Open source software for laser scanning microscopy

用于激光扫描显微镜的开源软件

• 批准号: 6752116
• 负责人: Karel Svoboda
• 金额: $ 29.6万
• 依托单位: COLD SPRING HARBOR LABORATORY
• 依托单位国家: 美国
• 财政年份: 2003
• 资助国家: 美国
• 起止时间: 2003-06-01 至 2008-03-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6752116
• 关键词: bioengineering /biomedical engineering; bioimaging /biomedical imaging; biomedical resource; computer program /software; computer system design /evaluation; confocal scanning microscopy; fluorescence microscopy; handbook; image processing; information dissemination; lasers; technical writing

DESCRIPTION (provided by applicant): Over the last decade the availability of new laser light sources and modern data acquisition engines has dramatically increased the range of applications of laser scanning microscopy (LSM). Today, LSM includes some of the most important optical imaging modalities in biology, including confocal and 2-photonmicroscopy. LSM is central to research in neurobiology, cancer research, immunology, pathology, developmental biology and other fields of research. Experimental systems amenable to LSM range from single biomolecules to whole living animals. Although numerous commercial LSMs exist, the most interesting and challenging applications of LSM demand custom hardware and software. However, few investigators have attempted this approach, mainly because of the difficulty of writing the complex software required to run a laser scanning microscope. Open source software for laser scanning microscopy is not available. In our laboratory we have developed a powerful program to control a laser scanning microscope. This program, Scanlmage, performs all of the typical functions a LSM performs with important advantages, i) Scanlmage is almost entirely written in Matlab, thereby fusing image acquisition with one of the most sophisticated image analysis environments; ii) Scanlmage uses a novel approach to signal conditioning and integration, and does not require complex custom electronics, removing significant obstacles to custom design; iii) Scanlmage miswritten in a modular and object-oriented style, making it easily expandable to accommodate emerging technologies. We propose to produce on-line help and documentation for Scanlmage and make the software available open source. We further propose to develop new modules for Scanlmage to address the need to integrate LSM with new imaging technologies. These new modules will include random access laser scanning, the simultaneous operation of two scanners (e.g. one for imaging and the other for photolytic release of bioactive substances), and the combination of laser scanning microscopy and fluorescence lifetime imaging. We believe that Scanlmage will facilitate exciting biological discovery in numerous laboratories.

描述（由申请人提供）：在过去的十年中，新的激光光源和现代数据采集引擎的可用性显着增加了激光扫描显微镜（LSM）的应用范围。如今，LSM包括生物学中一些最重要的光学成像方式，包括共聚焦和2-光子显微镜检查。 LSM对于神经生物学，癌症研究，免疫学，病理学，发育生物学和其他研究领域的研究至关重要。可以适应LSM的实验系统范围从单个生物分子到整个活体动物。尽管存在许多商业LSM，但LSM需求自定义硬件和软件的最有趣，最具挑战性的应用程序。但是，很少有人尝试这种方法，这主要是因为很难编写运行激光扫描显微镜所需的复杂软件。无法使用激光扫描显微镜的开源软件。在我们的实验室中，我们开发了一个强大的程序来控制激光扫描显微镜。该程序（ScanlMage）执行LSM具有重要优势的所有典型功能，i）scanlMage几乎完全用MATLAB编写，从而将图像采集与最复杂的图像分析环境之一融合在一起； ii）扫描使用一种新颖的方法来信号调理和集成，并且不需要复杂的自定义电子设备，从而消除了定制设计的重大障碍； iii）扫描以模块化和面向对象的样式误解，使其易于扩展以适应新兴技术。我们建议为扫描仪生成在线帮助和文档，并使软件提供开源。我们进一步建议开发扫描模块的新模块，以解决将LSM与新成像技术集成的需求。这些新模块将包括随机访问激光扫描，两个扫描仪的同时操作（例如，一个用于成像，另一个用于生物活性物质的光解释放）以及激光扫描显微镜和荧光寿命成像的组合。我们认为，扫描将有助于许多实验室中的激动人心的生物学发现。