Biophysical essentials - A full stack open-source software framework for conserved and advanced analysis of patch-clamp recordings

Background and objectives: Patch-Clamp recordings allow for in depth electrophysiological characterization of single cells, their general biophysical properties as well as characteristics of voltage- and ligand-gated ionic currents. Different acquisition modes, such as whole-cell patch-clamp recordings in the current or voltage clamp configuration, capacitance measurements or single channel recordings from cultured cells as well as acute brain slices are routinely performed for these purposes. Nevertheless, multipurpose transparent and adaptable software tools to perform reproducible state-of-the-art analysis of multiple experiment types and to manage larger sets of experimental data are currently unavailable.

Methods: Biophysical Essentials (BPE) was developed as an open-source full stack python software for transparent and reproducible analysis of electrophysiological recordings. For validation, BPE results were compared with manually analyzed single-cell patch-clamp data acquired from a human in vitro nociceptor-model and mouse dorsal root ganglia neurons.

Results: While initially designed to improve time consuming and repetitive analysis steps, BPE was further optimized as a technical software solution for entire workflow processing including data acquisition, data preprocessing, normalization and visualization and of single recordings up to stacked calculations and statistics of multiple experiments. BPE can operate with different file formats from different amplifier systems and producers. An in-process database logs all analysis steps reproducible review and serves as a central storage point for recordings. Statistical testing as well as advanced analysis functions like Boltzmann-fitting and dimensional reduction methods further support the researchers' needs in projects involving electrophysiology techniques.

Conclusions: BPE extends beyond available patch-clamp specific, open source - and commercial analysis tools in particular because of reproducible and sharable analysis workflows. BPE enables full analysis from raw data acquisition to publication ready result visualizations - all within one single program. Thereby, BPE significantly enhances transparency in the analytical process of patch-clamp data analysis. BPEs function scope is completely accessible through an easy-to-use graphical user interface eliminating the need for programing language proficiency as required by many community patch-clamp analysis frameworks and algorithms.