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bioRxiv · 10.1101/2025.04.15.648462

Fast and accessible morphology-free functional fluorescence imaging analysis

Estrada Berlanga, A. A.·Kang, G.·Kwok, A.·Broggini, T.·Lawlor, J.·Kuchibhotla, K.·Kleninfeld, D.·Mishne, G.·Charles, A.
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Abstract

Optical calcium imaging is a powerful tool for recording neural activity across a wide range of spatial scales, from dendrites and spines to whole-brain imaging through two-photon and widefield microscopy. Traditional methods for analyzing functional calcium imaging data rely heavily on spatial features, such as the compact shapes of somas, to extract regions of interest and their associated temporal traces. This spatial dependency can introduce biases in time trace estimation and limit the applicability of these methods across different neuronal morphologies and imaging scales. To address these limitations, the Graph Filtered Temporal Dictionary Learning (GraFT) uses a graph-based approach to identify neural components based on shared temporal activity rather than spatial proximity, enhancing generalizability across diverse datasets. Here we present significant advancements to the GraFT algorithm, including the integration of a more efficient solver for the L1 least absolute shrinkage and selection operator (LASSO) problem and the application of compressive sensing techniques to reduce computational complexity. By employing random projections to reduce data dimensionality, we achieve substantial speedups while maintaining analytical accuracy. These advancements significantly accelerate the GraFT algorithm, making it more scalable for larger and more complex datasets. Moreover, to increase accessibility, we developed a graphical user interface to facilitate running and analyzing the outputs of GraFT. Finally, we demonstrate the utility of GraFT to imaging data beyond meso-scale imaging, including vascular and axonal imaging.

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Estrada Berlanga, A. A., Kang, G., Kwok, A., Broggini, T., Lawlor, J., Kuchibhotla, K., Kleninfeld, D., Mishne, G., Charles, A.. 2025-04-20. Fast and accessible morphology-free functional fluorescence imaging analysis. https://doi.org/10.1101/2025.04.15.648462

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