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

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 .