751/incf.ni2018.0019 (DOI)

Funding

European Commission
HBP SGA2 - Human Brain Project Specific Grant Agreement 2 785907
European Commission
HBP SGA3 - Human Brain Project Specific Grant Agreement 3 945539
European Commission
HBP SGA1 - Human Brain Project Specific Grant Agreement 1 720270
European Commission
HBP - The Human Brain Project 604102