Three-dimensional biofilm structure quantification
Three-dimensional biofilm structure quantification
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DOI：
10.1016/j.mimet.2004.08.003
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发表时间：
2004-12-01
影响因子：
2.2
通讯作者：
Harkin, G
中科院分区：
文献类型：
--
作者：
Beyenal, H;Donovan, C;Harkin, G
描述生物膜物理结构的定量参数已从三维共聚焦激光扫描显微镜图像中提取，并用于比较生物膜结构，监测生物膜的发展，并量化影响生物膜结构的环境因素。研究人员以前使用生物体积，体积表面比，粗糙系数，平均和最大厚度比较生物膜结构。这些参数的选择取决于执行计算的软件的可用性。我们认为有必要开发更全面的参数来描述三维生物膜的异质性形态，本研究提出了描述三维生物膜异质性，大小和生物量形态的参数，从共聚焦激光扫描显微镜图像计算。这项研究扩展了以前的工作，从二维生物膜图像的形态特征提取定量参数的三维生物膜图像。我们描述了两种类型的参数：（1）纹理参数显示微尺度的生物膜的异质性和（2）体积参数描述的大小和形态的生物量。提出的三维特征是平均（ADD）和最大扩散距离（MDD），分形维数，平均游程长度（在X，Y和Z方向），纵横比，纹理熵能和均匀性。我们讨论了每个参数的含义，并提出了详细的计算。所开发的算法，包括自动阈值，在软件中实现的MATLAB程序，将可在www.erc.montana.edu网站之前，出版的文件。(C)2004 Elsevier B.V.保留所有权利。
Quantitative parameters describing biofilm physical structure have been extracted from three-dimensional confocal laser scanning microscopy images and used to compare biofilm structures, monitor biofilm development, and quantify environmental factors affecting biofilm structure. Researchers have previously used biovolume, volume to surface ratio, roughness coefficient, and mean and maximum thicknesses to compare biofilm structures. The selection of these parameters is dependent on the availability of software to perform calculations. We believe it is necessary to develop more comprehensive parameters to describe heterogeneous biofilm morphology in three dimensions.This research presents parameters describing three-dimensional biofilm heterogeneity, size, and morphology of biomass calculated from confocal laser scanning microscopy images. This study extends previous work which extracted quantitative parameters regarding morphological features from two-dimensional biofilm images to three-dimensional biofilm images. We describe two types of parameters: (1) textural parameters showing microscale heterogeneity of biofilms and (2) volumetric parameters describing size and morphology of biomass. The three-dimensional features presented are average (ADD) and maximum diffusion distances (MDD), fractal dimension, average run lengths (in X, Y and Z directions), aspect ratio, textural entropy energy and homogeneity. We discuss the meaning of each parameter and present the calculations in detail. The developed algorithms, including automatic thresholding, are implemented in software as MATLAB programs which will be available at www.erc.montana.edu site prior to publication of the paper. (C) 2004 Elsevier B.V. All rights reserved.