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Updated: Sep 11, 2025
Simultaneous Imaging of Microglial Dynamics and Neuronal Activity in Awake Mice
Published on: August 23, 2022
Protocol for detecting neuronal subnetworks from in vivo calcium imaging data using multiple clustering algorithms in
Jui-Yen Huang1, Gautam Chauhan2, Pei-Ying Chen3
1The Gill Institute for Neuroscience, Indiana University, Bloomington, IN 47405, USA; Department of Psychological and Brain Sciences, Indiana University, Bloomington, IN 47405, USA; Program in Neuroscience, Indiana University, Bloomington, IN 47405, USA.
Abstract:
Neuronal subnetworks, defined by co-activation patterns, are fundamental units of brain computation. We provide a step-by-step workflow to detect subnetworks from in vivo calcium imaging data using multiple clustering algorithms in MATLAB. We apply statistical modeling in R to evaluate group-level differences, followed by model selection and bootstrapping for robust estimation. Finally, we use an R Markdown template to generate a structured statistical report. For complete details on the use and execution of this protocol, please refer to Huang et al.1.
