Introduction

Recording neural activity is key to understanding neural circuit function, and ultimately, how the most complex organ known to humankind, the brain, works. However, electrophysiological recordings can produce large volumes of data, which need to be acquired, analyzed and visualized. While commercial software is available for these tasks, its source code is generally closed, which severely limits the experimental possibilities, as the integration of hardware and other software is limited and the existing functionality cannot be expanded. Thus, for many electrophysiological projects, especially novel and original ones extending beyond the established standards, custom-written, open source software is required. As the Ala-Laurila Laboratory is developing a novel multi-electrode patch clamp recording method, the need for custom data analysis software arose, as none of the existing software standards were optimized for the analysis of the resulting data structures.

SA-Labs-Analysis is a Matlab based data analysis toolbox for multi-electrode patch clamp recordings. It provides a graphical user interface to pre-process, analyze, and visualize the acquired data. Furthermore, the analysis toolbox is designed to support both streaming and post-acquisition analysis by using shared libraries and data structure.

The SA-Labs-Analysis toolbox is an extension to the sa-labs-analysis-core - a generic framework to build an analysis pipeline using Matlab. It also integrates features from different Github repositories. For example, common analysis functions for electrophysiological data analysis are maintained in the sa-labs-util repository, and the master configuration for managing the metadata of experiments such as cell class, cell type are saved in the sa-labs-analysis-preference repository. The raw data for the analysis is acquired using symphony-das - a Matlab based data acquisition system for electrophysiologists. The user interface and analysis architecture were inspired by source code from world-leading electrophysiology laboratories, such as Schwartz Lab Symphony Analysis, Rieke-Lab symphony-das and BrainardLab MatlabJobSupport.

As a way of promoting open science, the source code for the SA-Labs-Analysis toolbox, its dependent libraries, and its documentation is publicly available on Github and licensed under MIT.

Copyright (c) 2017 Schwartz-AlaLaurila-Labs