PatchView: A Python Package for Patch-clamp Data Analysis and Visualization
Ming Yan Hu, Xiaolong Jiang · The Journal of Open Source Software · 2022
PatchView is a Python package for visualizing and analyzing multi channel patch-clamp (multi-patch) data (Neher & Sakmann, 1992), including intrinsic membrane properties and firing pattern analysis (Komendantov et al., 2019;McKinney et al., 2022), mini-event analysis (Clements & Bekkers, 1997), synaptic connection detection (Jiang et al., 2015), morphological analysis (Palacios et al., 2022) and more.PatchView integrates multiple open-source tools and provides an intuitive graphic user interface (GUI) for navigating through the data files and analyses pipeline.It is aimed to enable users to perform most analysis quickly for the data collected in a typical patch-clamp experiment without managing a Python environment or writing any Python scripts.Please refer to the full documentation and the source code for detailed information. Statement of Need Research purposePatchView was designed to be used by neuroscientists for handling electrophysiology data recorded from cells in alive tissues (such as brain slice or cultured cells) in patch-clamp experiments.The target audience is anyone working with patch-clamp data, with or without programming skills. Problems solvedMain functionalities of PatchView: •Importing both Heka data and Axon Instruments data.Exporting to Python pickle file or NWB (Neurodata Without Borders) file format (Rübel et al., 2022).• Visualizing single and multiple traces with zoom, pan operations.• Automatically sorting experiments data according to predefined labels.