Quantitative and Real-Time Image Analysis for Advanced Light Microscopy.

在基于显微镜的研究中，获取和分析从经过不同处理的人群中采样的细胞的显微图像是很常见的。由于实验限制，常常需要采集数量不尽的样品(即细胞图像)，这些限制包括：采集周期有限、提供昂贵的设备或进行下一次实验的压力。随机抽样是一种用于代表性抽样的方法。然而，不随机抽样也有一些很好的理由。例如，细胞可能表达一种报告蛋白，该分子的拷贝数(数量)可能太高或太低，无法进行后续分析，因此对那些表达水平在一定范围内的例子表现出偏好。或者，区域中的细胞可能受到伪影的影响，不健康，或者对于特定的分析来说过于密集或稀疏。有许多因素会影响成像研究人员的选择，这些因素是完全合理的，但如何记录这些信息并与其他科学家分享，这是一个问题。将科学家从采集和分析管道中剔除是适得其反的，更好的解决方案是提供工具，允许他们记录和描述任何实验主观性，并通过自动化提高重复性。该项目第一部分(1-4)的目标围绕着解决记录、描述和自动化图像采集的问题，以便用户和实验室之间能够更好地交流实验设计。此外，我们希望开发工具和方法，为先进方法提供更好的可视化和实时反馈，以便在成像科学家进行研究和做出实验决策时更好地为他们提供信息。该项目的第二部分涉及这一目标，即目标5-6。

In microscopy based research it is common to acquire and analyze microscopy images of cells sampled from populations which have undergone differential treatments. A non-exhaustive number of samples (i.e. images of cells) are often acquired due to experimental limitations that include: restricted acquisition periods, provision of expensive equipment or pressures to move onto the next experiment. Random sampling is a methodology that is used to sample representatively. There are some good reasons however for not sampling randomly. For example, cells maybe expressing a reporter protein and the copy number (quantity) of this molecule maybe too high or too low for subsequent analysis and so preference is shown toward those examples where the expression levels are within a certain range. Or, alternatively, the cells in an area maybe compromised by an artifact, be unhealthy, or too dense or sparse for a particular analysis. There are many factors that will influence the choices of an imaging researcher that are fully justifiable, but it is a problem as to how this information is documented and shared with other scientists. Removing the scientist from the pipeline of acquisition and analysis is counter-productive, a better solution is to provide tools that allow them to document and describe any experimental subjectivity as well as boosting reproducibility through automation. The objectives of this first part of the project (1-4) revolve around solving these issues of documenting, describing and automating image acquisition so that experimental design can be better communicated between users and laboratories. Furthermore, we would like to develop tools and approaches, which allow better visualization and real-time feedback for advanced approaches so as to better inform imaging scientists as they perform their research and make experimental decisions. The second part of the project relates to this goal, objectives 5-6.