Software

sigInspect - Matlab GUI for MER signal annotation 

sigInspect is a graphical user interface (GUI) application for Matlab, developed for inspection and
annotation of extracellular microelectrode recordings (MER). The tool allows concurrent visualizationof multiple parallel channels, playback and spectrogram plot of selected channels (to identify specific firing patterns) and especially annotation of individual channels. Parallel signals are displayed in one-second segments, which can be easily annotated using the GUI controls or shortcut keys. SigInspect also contains tools for automatic annotation of microelectrode recording data, based on published methods. This can provide starting point for manual annotation and speed up the data-cleaning process considerably.

sigInspect and manual available at github.com/ebakstein/sigInspect

Refer also to our paper, describing the classification methodology:

Bakštein, E., Sieger, T., Wild, J., Novák, D., Schneider, J., Vostatek, P., Urgošík, D., Jech, R. (2017). Methods for automatic detection of artifacts in microelectrode recordings. In: Journal of Neuroscience Methods, 290, 39–51. [PDF, supplementary: PDF, matlab codes, data (18MB)]

idendro - Interactive Dendrograms

idendro is an  R package enabling to inspect dendrograms, resulting from hierarchical cluster analysis, interactively: to select and color clusters, to zoom and pan the dendrogram, and to visualize the clustered data not only in a built-in heat map, but also in any interactive plot implemented in the cranvas R package.

idendro is a visualization and exploration tool suitable for interactive analysis of general data, but it comes extremely helpful when analysing moderate- or high-dimensional data. idendro has been successfully applied on flow cytometry data, spectroscopic data, neurophysiological data, and more.

To install a version implemented using Qt graphics, please visit github.com/tsieger/idendro (available for Linux and MacOS, Windows support is limited).
To install a fully cross-platform version implemented using base R graphics and Tcl/Tk GUI, please visit github.com/tsieger/idendr0.

A comprehensive description of idendro is available in Sieger T, Hurley CB, Fišer K, Beleites C. Interactive Dendrograms: The R Packages idendro and idendr0. Journal of Statistical Software 76(10), doi: 10.18637/jss.v076.i10.