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Related Concept Videos

Patch Clamp

Patch Clamp

Many fundamental cell functions such as muscle contraction and nerve transmission rely on the electrical signals produced by the movement of positively and negatively charged ions across the cell membrane. One competent method to record current flowing across the whole cell or single ion channel is the patch-clamp technique.
In this method, a glass micropipette containing electrolyte solution is tightly sealed against a small portion of the cell membrane. As a result, a patch of the cell...

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Related Experiment Video

Updated: Jun 20, 2025

One-channel Cell-attached Patch-clamp Recording

One-channel Cell-attached Patch-clamp Recording

Published on: June 9, 2014

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

David Zimmermann¹, Michaela Kress¹, Maximilian Zeidler²

¹Institute of Physiology, Medical University of Innsbruck, Innsbruck, Austria.

Computer Methods and Programs in Biomedicine

|July 22, 2024

Summary

Biophysical Essentials (BPE) is a new open-source software for electrophysiology data analysis. It streamlines patch-clamp recordings from acquisition to visualization, enhancing reproducibility and transparency for researchers.

Keywords:

Current kinetics Curve fitting Electrophysiology Open-source analysis Patch-clamp recording

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Patch Clamp Recordings from Embryonic Zebrafish Mauthner Cells

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Last Updated: Jun 20, 2025

One-channel Cell-attached Patch-clamp Recording

One-channel Cell-attached Patch-clamp Recording

Published on: June 9, 2014

Whole-cell Patch-clamp Recordings from Morphologically- and Neurochemically-identified Hippocampal Interneurons

Whole-cell Patch-clamp Recordings from Morphologically- and Neurochemically-identified Hippocampal Interneurons

Published on: September 30, 2014

Patch Clamp Recordings from Embryonic Zebrafish Mauthner Cells

Patch Clamp Recordings from Embryonic Zebrafish Mauthner Cells

Published on: September 10, 2013

Area of Science:

Electrophysiology
Neuroscience
Computational Biology

Background:

Patch-clamp recordings are crucial for characterizing cellular electrophysiology.
Current software lacks comprehensive, adaptable tools for reproducible analysis of diverse patch-clamp data.
Managing large electrophysiological datasets and ensuring analysis transparency remains a challenge.

Purpose of the Study:

To introduce Biophysical Essentials (BPE), an open-source software solution for electrophysiological data analysis.
To provide a transparent, reproducible, and adaptable platform for the entire workflow of patch-clamp experiments.
To address the limitations of existing tools in managing and analyzing complex electrophysiological datasets.

Main Methods:

Development of Biophysical Essentials (BPE) as a full-stack Python software.
Implementation of features for data acquisition, preprocessing, normalization, and visualization.
Validation through comparison with manually analyzed patch-clamp data from human and mouse neurons.

Main Results:

BPE offers a comprehensive solution for the entire electrophysiology workflow, from data acquisition to publication-ready visualizations.
The software supports various file formats and includes an in-process database for reproducible logging of analysis steps.
Advanced functions like Boltzmann-fitting and dimensional reduction are integrated, alongside statistical testing capabilities.

Conclusions:

BPE surpasses existing open-source and commercial tools by offering reproducible and sharable analysis workflows for patch-clamp data.
The software enhances transparency in electrophysiological data analysis, enabling full processing within a single program.
BPE's graphical user interface makes advanced electrophysiology analysis accessible without requiring programming expertise.