IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v16y2025i1d10.1038_s41467-025-58817-z.html
   My bibliography  Save this article

A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging

Author

Listed:
  • Pablo Vergara

    (University of Tsukuba)

  • Yuteng Wang

    (University of Tsukuba
    University of Tsukuba)

  • Sakthivel Srinivasan

    (University of Tsukuba)

  • Zhe Dong

    (Icahn School of Medicine at Mount Sinai)

  • Yu Feng

    (Icahn School of Medicine at Mount Sinai)

  • Iyo Koyanagi

    (University of Tsukuba)

  • Deependra Kumar

    (University of Tsukuba)

  • Yoan Chérasse

    (University of Tsukuba)

  • Toshie Naoi

    (University of Tsukuba)

  • Yuki Sugaya

    (The University of Tokyo
    The University of Tokyo Institutes for Advanced Study (UTIAS))

  • Takeshi Sakurai

    (University of Tsukuba)

  • Masanobu Kano

    (The University of Tokyo
    The University of Tokyo Institutes for Advanced Study (UTIAS))

  • Tristan Shuman

    (Icahn School of Medicine at Mount Sinai)

  • Denise Cai

    (Icahn School of Medicine at Mount Sinai)

  • Masashi Yanagisawa

    (University of Tsukuba
    University of Tsukuba
    University of Tsukuba)

  • Masanori Sakaguchi

    (University of Tsukuba
    University of Tsukuba
    University of Tsukuba)

Abstract

We developed CaliAli, a comprehensive suite designed to extract neuronal signals from one-photon calcium imaging data collected across multiple sessions in free-moving conditions in mice. CaliAli incorporates information from blood vessels and neurons to correct inter-session misalignments, making it robust against non-rigid brain deformations even after substantial changes in the field of view across sessions. This also makes CaliAli robust against high neuron overlap and changes in active neuron population across sessions. CaliAli performs computationally efficient signal extraction from concatenated video sessions that enhances the detectability of weak calcium signals. Notably, CaliAli enhanced the spatial coding accuracy of extracted hippocampal CA1 neuron activity across sessions. An optogenetic tagging experiment showed that CaliAli enhanced neuronal trackability in the dentate gyrus across a time scale of weeks. Finally, dentate gyrus neurons tracked using CaliAli exhibited stable population activity for 99 days. Overall, CaliAli advances our capacity to understand the activity dynamics of neuronal ensembles over time, which is crucial for deciphering the complex neuronal substrates of natural animal behaviors.

Suggested Citation

  • Pablo Vergara & Yuteng Wang & Sakthivel Srinivasan & Zhe Dong & Yu Feng & Iyo Koyanagi & Deependra Kumar & Yoan Chérasse & Toshie Naoi & Yuki Sugaya & Takeshi Sakurai & Masanobu Kano & Tristan Shuman , 2025. "A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging," Nature Communications, Nature, vol. 16(1), pages 1-18, December.
    • Handle: RePEc:nat:natcom:v:16:y:2025:i:1:d:10.1038_s41467-025-58817-z
    DOI: 10.1038/s41467-025-58817-z
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-025-58817-z
    File Function: Abstract
    Download Restriction: no
    File URL: https://libkey.io/10.1038/s41467-025-58817-z?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
    ---><---

    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:16:y:2025:i:1:d:10.1038_s41467-025-58817-z. 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.

    We have no bibliographic references for this item. You can help adding them by using 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.