Optical imaging is a valuable tool to visualise biological processes in the context of the tissue. Each imaging modality provides the biologist with different types of information – cell dynamics and migration over time can be tracked with time-lapse imaging (e.g. intra-vital imaging); an overview of whole tissues can be acquired using optical clearing in conjunction with light sheet microscopy; finer details such as cellular morphology and fine nerve tortuosity can be imaged at higher resolution using the confocal microscope. Multi-modal imaging combined with image cytometry – a form of quantitative analysis of image datasets – provides an objective basis for comparing between sample groups. Here, we provide an overview of technical aspects to look out for in an image cytometry workflow, and discuss issues related to sample preparation, image post-processing and analysis for intra-vital and whole organ imaging.

光学成像是在组织环境中可视化生物过程的宝贵工具。每种成像方式都会为生物学家提供不同类型的信息-可以通过延时成像（例如，活体成像）跟踪细胞动力学和随时间的迁移。可以使用光学清除结合光片显微镜来获取整个组织的概况；可以使用共聚焦显微镜以更高的分辨率对诸如细胞形态和精细神经弯曲等更精细的细节进行成像。多模式成像与图像细胞术相结合-一种对图像数据集进行定量分析的形式-为在样本组之间进行比较提供了客观的依据。在这里，我们概述了在图像细胞仪工作流程中需要注意的技术方面，并讨论了与样品制备有关的问题，