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An interactive time series image analysis software for dendritic spines.

ABSTRACT: Live fluorescence imaging has demonstrated the dynamic nature of dendritic spines, with changes in shape occurring both during development and in response to activity. The structure of a dendritic spine correlates with its functional efficacy. Learning and memory studies have shown that a great deal of the information stored by a neuron is contained in the synapses. High precision tracking of synaptic structures can give hints about the dynamic nature of memory and help us understand how memories evolve both in biological and artificial neural networks. Experiments that aim to investigate the dynamics behind the structural changes of dendritic spines require the collection and analysis of large time-series datasets. In this paper, we present an open-source software called SpineS for automatic longitudinal structural analysis of dendritic spines with additional features for manual intervention to ensure optimal analysis. We have tested the algorithm on in-vitro, in-vivo, and simulated datasets to demonstrate its performance in a wide range of possible experimental scenarios.

SUBMITTER: Argunsah AO

PROVIDER: S-EPMC9300710 | biostudies-literature | 2022 Jul

REPOSITORIES: biostudies-literature

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An interactive time series image analysis software for dendritic spines.

Argunşah Ali Özgür AÖ Erdil Ertunç E Ghani Muhammad Usman MU Ramiro-Cortés Yazmín Y Hobbiss Anna F AF Karayannis Theofanis T Çetin Müjdat M Israely Inbal I Ünay Devrim D

Scientific reports 20220720 1

Live fluorescence imaging has demonstrated the dynamic nature of dendritic spines, with changes in shape occurring both during development and in response to activity. The structure of a dendritic spine correlates with its functional efficacy. Learning and memory studies have shown that a great deal of the information stored by a neuron is contained in the synapses. High precision tracking of synaptic structures can give hints about the dynamic nature of memory and help us understand how memorie ...[more]

PMID: 35859092

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Project description:SignificanceAdvances in genetically encoded sensors and two-photon imaging have unlocked functional imaging at the level of single dendritic spines. Synaptic activity can be measured in real time in awake animals. However, tools are needed to facilitate the analysis of the large datasets acquired by the approach. Commonly available software suites for imaging calcium transients in cell bodies are ill-suited for spine imaging as dendritic spines have structural characteristics distinct from those of the cell bodies. We present an automated tuning analysis tool (AUTOTUNE), which provides analysis routines specifically developed for the extraction and analysis of signals from subcellular compartments, including dendritic subregions and spines.AimAlthough the acquisition of in vivo functional synaptic imaging data is increasingly accessible, a hurdle remains in the computation-heavy analyses of the acquired data. The aim of this study is to overcome this barrier by offering a comprehensive software suite with a user-friendly interface for easy access to nonprogrammers.ApproachWe demonstrate the utility and effectiveness of our software with demo analyses of dendritic imaging data acquired from layer 2/3 pyramidal neurons in mouse V1 in vivo. A user manual and demo datasets are also provided.ResultsAUTOTUNE provides a robust workflow for analyzing functional imaging data from neuronal dendrites. Features include source image registration, segmentation of regions-of-interest and detection of structural turnover, fluorescence transient extraction and smoothing, subtraction of signals from putative backpropagating action potentials, and stimulus and behavioral parameter response tuning analyses.ConclusionsAUTOTUNE is open-source and extendable for diverse functional synaptic imaging experiments. The ease of functional characterization of dendritic spine activity provided by our software can accelerate new functional studies that complement decades of morphological studies of dendrites, and further expand our understanding of neural circuits in health and in disease.

Dataset Information

An interactive time series image analysis software for dendritic spines.

Publications

An interactive time series image analysis software for dendritic spines.

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