Open Source Microscopy Software

开源显微镜软件

• 批准号: 8721211
• 负责人: RONALD D VALE
• 金额: $ 37.43万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2008
• 资助国家: 美国
• 起止时间: 2008-08-01 至 2016-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8721211
• 关键词: Academia; Address; Adopted; Advanced Development; Automation; Biomedical Research; Code; Communities; Computer software; Cost Savings; Data; Development; Devices; Documentation; Environment; Equipment; Fiji; Foundations; Grant; Image; Image Analysis; Individual; Industry; Life; Light Microscope; Lighting; Linux; Maintenance; Methods; Microscope; Microscopy; Modification; Nature; Optics; Pain; Procedures; Process; Protocols documentation; Quality Control; Reporting; Research; Research Personnel; Running; Savings; Scientist; Solutions; Source Code; Staging; Stress; Structure; System; Techniques; Time; United States National Institutes of Health; Vendor; Work; Writing; base; cost; design; digital; flexibility; improved; innovation; instrument; light microscopy; meetings; novel; open source; operation; programs; repository; research study; software development; tool; user-friendly

DESCRIPTION (provided by applicant): Modern light microscopes use digital cameras, motorized stages, shutters, filter wheels, etc., that need to be controlled by computer software. Various commercial solutions exists, all of which have shortfalls. The ?Manager software application is open source, freely available software for microscope automation written for and by scientists that runs on Windows, Mac OS X, and Linux. It provides an easy-to-use interface through which most microscope hardware can be controlled making it simple for scientists to carry out experiments using equipment from different vendors. The software is used at about 2000 microscopes world-wide, and provides significant savings to the NIH since individual copies of commercial alternatives cost $5-15k. ?Manager also provides a hardware abstraction layer that is used by scientists with programming abilities to automate their microscope hardware in novel and creative ways. The open source nature of this project not only makes it possible to see exactly how acquisition protocols are carried out (which is important in research), but also attracts many code contributions from industry and academia. Many companies already make sure that their equipment works within ?Manager and maintain the source code for their equipment in the ?Manager source code repository. More than 50 programmers have contributed code, a number that continues to rise. This grant will be used to continue stewardship of these many code contributions, regularly release user-friendly installers for the software, improve documentation, address bug reports, etc. It will also be used to add novel capabilities to the software such as live STORM/PALM imaging, structured illumination-based optical sectioning, and photo-bleaching/photo-activation using digital mirror devices. In addition, integration with existing open source microscopy-related software packages will be improved.

描述（由申请人提供）：现代光学显微镜使用数码相机、电动载物台、快门、滤光轮等，需要由计算机软件控制。存在各种商业解决方案，但它们都有不足之处。 ?Manager 软件应用程序是开源、免费的显微镜自动化软件，由科学家编写并由科学家编写，可在 Windows、Mac OS X 和 Linux 上运行。它提供了一个易于使用的界面，通过该界面可以控制大多数显微镜硬件，使科学家可以轻松地使用不同供应商的设备进行实验。该软件在全球约 2000 台显微镜中使用，为 NIH 节省了大量成本，因为商业替代品的单个副本成本为 5-15,000 美元。 Manager 还提供了一个硬件抽象层，具有编程能力的科学家可以使用该层以新颖且富有创意的方式自动化其显微镜硬件。该项目的开源性质不仅可以准确地了解采集协议的执行方式（这对于研究很重要），而且还吸引了来自工业界和学术界的许多代码贡献。许多公司已经确保他们的设备在 ?Manager 中工作，并在 ?Manager 源代码存储库中维护其设备的源代码。超过 50 名程序员贡献了代码，而且这个数字还在持续上升。这笔赠款将用于继续管理这些众多的代码贡献，定期发布用户友好的软件安装程序，改进文档，解决错误报告等。它还将用于为软件添加新颖的功能，例如实时 STORM/ PALM 成像、基于结构化照明的光学切片以及使用数字镜装置的光漂白/光激活。此外，与现有开源显微镜相关软件包的集成也将得到改进。

项目成果

Advanced methods of microscope control using μManager software.

使用μManager 软件进行显微镜控制的先进方法。

• DOI: 10.14440/jbm.2014.36
• 发表时间: 2014-11-07
• 期刊: Journal of biological methods
• 作者: A. Edelstein;Mark A. Tsuchida;Nenad Amodaj;H. Pinkard;R. Vale;N. Stuurman
• 通讯作者: N. Stuurman

An acquisition and analysis pipeline for scanning angle interference microscopy.

用于扫描角干涉显微镜的采集和分析管道。

• 发表时间: 2016-10-31
• 影响因子: 48
• 作者: Carbone, Catherine B;Vale, Ronald D;Stuurman, Nico
• 通讯作者: Stuurman, Nico

Computer control of microscopes using µManager.

使用 µManager 对显微镜进行计算机控制。

• 发表时间: 2010-10
• 作者: Edelstein, Arthur;Amodaj, Nenad;Hoover, Karl;Vale, Ron;Stuurman, Nico
• 通讯作者: Stuurman, Nico

Micropilot: automation of fluorescence microscopy-based imaging for systems biology.

Micropilot：基于荧光显微镜的系统生物学成像自动化。

• 发表时间: 2011-03
• 影响因子: 48
• 作者: Conrad, Christian;Wünsche, Annelie;Tan, Tze Heng;Bulkescher, Jutta;Sieckmann, Frank;Verissimo, Fatima;Edelstein, Arthur;Walter, Thomas;Liebel, Urban;Pepperkok, Rainer;Ellenberg, Jan
• 通讯作者: Ellenberg, Jan

Impact of New Camera Technologies on Discoveries in Cell Biology.

新相机技术对细胞生物学发现的影响。

• 发表时间: 2016
• 作者: Stuurman, Nico;Vale, Ronald D
• 通讯作者: Vale, Ronald D