Optimizing Neuronal Calcium Flux Analysis: A Python Framework for Alzheimer's and TBI Studies
<p dir="ltr">This study presents a Python-based framework for analyzing calcium flux in cortical neurons, particularly in the context of Alzheimer’s disease and traumatic brain injury (TBI). Cortical neurons, central to memory and cognition, are highly susceptible to calcium dysregul...
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2025
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| Summary: | <p dir="ltr">This study presents a Python-based framework for analyzing calcium flux in cortical neurons, particularly in the context of Alzheimer’s disease and traumatic brain injury (TBI). Cortical neurons, central to memory and cognition, are highly susceptible to calcium dysregulation in neurodegenerative conditions. The research focuses on comparing calcium ion fluctuations following Laser-Induced Shockwave—a method simulating TBI—in both healthy and diseased mouse neurons. Previous approaches relied on MATLAB, which proved inefficient and error-prone. The new Python pipeline significantly enhances accessibility and speed, reducing analysis time from four hours to twenty seconds.</p><p dir="ltr">The multistep process begins with user input of Fluo-4 and phase images, including Dead Red and empty channels. Dead cells are identified via watershed algorithms, and all cells are segmented using Cellpose, an AI-based tool. The code checks overlap between dead and alive cells, detects the shockwave frame, and validates calcium intensity data. For viable cells, it calculates ΔF/F₀, detects peaks, estimates calcium transient half-lives using a two-phase exponential decay model, and performs statistical analyses. Visualizations are generated and results exported to CSV for downstream analysis.</p><p dir="ltr">This automated approach eliminates manual masking and error-prone cell classification, streamlining the workflow and improving reproducibility. By transitioning to Python, researchers gain better debugging capabilities and enhanced performance. The framework is designed to support future studies in calcium dynamics and may accelerate discoveries in neurodegenerative disease research and therapeutic development.</p> |
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