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01.07.2022 | Software Original Article

3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines

verfasst von: Nirmal Das, Ewa Baczynska, Monika Bijata, Blazej Ruszczycki, Andre Zeug, Dariusz Plewczynski, Punam Kumar Saha, Evgeni Ponimaskin, Jakub Wlodarczyk, Subhadip Basu

Erschienen in: Neuroinformatics | Ausgabe 3/2022

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Abstract

Three-dimensional segmentation and analysis of dendritic spine morphology involve two major challenges: 1) how to segment individual spines from the dendrites and 2) how to quantitatively assess the morphology of individual spines. To address these two issues, we developed software called 3dSpAn (3-dimensional Spine Analysis), based on implementing a previously published method, 3D multi-scale opening algorithm in shared intensity space. 3dSpAn consists of four modules: a) Preprocessing and Region of Interest (ROI) selection, b) Intensity thresholding and seed selection, c) Multi-scale segmentation, and d) Quantitative morphological feature extraction. In this article, we present the results of segmentation and morphological analysis for different observation methods and conditions, including in vitro and ex vivo imaging with confocal microscopy, and in vivo observations using high-resolution two-photon microscopy. In particular, we focus on software usage, the influence of adjustable parameters on the obtained results, user reproducibility, accuracy analysis, and also include a qualitative comparison with a commercial benchmark. 3dSpAn software is freely available for non-commercial use at www.3dSpAn.org.

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Titel: 3dSpAn: An interactive software for 3D segmentation and analysis of dendritic spines
verfasst von: Nirmal Das
Ewa Baczynska
Monika Bijata
Blazej Ruszczycki
Andre Zeug
Dariusz Plewczynski
Punam Kumar Saha
Evgeni Ponimaskin
Jakub Wlodarczyk
Subhadip Basu
Publikationsdatum: 01.07.2022
Verlag: Springer US
Erschienen in: Neuroinformatics / Ausgabe 3/2022
Print ISSN: 1539-2791
Elektronische ISSN: 1559-0089
DOI: https://doi.org/10.1007/s12021-021-09549-0

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