  Over the last ten years, developments in whole-brain microscopy now allow for
high-resolution imaging of intact brains of small rodents 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.
