Over the last ten years, developments in whole-brain microscopy now allow for high-resolution imaging of intact brains of small animals such as mice. These complex images contain a wealth of information, but many neuroscience laboratories do not have all of the computational knowledge and tools needed to process these data. We review recent open source tools for registration of images to atlases, and the segmentation, visualisation and analysis of brain regions and labelled structures such as neurons. Since the field lacks fully integrated analysis pipelines for all types of whole-brain microscopy analysis, we propose a pathway for tool developers to work together to meet this challenge.

在过去的十年中，全脑显微镜的发展现在可以对小鼠等小动物的完整大脑进行高分辨率成像。这些复杂的图像包含丰富的信息，但许多神经科学实验室不具备处理这些数据所需的所有计算知识和工具。我们回顾了最新的开源工具，用于将图像注册到图册，以及大脑区域和标记结构（如神经元）的分割、可视化和分析。由于该领域缺乏适用于所有类型全脑显微镜分析的完全集成的分析流程，我们为工具开发人员提出了一条共同应对这一挑战的途径。