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Over the last ten years, developments in whole-brain microscopy now allow forhigh-resolution imaging of intact brains of small rodents such as mice. Thesecomplex images contain a wealth of information, but many neurosciencelaboratories do not have all of the computational knowledge and tools needed toprocess these data. We review recent open source tools for registration ofimages to atlases, and the segmentation, visualisation and analysis of brainregions and labelled structures such as neurons. Since the field lacks fullyintegrated analysis pipelines for all types of whole-brain microscopy analysis,we propose a pathway for tool developers to work together to meet thischallenge.

Mesoscale microscopy for micromammals: image analysis tools for understanding the rodent brain