. The Allen Mouse Brain Common Coordinate Framework: A 3D Reference Atlas. Cell. 2020 Apr 30; PubMed.


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  1. This three-dimensional reference atlas is a true tour de force that will be hugely useful for the neuroscience community and for AD researchers working with mouse models on a C57Bl6/J background. One example is the detailed projection data will be very useful for studies of pathological protein propagation through neural circuits. In future, it would be amazing if this atlas could get to even higher resolution to integrate synaptic structure and connectivity data.

    View all comments by Tara Spires-Jones
  2. The mouse brain is the most widely used model in modern neuroscience. This essential new paper describes the latest release (v3) of the Allen Mouse Brain Common Coordinate Framework (CCF). This is based on averaging images from 1,675 genetically identical mouse brains and various datasets from histological staining, immunohistochemistry, analysis of transgenic expression, in situ hybridization, and tracer connectivity analysis. Integration of all this data results in a cellular-level resolution three-dimensional mouse reference brain, with delineated gray-matter structures, fiber tracts, and ventricular structures.

     As both basic and translational research continue to move toward combining various types of analysis at different spatial resolutions (from functional studies to single-cell transcriptomics), tools that enable integration of these datasets become more and more essential. The CCF provides the dataset and resources needed for this integration.

    Perhaps most critically, kudos to the Allen Institute for Brain Science team for being a model of open science. They have enabled unrestricted access to over 100 mouse lines that express cre in specific neuronal populations that were used to help define brain structures in this paper, as well as dozens of cre reporter lines. The data described here are available for download, as well as accessible via a user-friendly interactive Atlas Viewer and supported by an active, well-supported online community forum. This will no doubt be a useful teaching tool, in addition to its great utility to the research community. 

    Full disclosure: I have a research collaboration with one of the lead authors.

    View all comments by Michael Sasner

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  1. Mouse Brain Mapped in 3D, at High Resolution