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DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas

Author

Listed:
  • Harry Carey

    (Macquarie University
    University of Oslo)

  • Michael Pegios

    (Macquarie University)

  • Lewis Martin

    (OpenBench)

  • Chris Saleeba

    (Macquarie University)

  • Anita J. Turner

    (Macquarie University)

  • Nicholas A. Everett

    (University of Sydney)

  • Ingvild E. Bjerke

    (University of Oslo)

  • Maja A. Puchades

    (University of Oslo)

  • Jan G. Bjaalie

    (University of Oslo)

  • Simon McMullan

    (Macquarie University)

Abstract

Registration of data to a common frame of reference is an essential step in the analysis and integration of diverse neuroscientific data. To this end, volumetric brain atlases enable histological datasets to be spatially registered and analyzed, yet accurate registration remains expertise-dependent and slow. In order to address this limitation, we have trained a neural network, DeepSlice, to register mouse brain histological images to the Allen Brain Common Coordinate Framework, retaining registration accuracy while improving speed by >1000 fold.

Suggested Citation

  • Harry Carey & Michael Pegios & Lewis Martin & Chris Saleeba & Anita J. Turner & Nicholas A. Everett & Ingvild E. Bjerke & Maja A. Puchades & Jan G. Bjaalie & Simon McMullan, 2023. "DeepSlice: rapid fully automatic registration of mouse brain imaging to a volumetric atlas," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41645-4
    DOI: 10.1038/s41467-023-41645-4
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    References listed on IDEAS

    as
    1. Ed S. Lein & Michael J. Hawrylycz & Nancy Ao & Mikael Ayres & Amy Bensinger & Amy Bernard & Andrew F. Boe & Mark S. Boguski & Kevin S. Brockway & Emi J. Byrnes & Lin Chen & Li Chen & Tsuey-Ming Chen &, 2007. "Genome-wide atlas of gene expression in the adult mouse brain," Nature, Nature, vol. 445(7124), pages 168-176, January.
    2. Seung Wook Oh & Julie A. Harris & Lydia Ng & Brent Winslow & Nicholas Cain & Stefan Mihalas & Quanxin Wang & Chris Lau & Leonard Kuan & Alex M. Henry & Marty T. Mortrud & Benjamin Ouellette & Thuc Ngh, 2014. "A mesoscale connectome of the mouse brain," Nature, Nature, vol. 508(7495), pages 207-214, April.
    3. Bowen Dempsey & Selvee Sungeelee & Phillip Bokiniec & Zoubida Chettouh & Séverine Diem & Sandra Autran & Evan R. Harrell & James F. A. Poulet & Carmen Birchmeier & Harry Carey & Auguste Genovesio & Si, 2021. "A medullary centre for lapping in mice," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
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