OpenFIBSEM: A universal API for FIBSEM control

IF 3 3区生物学 Q3 BIOCHEMISTRY & MOLECULAR BIOLOGY

Journal of structural biology Pub Date : 2023-09-01 DOI:10.1016/j.jsb.2023.107967

Patrick Cleeve , David Dierickx , Lucile Naegele , Rohit Kannachel , Lachlan Burne , Genevieve Buckley , Sergey Gorelick , James C. Whisstock , Alex de Marco

{"title":"OpenFIBSEM: A universal API for FIBSEM control","authors":"Patrick Cleeve , David Dierickx , Lucile Naegele , Rohit Kannachel , Lachlan Burne , Genevieve Buckley , Sergey Gorelick , James C. Whisstock , Alex de Marco","doi":"10.1016/j.jsb.2023.107967","DOIUrl":null,"url":null,"abstract":"<div><p>This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development.</p><p>OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (<span>https://github.com/DeMarcoLab/fibsem</span><svg><path></path></svg>).</p></div>","PeriodicalId":17074,"journal":{"name":"Journal of structural biology","volume":null,"pages":null},"PeriodicalIF":3.0000,"publicationDate":"2023-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Journal of structural biology","FirstCategoryId":"99","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S1047847723000308","RegionNum":3,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q3","JCRName":"BIOCHEMISTRY & MOLECULAR BIOLOGY","Score":null,"Total":0}

引用次数: 0

Abstract

This paper introduces OpenFIBSEM, a universal API to control Focused Ion Beam Scanning Electron Microscopes (FIBSEM). OpenFIBSEM aims to improve the programmability and automation of electron microscopy workflows in structural biology research. The API is designed to be cross-platform, composable, and extendable: allowing users to use any portion of OpenFIBSEM to develop or integrate with other software tools. The package provides core functionality such as imaging, movement, milling, and manipulator control, as well as system calibration, alignment, and image analysis modules. Further, a library of reusable user interface components integrated with napari is provided, ensuring easy and efficient application development.

OpenFIBSEM currently supports ThermoFisher and TESCAN hardware, with support for other manufacturers planned. To demonstrate the improved automation capabilities enabled by OpenFIBSEM, several example applications that are compatible with multiple hardware manufacturers are discussed. We argue that OpenFIBSEM provides the foundation for a cross-platform operating system and development ecosystem for FIBSEM systems. The API and applications are open-source and available on GitHub (https://github.com/DeMarcoLab/fibsem).

查看原文本刊更多论文

OpenFIBSEM：用于FIBSEM控制的通用API

本文介绍了一种控制聚焦离子束扫描电子显微镜的通用API——OpenFIBSEM。OpenFIBSEM旨在提高结构生物学研究中电子显微镜工作流程的可编程性和自动化。API被设计为跨平台、可组合和可扩展的：允许用户使用OpenFIBSEM的任何部分来开发或与其他软件工具集成。该软件包提供核心功能，如成像、移动、铣削和机械手控制，以及系统校准、对准和图像分析模块。此外，还提供了一个与napari集成的可重用用户界面组件库，确保了应用程序开发的简单高效。OpenFIBSEM目前支持ThermoFisher和TESCAN硬件，并计划支持其他制造商。为了展示OpenFIBSEM实现的改进的自动化功能，讨论了几个与多个硬件制造商兼容的示例应用程序。我们认为OpenFIBSEM为FIBSEM系统的跨平台操作系统和开发生态系统提供了基础。API和应用程序是开源的，可在GitHub上使用(https://github.com/DeMarcoLab/fibsem)。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

求助全文

约1分钟内获得全文求助全文

来源期刊

Journal of structural biology 生物-生化与分子生物学

CiteScore

6.30

自引率

3.30%

发文量

审稿时长

65 days

期刊介绍： Journal of Structural Biology (JSB) has an open access mirror journal, the Journal of Structural Biology: X (JSBX), sharing the same aims and scope, editorial team, submission system and rigorous peer review. Since both journals share the same editorial system, you may submit your manuscript via either journal homepage. You will be prompted during submission (and revision) to choose in which to publish your article. The editors and reviewers are not aware of the choice you made until the article has been published online. JSB and JSBX publish papers dealing with the structural analysis of living material at every level of organization by all methods that lead to an understanding of biological function in terms of molecular and supermolecular structure. Techniques covered include: • Light microscopy including confocal microscopy • All types of electron microscopy • X-ray diffraction • Nuclear magnetic resonance • Scanning force microscopy, scanning probe microscopy, and tunneling microscopy • Digital image processing • Computational insights into structure