MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images.
MDL constrained 3-D grayscale skeletonization algorithm for automated extraction of dendrites and spines from fluorescence confocal images.
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MDL 约束 3-D 灰度骨架化算法，用于从荧光共焦图像中自动提取树突和脊柱。
DOI：
10.1007/s12021-009-9057-y
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发表时间：
2009-12
期刊：
影响因子：
3
通讯作者：
Roysam, Badrinath
中科院分区：
文献类型：
--
作者：
Yuan, Xiaosong;Trachtenberg, Joshua T.;Potter, Steve M.;Roysam, Badrinath
关键词：
本文提出了一种改进的方法，用于从共焦或多光子荧光显微镜获取的神经元的三维图像中自动描绘树突和棘突。这里提出的核心改进是一种直接的灰度骨架化算法，该算法受到使用最小描述长度(MDL)原则的结构复杂性惩罚的约束，以及附加的神经解剖学特定的约束。3-D骨架直接从灰度图像数据中提取，避免了图像二值化带来的误差。MDL方法在骨架的复杂性和其对荧光信号的覆盖之间实现了实际的折衷。其他进展包括使用树突的3-D样条线平滑来改进脊椎检测，以及使用强度加权最小生成树(IW-MST)算法从灰度骨架中探索和提取树枝结构的图论算法。该算法在来自多个实验室的8组30个数据集上进行了评估。在大多数数据集上，脊椎检测的假阴性率低于10%(平均为7.1%)，平均假阳性率为11.8%。该软件以开放源代码的形式提供。
This paper presents a method for improved automatic delineation of dendrites and spines from three-dimensional (3-D) images of neurons acquired by confocal or multi-photon fluorescence microscopy. The core advance presented here is a direct grayscale skeletonization algorithm that is constrained by a structural complexity penalty using the minimum description length (MDL) principle, and additional neuroanatomy-specific constraints. The 3-D skeleton is extracted directly from the grayscale image data, avoiding errors introduced by image binarization. The MDL method achieves a practical tradeoff between the complexity of the skeleton and its coverage of the fluorescence signal. Additional advances include the use of 3-D spline smoothing of dendrites to improve spine detection, and graph-theoretic algorithms to explore and extract the dendritic structure from the grayscale skeleton using an intensity-weighted minimum spanning tree (IW-MST) algorithm. This algorithm was evaluated on 30 datasets organized in 8 groups from multiple laboratories. Spines were detected with false negative rates less than 10% on most datasets (the average is 7.1%), and the average false positive rate was 11.8%. The software is available in open source form.
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