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

Abstract

Background: 3D segmentation and analysis of dendritic spines involve two major challenges: 1) how to segment individual spines in 3D from the dendrites and 2) how to quantitatively assess the 3D morphology of individual spines. We developed software named 3dSpAn to address these two issues by implementing a 3D multiscale opening algorithm in shared intensity space and using effective morphological features, for individual dendritic spine plasticity analysis.Results: 3dSpAn works in four main modules: Preprocessing and ROI selection, Intensity thresholding and seed selection, Multiscale segmentation and Quantitative morphological feature extraction. Experimental results show that 3dSpAn can segment individual spines from dendrites from in vitro and ex vivo samples, imaged using confocal microscopy, and in vivo samples, using high-resolution two-photon microscopy.Conclusions: This freely available software will fulfill the requirement of an interactive software for quantitative morphological analysis of individual dendritic spine in 3D. The source code, windows installer, software manual and video tutorial are available at: https://sites.google.com/view/3dSpAn/.

Quantification of Dendritic Spines Remodeling under Physiological Stimuli and in Pathological Conditions

“…The diversity of images and a presence of artifacts is the major obstacle for using fully automatic segmentation algorithms, which often require setting the parameters controlling the segmentation according to data modalities and might be insufficiently flexible to cope with complicated structures [ 151 ]. Thus, many analyses are based on manual or semi-manual processing of images [ 152 ]. Several methods based on conventional/deep machine learning have recently been reported for automatic segmentation and analysis of dendritic spines [ 153 , 154 , 155 ].…”

“…The most popular software tools that were reported in experimental protocols to be used for spines segmentation and analysis are SpineMagick (patent no. WO/2013/021001), 3dSpAn [ 152 ], Neurolucida [ 156 ], SpineLab [ 157 ], Imaris Editing Tools of FilamentTracer [ 158 ], NeuronIQ [ 159 ], MetaMorph [ 160 ], 3DMA-Neuron [ 161 ], NeuronStudio [ 162 ].…”

SpineS: An interactive time-series analysis software for dendritic spines

“…SpineJ 22 is a recently released good alternative for super-resolution microscopy image stacks but whether it would work for CLSM or 2PLSM images is an open question and it does not offer time-series analysis. 2dSpAn 23 and its 3D version 3dSpAn 24,25 are two other alternative available software packages for morphological analysis of dendritic spines. Although these software packages are providing good results, they also do not offer longitudinal analysis and do not allow for manual correction, and either report spine head and neck volume together as one entity or the total length of the spine head from the tip to base, neither of which have reported biological correlates.…”