The ERGtools2 package: a toolset for processing and analysing visual electrophysiology data.

IF 2.6 4区医学 Q2 OPHTHALMOLOGY

Documenta Ophthalmologica Pub Date : 2025-04-12 DOI:10.1007/s10633-025-10017-2

Moritz Lindner

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引用次数: 0

Abstract

Purpose: To introduce ERGtools2, an open-source R package for processing, analysing and long-term storing visual electrophysiology data.

Methods: A dataset comprising Electroretinogram (ERG) recordings of C57Bl/6J mice, subjected to standard ISCEV stimuli, was used to present the functionality of ERGtools2. ERGtools2 stores and organizes all recordings, metadata, and measurement information from an individual examination in a single object, maintaining raw data throughout the analysis process.

Results: A standard workflow is presented exemplifying how ERGtools2 can be used to efficiently import, pre-process and analyse ERG data. Following this workflow, basic ERG measurements and visualisation of a single exam as well as group statistics are obtained. Moreover, special use cases are described, including for the handling of noisy data and the storage of data in the HDF5 format to ensure long-term preservation and accessibility.

Conclusions: ERGtools2 provides a comprehensive, flexible, and device-independent solution for visual electrophysiology data analysis. Its emphasis on maintaining raw data integrity, combined with advanced processing and analysis capabilities, makes it a useful tool for preclinical and clinical research applications. The open-source nature and the use of open data formats promote reproducibility and data sharing in visual neurosciences.

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ERGtools2包：用于处理和分析视觉电生理数据的工具集。

目的：介绍用于处理、分析和长期存储视觉电生理数据的开源R包ERGtools2。方法：使用标准ISCEV刺激下C57Bl/6J小鼠视网膜电图（ERG）记录数据集来展示ERGtools2的功能。ERGtools2存储和组织来自单个对象的单个检查的所有记录、元数据和测量信息，在整个分析过程中维护原始数据。结果：提出了一个标准的工作流程，举例说明如何使用ERGtools2有效地导入、预处理和分析ERG数据。按照这个工作流程，可以获得基本的ERG测量和单个检查的可视化以及组统计数据。此外，还描述了特殊用例，包括处理噪声数据和以HDF5格式存储数据，以确保长期保存和可访问性。结论：ERGtools2为视觉电生理数据分析提供了一个全面、灵活且与设备无关的解决方案。它强调保持原始数据的完整性，结合先进的处理和分析能力，使其成为临床前和临床研究应用的有用工具。开放源代码的性质和开放数据格式的使用促进了视觉神经科学的再现性和数据共享。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Documenta Ophthalmologica 医学-眼科学

CiteScore

3.50

自引率

21.40%

发文量

审稿时长

>12 weeks

期刊介绍： Documenta Ophthalmologica is an official publication of the International Society for Clinical Electrophysiology of Vision. The purpose of the journal is to promote the understanding and application of clinical electrophysiology of vision. Documenta Ophthalmologica will publish reviews, research articles, technical notes, brief reports and case studies which inform the readers about basic and clinical sciences related to visual electrodiagnosis and means to improve diagnosis and clinical management of patients using visual electrophysiology. Studies may involve animals or humans. In either case appropriate care must be taken to follow the Declaration of Helsinki for human subject or appropriate humane standards of animal care (e.g., the ARVO standards on Animal Care and Use).