Mesoscale microscopy and image analysis tools for understanding the brain

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.

Automated summary

In the past decade, advances in whole-brain microscopy have made it possible to obtain high-resolution images of intact brains of small animals, such as mice. These complex images contain a wealth of information, but many neuroscience laboratories lack the computational knowledge and tools necessary to process this data. To address this, we review recent open source tools and propose a pathway for tool developers to collaborate and meet this challenge.