SynapFlow: A Modular Framework Towards Large-Scale Analysis of Dendritic Spines

• URL: http://arxiv.org/abs/2509.18926v1
• Date: Tue, 23 Sep 2025 12:47:43 GMT
• Title: SynapFlow: A Modular Framework Towards Large-Scale Analysis of Dendritic Spines
• Abstract summary: Dendritic spines are key structural components of excitatory synapses in the brain.<n>Despite their relevance, large-scale analyses of the structural dynamics of dendritic spines in 3D+time microscopy data remain challenging.<n>Here, we present a modular machine learning-based pipeline designed to automate the detection, time-tracking, and feature extraction of dendritic spines.
• Score: 4.377081487137802
• License: http://creativecommons.org/licenses/by-nc-nd/4.0/
• Abstract: Dendritic spines are key structural components of excitatory synapses in the brain. Given the size of dendritic spines provides a proxy for synaptic efficacy, their detection and tracking across time is important for studies of the neural basis of learning and memory. Despite their relevance, large-scale analyses of the structural dynamics of dendritic spines in 3D+time microscopy data remain challenging and labor-intense. Here, we present a modular machine learning-based pipeline designed to automate the detection, time-tracking, and feature extraction of dendritic spines in volumes chronically recorded with two-photon microscopy. Our approach tackles the challenges posed by biological data by combining a transformer-based detection module, a depth-tracking component that integrates spatial features, a time-tracking module to associate 3D spines across time by leveraging spatial consistency, and a feature extraction unit that quantifies biologically relevant spine properties. We validate our method on open-source labeled spine data, and on two complementary annotated datasets that we publish alongside this work: one for detection and depth-tracking, and one for time-tracking, which, to the best of our knowledge, is the first data of this kind. To encourage future research, we release our data, code, and pre-trained weights at https://github.com/pamelaosuna/SynapFlow, establishing a baseline for scalable, end-to-end analysis of dendritic spine dynamics.

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