Friday, September 6, 2013

Spyke Viewer 0.4.0 released

We are pleased to announce the release of spykeutils and Spyke Viewer 0.4.0, available on PyPi, NeuroDebian and as binary version.

Spyke Viewer is a multi-platform GUI application for navigating, analyzing and visualizing data from electrophysiological experiments or neural simulations.  It is based on the Neo library, which enables it to load a wide variety of data formats used in electrophysiology. At its core, Spyke Viewer includes functionality for navigating Neo object hierarchies and performing operations on them. spykeutils is a Python library containing analysis functions and plots for Neo objects.

A central design goal of Spyke Viewer is flexibility. For this purpose, it includes an embedded Python console for exploratory analysis, a filtering system, and a plugin system. Filters are used to semantically define data subsets of interest. Spyke Viewer comes with a variety of plugins implementing common neuroscientific plots (e.g. rasterplot, peristimulus time histogram, correlogram, and signal plot). Custom plugins for other analyses or plots can be easily created and modified using the integrated Python editor or external editors. Documentation and installation instructions are at

In addition, the Spyke Repository is now online. Find Spyke Viewer extensions (e.g. plugins, startup script snippets, IO plugins etc.) or share your own at Among the extensions currently hosted at the site are plugins for spike detection and spike sorting.

Some highlights from the changelogs since 0.2.0 (available for spykeutils and Spyke Viewer):
  • spykeutils & Spyke Viewer: Support for lazy loading features in current Neo development version 
  • spykeutils & Spyke Viewer: New features for spike waveform and correlogram plots 
  • Spyke Viewer: Splash screen while loading the application 
  • Spyke Viewer: Better support for starting plugins remotely: Progress bar and console output available 
  • Spyke Viewer: Additional data export formats 
  • Spyke Viewer: A startup script and an API enable more configuration and customization 
  • Spyke Viewer: Forcing a specific IO class is now possible. Graphical options for IOs with parameters 
  • Spyke Viewer: Filters are automatically deactivated on loading a selection if they prevent parts of it to be shown 
  • Spyke Viewer: Modified plugins are saved automatically before starting the plugin 
  • Spyke Viewer: Plugin configurations are now restored when saving or refreshing plugins and when restarting the program 
  • Spyke Viewer: Added context menu for navigation. Includes entries for removing objects and an annotation editor. 
  • Spyke Viewer: The editor now has search and replace functionality (access wiht Ctrl+F and Ctrl+H) 
  • spykeutils: Fast and well tested implementations for many spike train metrics (contributed by Jan Gosmann) 

The new version can be installed over older versions and will keep previous configuration, filters and plugins.