Open source software for laser scanning microscopy

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大大增加了激光扫描显微镜（LSM）的应用范围。今天，LSM包括生物学中一些最重要的光学成像模式，包括共聚焦和双光子显微镜。LSM是神经生物学、癌症研究、免疫学、病理学、发育生物学和其他研究领域的核心。适用于LSM的实验系统范围从单个生物分子到整个活体动物。虽然存在许多商业LSM，但LSM最有趣和最具挑战性的应用需要定制硬件和软件。然而，很少有研究人员尝试这种方法，主要是因为编写运行激光扫描显微镜所需的复杂软件的难度。激光扫描显微镜的开源软件不可用。在我们的实验室里，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执行的所有典型功能，具有重要的优点，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; ii）Scanlmage使用新颖的信号调节和积分方法，并且不需要复杂的定制电子器件，消除了定制设计的重大障碍; iii）以模块化和面向对象的风格编写的扫描图像，使其易于扩展以适应新兴技术。我们建议为Scanlmage制作在线帮助和文档，并使软件开放源代码。我们还建议为Scanlmage开发新模块，以满足将LSM与新成像技术集成的需求。这些新的模块将包括随机存取激光扫描、两台扫描仪的同时操作（例如，一台用于成像，另一台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。我们相信Scanlmage将促进众多实验室令人兴奋的生物发现。

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.