Developing a new analysis method for capturing long-term brain activity in freely moving mice

Tsukuba, Japan—Calcium imaging with ultra-small microscopes has become a widely used method for visualizing brain activity in mice during natural behaviors, including sleep. However, current analysis techniques struggle to follow the same neuronal populations over time due to shifts in the imaging field of view and subtle tissue deformations between sessions. These issues make it difficult to reliably identify and track individual neurons across days or weeks.

To overcome these limitations, the research team developed CaliAli (Calcium Imaging inter-session Alignment), an advanced analytical framework designed specifically for aligning data across multiple sessions. CaliAli corrects image misalignments by systematically integrating data from each processing step, ultimately reconstructing a continuous and coherent video. It also incorporates an optimized algorithm to automatically extract neural signals from the aligned video while filtering out noise and eliminating redundant detections.

Using this method, researchers were able to track and record the same group of neurons continuously for up to 99 days with a standard ultra-miniature microscope—a world first. CaliAli opens new possibilities for long-term brain activity studies and could significantly advance our understanding of memory formation, retention, and the gradual changes in brain function associated with neurological diseases.

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This work was partially supported by the Japan Agency for Medical Research and Development (JP21zf0127005, JP23wm0525003), Japan Society for the Promotion of Science (JSPS)(24H00894, 23H02784, 22H00469, 16H06280, 20H03552, 21H05674, 21F21080), Takeda Science Foundation, Uehara Memorial Foundation, The Mitsubishi Foundation, and G-7 Scholarship Foundation to M.S., JSPS (23K19393, 24K18212) to I.K. and the Japan Science and Technology Agency (JPMJSP2124) to Y.W.

_{Original Paper}

Title of original paper:
A comprehensive suite for extracting neuron signals across multiple sessions in one-photon calcium imaging

Journal:
Nature Communications

DOI:
10.1038/s41467-025-58817-z

_{Correspondence}

Associate Professor SAKAGUCHI, Masanori
Institute of Medicine / International Institute for Integrative Sleep Medicine (WPI-IIIS), University of Tsukuba

_{Related Link}

International Institute for Integrative Sleep Medicine (WPI-IIIS)
Institute of Medicine

About the World Premier International Research Center Initiative (WPI)
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About International Institute for Integrative Sleep Medicine (IIIS), University of Tsukuba
World-class institute for sleep medicine, aiming to solve the mechanism of sleep/wakefulness by conducting basic to translational research
The mission of IIIS is to be a multidisciplinary, international hub for the research to elucidate the function of sleep and the fundamental mechanisms of sleep/wake regulation, to elucidate molecular pathogenesis of sleep disorders and related diseases, to develop preventive measures, diagnostic methods, and treatments for sleep.