Milestone v0.2

[skim0119]

Milestone v0.2

Not all features will be included for v0.2, and the remaining will be pushed to the next release.
If an external package is already available, a simple wrapper (if needed) with detailed documentation on how to use that package could be sufficient.

New Features

For each category, the sublist is in the order of priority.

• Data Conversion
  • List of SpikeTrains to scipy sparse matrix format @skim0119 (Included in elephant.conversion)
• Connectivity
  • Connectivity: cross-correlation #41 @Gauravu2
  • Connectivity: cross-entropy and directed information #58 @Gauravu2
  • coherence Connectivity: granger causality and cross-entropy #51 @Gauravu2
  • granger causality Connectivity: granger causality and cross-entropy #51 @Gauravu2
  • spike triggered average #70
  • spike field coherence #69
  • directed transfer information Connectivity: cross-entropy and directed information #58 @Gauravu2
  • mutual information Connectivity: cross-entropy and directed information #58 @Gauravu2
  • misc information theory Connectivity: cross-entropy and directed information #58 @Gauravu2
    • shannon-entropy
    • block entropy
    • entropy rate
    • active information
    • relative entropy
    • conditional entropy
    • transfer entropy
• Criticality
  • Avalanche detection #40 @frthjf
  • Example Dataset (7bb3486) @skim0119
• Spike Classification / Quantification
  • Wavelet/PCA characterization
  • Correlation Matrix 74f7a47 @jihugo
• Statistics / Analysis
  • Inter-spike interval histogram (ISIH) #43 @armantekinalp
  • Coefficient variation #46 @skim0119
  • Peri-stimulus time histogram (PSTH) #49 @armantekinalp
  • Burst Analysis #54 @Gauravu2
  • Fano Factor Fano Factor #65 @Gauravu2
  • Tuning curves
• Visualization
  • MEA geometry visualization (MEA - Geometry module #24) @skim0119
  • Visualization: connectivity network #47 @Gauravu2
  • Multi-channel signal replay #59 @armantekinalp

Additional Functions

Here is the list of functions we would like to implement using our code. Some could be accomplished by having "how-to" documentation, some might need additional implementations on the modules. Feel free to make a separate issue and propose ideas if you want to take a shot.

• Automatic channel masking #36 @jihugo

Data Organization

• Simple practice dataset Create a validated data set for development and testing of prototype data format #38 Update: Sample dataset and utilities to install #39
• External data installation utilities Update: Sample dataset and utilities to install #39
  • In-line download for Colab or remote-server
  • Hash check for large file
  • Archive extraction

Documentation

Coverage

• Improve coverage of MiV-OS #64

Others

• Plugin interface for MiV-Simulator

[skim0119]

It looks like we have many implementations finished. I'll try to wrap up the version and make a release.