PatchView: A Python Package for Patch-clamp Data
Analysis and Visualization

Hu, Ming; Jiang, Xiaolong

doi:10.21105/joss.04706

Cited by 5 publications

(3 citation statements)

References 10 publications

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“…A custom-made Python software kit named as Patchview was developed to analyze the electrophysiology data offline (Ming Hu, 2022). We extracted 13 electrophysiological properties from each neuron, following a similar method as used in previous studies (Gouwens et al, 2019;Scala et al, 2021).…”

Section: Electrophysiological Features Extractionmentioning

confidence: 99%

Cellular and Circuit Organization of the Locus Coeruleus of Adult Mice

McKinney

Jing

et al. 2022

Preprint

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The locus coeruleus (LC) houses the vast majority of noradrenergic neurons in the brain and regulates many fundamental functions. While efferent projections of the LC have been extensively investigated, little is known about its local circuit organization. Here, we performed large-scale multi-patch recordings of LC noradrenergic neurons to profile their morpho-electric properties while simultaneously examining their interactions. LC neurons were diverse and could be classified into two major morpho-electric types. While chemical transmission was not detected, these neurons electrically connected at a rate comparable to many brain regions. Most connections form between dendrites and were restricted to narrowly spaced pairs or small clusters of neurons of the same type. Furthermore, more than two coupled pairs were often identified from individual recording sets that follow a train-like organizational pattern. The assembly of LC neurons follows a spatial and cell type-specific wiring principle that may be imposed by a unique train-like rule.

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Section: Electrophysiological Features Extractionmentioning

confidence: 99%

Cellular and Circuit Organization of the Locus Coeruleus of Adult Mice

McKinney

Jing

et al. 2022

Preprint

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“…Electrophysiological data were analyzed with a python-based GUI named PatchView that we have developed (Ming Hu, 2022) or a custom-made IDL code. To access the IDL code, the raw electrophysiological data was exported to ASCII format using Nest-o-Patch.…”

Section: Quantification and Statistical Analysismentioning

confidence: 99%

Molecular logic for cellular specializations that initiate the auditory parallel processing pathways

Jing

Ngodup

et al. 2023

Preprint

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SummaryThe cochlear nucleus (CN), the starting point for all auditory processing in the brain, comprises a suite of well-defined cell types that are morphologically and biophysically specialized for initiating parallel processing pathways, yet their molecular distinctions are largely unknown. To determine how their functional specialization is determined at the molecular level, we employed a single-nucleus RNA sequencing analysis of the mouse CN to transcriptomically define its cell types and then related each molecularly distinct cell type to well-established cell type via Patch-seq, an approach linking single-cell transcriptome to their morphological/electrophysiological features. We reveal a one-to-one correspondence between an expanded set of molecular cell types and all previously described major types. Our approach also yields a set of novel markers for these cell types, as well as clear molecular subtypes for several major principal cell types. This study thus establishes the CN as a brain region with clearly defined cell types from the molecular to the circuit level, opening a new window for genetic dissection of auditory processing and hearing disorders.

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“…BPEs ability to keep track of intra-and extracellular recording solution as well as stimulation protocols enables to compare data taking into account different recording conditions such as ionic strength and will be further developed to correct for these differences relevant for data comparison. BPE extends beyond already available patch clamp specific, open source and full stack analysis tools such as the python tool PatchView(Hu & Jiang, 2022) or the C++ based software StimFit(Guzman et al, 2014). since it was developed in particular for reproducible analysis workflow which is documented in detail and stored in the background database.…”

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confidence: 99%

Biophysical Essentials – A Full Stack Open-Source Software Framework for Conserved and Advanced Analysis of Patch-Clamp Recordings

Zimmermann,

Kress,

Zeidler

2024

Preprint

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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. We therefore developed Biophysical Essentials (BPE) as an open-source python software for transparent and reproducible analysis of electrophysiological recordings. While initially designed to improve time consuming and repetitive analysis steps, BPE was optimized to cover entire workflows from data acquisition, preprocessing, visualization and normalization 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 for later 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.

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PatchView: A Python Package for Patch-clamp Data Analysis and Visualization

Cited by 5 publications

References 10 publications

Cellular and Circuit Organization of the Locus Coeruleus of Adult Mice

Cellular and Circuit Organization of the Locus Coeruleus of Adult Mice

Molecular logic for cellular specializations that initiate the auditory parallel processing pathways

Biophysical Essentials – A Full Stack Open-Source Software Framework for Conserved and Advanced Analysis of Patch-Clamp Recordings

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