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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
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    References listed on IDEAS

    as
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