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

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, Denise Cai, Masashi Yanagisawa and Masanori Sakaguchi ()
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Pablo Vergara: University of Tsukuba
Yuteng Wang: 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
Takeshi Sakurai: University of Tsukuba
Masanobu Kano: The University of Tokyo
Tristan Shuman: Icahn School of Medicine at Mount Sinai
Denise Cai: Icahn School of Medicine at Mount Sinai
Masashi Yanagisawa: University of Tsukuba
Masanori Sakaguchi: University of Tsukuba

Nature Communications, 2025, vol. 16, issue 1, 1-18

Abstract: 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.

Date: 2025
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DOI: 10.1038/s41467-025-58817-z

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