Sub-cellular population imaging tools reveal stable apical dendrites in hippocampal area CA3

Jason J. Moore (), Shannon K. Rashid, Emmett Bicker, Cara D. Johnson, Naomi Codrington, Dmitri B. Chklovskii and Jayeeta Basu ()
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Jason J. Moore: New York University Langone Health
Shannon K. Rashid: New York University Langone Health
Emmett Bicker: New York University Langone Health
Cara D. Johnson: New York University Langone Health
Naomi Codrington: New York University Langone Health
Dmitri B. Chklovskii: New York University Langone Health
Jayeeta Basu: New York University Langone Health

Nature Communications, 2025, vol. 16, issue 1, 1-21

Abstract: Abstract Apical and basal dendrites of pyramidal neurons receive anatomically and functionally distinct inputs, implying compartment-level functional diversity during behavior. To test this, we imaged in vivo calcium signals from soma, apical dendrites, and basal dendrites in mouse hippocampal CA3 pyramidal neurons during head-fixed navigation. To capture compartment-specific population dynamics, we developed computational tools to automatically segment dendrites and extract accurate fluorescence traces from densely labeled neurons. We validated the method on sparsely labeled preparations and synthetic data, predicting an optimal labeling density for high experimental throughput and analytical accuracy. Our method detected rapid, local dendritic activity. Dendrites showed robust spatial tuning, similar to soma but with higher activity rates. Across days, apical dendrites remained more stable and outperformed in decoding of the animal’s position. Thus, population-level apical and basal dendritic differences may reflect distinct compartment-specific input-output functions and computations in CA3. These tools will facilitate future studies mapping sub-cellular activity and their relation to behavior.

Date: 2025
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DOI: 10.1038/s41467-025-56289-9

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