IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-41645-4.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-41645-4
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-023-41645-4?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    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. 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.
    3. 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.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    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. Ayelet M. Rosenberg & Manish Saggar & Anna S. Monzel & Jack Devine & Peter Rogu & Aaron Limoges & Alex Junker & Carmen Sandi & Eugene V. Mosharov & Dani Dumitriu & Christoph Anacker & Martin Picard, 2023. "Brain mitochondrial diversity and network organization predict anxiety-like behavior in male mice," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    3. Jun Ding & Jian Ji & Zachary Rabow & Tong Shen & Jacob Folz & Christopher R. Brydges & Sili Fan & Xinchen Lu & Sajjan Mehta & Megan R. Showalter & Ying Zhang & Renee Araiza & Lynette R. Bower & K. C. , 2021. "A metabolome atlas of the aging mouse brain," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    4. Stuart Oldham & Gareth Ball, 2023. "A phylogenetically-conserved axis of thalamocortical connectivity in the human brain," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Fae N. Kronman & Josephine K. Liwang & Rebecca Betty & Daniel J. Vanselow & Yuan-Ting Wu & Nicholas J. Tustison & Ashwin Bhandiwad & Steffy B. Manjila & Jennifer A. Minteer & Donghui Shin & Choong Heo, 2024. "Developmental mouse brain common coordinate framework," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    6. Federico Malizia & Santiago Lamata-Otín & Mattia Frasca & Vito Latora & Jesús Gómez-Gardeñes, 2025. "Hyperedge overlap drives explosive transitions in systems with higher-order interactions," Nature Communications, Nature, vol. 16(1), pages 1-10, December.
    7. S. Vickovic & B. Lötstedt & J. Klughammer & S. Mages & Å Segerstolpe & O. Rozenblatt-Rosen & A. Regev, 2022. "SM-Omics is an automated platform for high-throughput spatial multi-omics," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    8. Wenqi Chen & Jiejunyi Liang & Qiyun Wu & Yunyun Han, 2024. "Anterior cingulate cortex provides the neural substrates for feedback-driven iteration of decision and value representation," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    9. Wen-Hao Zhang & Si Wu & Krešimir Josić & Brent Doiron, 2023. "Sampling-based Bayesian inference in recurrent circuits of stochastic spiking neurons," Nature Communications, Nature, vol. 14(1), pages 1-19, December.
    10. Léa J. Becker & Clémentine Fillinger & Robin Waegaert & Sarah H. Journée & Pierre Hener & Beyza Ayazgok & Muris Humo & Meltem Karatas & Maxime Thouaye & Mithil Gaikwad & Laetitia Degiorgis & Marie des, 2023. "The basolateral amygdala-anterior cingulate pathway contributes to depression-like behaviors and comorbidity with chronic pain behaviors in male mice," Nature Communications, Nature, vol. 14(1), pages 1-23, December.
    11. Alessandra Griffa & Mathieu Mach & Julien Dedelley & Daniel Gutierrez-Barragan & Alessandro Gozzi & Gilles Allali & Joanes Grandjean & Dimitri Ville & Enrico Amico, 2023. "Evidence for increased parallel information transmission in human brain networks compared to macaques and male mice," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    12. Marcus N. Leiwe & Satoshi Fujimoto & Toshikazu Baba & Daichi Moriyasu & Biswanath Saha & Richi Sakaguchi & Shigenori Inagaki & Takeshi Imai, 2024. "Automated neuronal reconstruction with super-multicolour Tetbow labelling and threshold-based clustering of colour hues," Nature Communications, Nature, vol. 15(1), pages 1-19, December.
    13. Tingting Bo & Jie Li & Ganlu Hu & Ge Zhang & Wei Wang & Qian Lv & Shaoling Zhao & Junjie Ma & Meng Qin & Xiaohui Yao & Meiyun Wang & Guang-Zhong Wang & Zheng Wang, 2023. "Brain-wide and cell-specific transcriptomic insights into MRI-derived cortical morphology in macaque monkeys," Nature Communications, Nature, vol. 14(1), pages 1-15, December.
    14. Adrienne I. Kinman & Derek N. Merryweather & Sarah R. Erwin & Regan E. Campbell & Kaitlin E. Sullivan & Larissa Kraus & Margarita Kapustina & Brianna N. Bristow & Mingjia Y. Zhang & Madeline W. Elder , 2025. "Atypical hippocampal excitatory neurons express and govern object memory," Nature Communications, Nature, vol. 16(1), pages 1-19, December.
    15. E. R. Velasco & A. Florido & Á Flores & E. Senabre & A. Gomez-Gomez & A. Torres & A. Roca & S. Norrholm & E. L. Newman & P. Das & R. A. Ross & A. Lori & O. J. Pozo & K. J. Ressler & L. L. Garcia-Estev, 2022. "PACAP-PAC1R modulates fear extinction via the ventromedial hypothalamus," Nature Communications, Nature, vol. 13(1), pages 1-17, December.
    16. Marghoti, Gabriel & de Lima Prado, Thiago & Conte, Arturo Cagnato & Ferrari, Fabiano Alan Serafim & Lopes, Sergio Roberto, 2022. "Intermittent chimera-like and bi-stable synchronization states in network of distinct Izhikevich neurons," Chaos, Solitons & Fractals, Elsevier, vol. 162(C).
    17. Vincent Bazinet & Justine Y. Hansen & Reinder Vos de Wael & Boris C. Bernhardt & Martijn P. Heuvel & Bratislav Misic, 2023. "Assortative mixing in micro-architecturally annotated brain connectomes," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    18. Vincent Paget-Blanc & Marlene E. Pfeffer & Marie Pronot & Paul Lapios & Maria-Florencia Angelo & Roman Walle & Fabrice P. Cordelières & Florian Levet & Stéphane Claverol & Sabrina Lacomme & Mélina Pet, 2022. "A synaptomic analysis reveals dopamine hub synapses in the mouse striatum," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    19. Xiaomeng Wan & Jiashun Xiao & Sindy Sing Ting Tam & Mingxuan Cai & Ryohichi Sugimura & Yang Wang & Xiang Wan & Zhixiang Lin & Angela Ruohao Wu & Can Yang, 2023. "Integrating spatial and single-cell transcriptomics data using deep generative models with SpatialScope," Nature Communications, Nature, vol. 14(1), pages 1-22, December.
    20. Maxime Brunner & David Lopez-Rodriguez & Judith Estrada-Meza & Rafik Dali & Antoine Rohrbach & Tamara Deglise & Andrea Messina & Bernard Thorens & Federico Santoni & Fanny Langlet, 2024. "Fasting induces metabolic switches and spatial redistributions of lipid processing and neuronal interactions in tanycytes," Nature Communications, Nature, vol. 15(1), pages 1-19, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-41645-4. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.