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Enhanced and unified anatomical labeling for a common mouse brain atlas

Author

Listed:
  • Uree Chon

    (Penn State University)

  • Daniel J. Vanselow

    (Penn State University)

  • Keith C. Cheng

    (Penn State University)

  • Yongsoo Kim

    (Penn State University)

Abstract

Anatomical atlases in standard coordinates are necessary for the interpretation and integration of research findings in a common spatial context. However, the two most-used mouse brain atlases, the Franklin-Paxinos (FP) and the common coordinate framework (CCF) from the Allen Institute for Brain Science, have accumulated inconsistencies in anatomical delineations and nomenclature, creating confusion among neuroscientists. To overcome these issues, we adopt here the FP labels into the CCF to merge the labels in the single atlas framework. We use cell type-specific transgenic mice and an MRI atlas to adjust and further segment our labels. Moreover, detailed segmentations are added to the dorsal striatum using cortico-striatal connectivity data. Lastly, we digitize our anatomical labels based on the Allen ontology, create a web-interface for visualization, and provide tools for comprehensive comparisons between the CCF and FP labels. Our open-source labels signify a key step towards a unified mouse brain atlas.

Suggested Citation

  • Uree Chon & Daniel J. Vanselow & Keith C. Cheng & Yongsoo Kim, 2019. "Enhanced and unified anatomical labeling for a common mouse brain atlas," Nature Communications, Nature, vol. 10(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:10:y:2019:i:1:d:10.1038_s41467-019-13057-w
    DOI: 10.1038/s41467-019-13057-w
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    Cited by:

    1. Dongsheng Xiao & Brandon J. Forys & Matthieu P. Vanni & Timothy H. Murphy, 2021. "MesoNet allows automated scaling and segmentation of mouse mesoscale cortical maps using machine learning," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    2. Diek W. Wheeler & Shaina Banduri & Sruthi Sankararaman & Samhita Vinay & Giorgio A. Ascoli, 2024. "Unsupervised classification of brain-wide axons reveals the presubiculum neuronal projection blueprint," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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