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

TL;DR

This paper reviews open source image analysis tools for high-resolution whole-brain microscopy in small rodents, highlighting the need for integrated pipelines to advance neuroscience research.

Contribution

It provides an overview of current tools for brain image registration, segmentation, and visualization, and proposes a collaborative pathway for developing comprehensive analysis pipelines.

Findings

Existing tools facilitate registration, segmentation, and visualization.

Field lacks fully integrated analysis pipelines.

Collaboration among developers can improve analysis workflows.

Abstract

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.