Open Source Microscopy Software

开源显微镜软件

• 批准号: 7426511
• 负责人: RONALD D VALE
• 金额: $ 40.08万
• 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 2012-05-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/7426511
• 关键词: Architecture; Biological Sciences; Boxing; Case Study; Charge; Clinical Research; Code; Complex; Computer software; Computers; Condition; Cost Savings; Custom; Data; Data Collection; Databases; Development; Devices; Documentation; Electronic Mail; Environment; Foundations; Generations; Grant; Hand; Image; Image Analysis; Imaging Techniques; Informatics; Java; Laboratories; Language; Light; Light Microscope; Linux; Metadata; Microscope; Microscopy; Motion; Names; Numbers; Online Systems; Operating System; Operative Surgical Procedures; Output; Plug-in; Positioning Attribute; Procedures; Process; Protocols documentation; Range; Research; Research Personnel; Sampling; Scanning; Scientist; Shapes; Source; Source Code; Specific qualifier value; Speed; Staging; Standards of Weights and Measures; Stream; Support System; Syndrome; Systems Analysis; Technology; Testing; Time; Today; Trees; United States National Institutes of Health; Work; Writing; base; cellular imaging; cost; data mining; design; digital; experience; file format; improved; interest; interoperability; light microscopy; new technology; novel; open source; platform-independent; programs; research study; software development; syntax; tool; tool development

DESCRIPTION (provided by applicant): Ever since the inception of the microscope by van Leeuwenhoek in the 17th century, microscopy has been the cornerstone technology of biological sciences. Today, digital microscopy is revolutionizing basic life science and clinical research. Direct observation through an eyepiece is becoming uncommon and is rapidly being replaced by data collection using digital cameras. In addition to a digital camera, contemporary microscopes have several motion devices (shutters, motorized states, filter wheels or turrets, z-drives, etc.) whose operation needs to be orchestrated according to the researcher's experimental needs. Thus, software control of microscope image acquisition has become indispensable. There are several commercial software packages available, but they suffer from 1) limitations in the hardware they can control, 2) impossibility of adding hardware support to change their hardwired experimental strategies, 3) the 'black box' syndrome, i.e. the tendency to make it difficult to work together with other software and databases, and 4) high cost. To remedy this situation, we have developed Open Source Software that controls microscope image acquisition. The software is easy to install and operate, yet can be extended at any level. For instance, hardware support can be added by the end-user and experimental strategies can be changed using a built-in scripting language. The user interface has been shaped with extensive help of researchers in the lab. The software is maintained on multiple platforms (Windows, Mac, Linux). Here, we aim to extend our initial software by greatly increasing the number of supported hardware and by enabling high speed and multi-position acquisition. We plan to make it easier for researchers to change the software by adding automatic code generation and strengthening the existing scripting facilities. We also propose adding features needed to drive automated, high -throughput microscopes and to integrate the software with databases and analysis environments. Through these and additional improvements, we expect that this software (provided free of charge) will ultimately be used in at least 5,000 microscope workstations worldwide. With Open Source software, researchers also will be able to more easily execute creative, novel imaging strategies. Narrative: This project will result in flexible, extendible software that researchers will use to operate light microscopes. The software will be freely available, and will not only make possible novel experimental approaches, but also make digital microscopy much more accessible to researchers world-wide.

描述（由申请人提供）：自从17世纪van Leeuwenhoek发明显微镜以来，显微镜一直是生物科学的基石技术。如今，数字显微镜正在彻底改变基础生命科学和临床研究。通过目镜直接观察变得不常见，并迅速被使用数码相机进行数据收集所取代。除了数码相机外，当代显微镜还有几个运动设备（快门、电动状态、滤光轮或转塔、z驱动器等）其操作需要根据研究者的实验需要来编排。因此，显微镜图像采集的软件控制已成为不可或缺的。有几个商业软件包可用，但它们遭受1）它们可以控制的硬件的限制，2）不可能添加硬件支持来改变它们的硬连线实验策略，3）"黑盒"综合症，即难以与其他软件和数据库一起工作的趋势，以及4）高成本。为了弥补这种情况，我们开发了控制显微镜图像采集的开源软件。该软件易于安装和操作，但可以在任何级别上扩展。例如，硬件支持可以由最终用户添加，实验策略可以使用内置的脚本语言进行更改。在实验室研究人员的广泛帮助下，用户界面已经成型。该软件可在多个平台上维护（Windows、Mac、Linux）。在这里，我们的目标是通过大大增加支持的硬件数量并实现高速和多位置采集来扩展我们的初始软件。我们计划通过增加自动代码生成和加强现有的脚本工具，使研究人员更容易改变软件。我们还建议增加驱动自动化、高通量显微镜所需的功能，并将软件与数据库和分析环境集成。通过这些和其他改进，我们预计该软件（免费提供）最终将在全球至少5，000个显微镜工作站中使用。有了开源软件，研究人员也将能够更容易地执行创造性的，新颖的成像策略。该项目将产生灵活，可扩展的软件，研究人员将使用该软件操作光学显微镜。该软件将免费提供，不仅使新的实验方法成为可能，而且还使全世界的研究人员更容易获得数字显微镜。