daime, a novel image analysis program for microbial ecology and biofilm research
daime, a novel image analysis program for microbial ecology and biofilm research
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DOI：
10.1111/j.1462-2920.2005.00880.x
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发表时间：
2006-02-01
影响因子：
5.1
通讯作者：
Wagner, M
中科院分区：
文献类型：
--
作者：
Daims, H;Lücker, S;Wagner, M
结合显微镜和分子技术来检测、鉴定和表征环境和医学样品中的微生物被广泛用于微生物生态学和生物膜研究。这些方法的范围，其中包括荧光原位杂交（FISH）与rRNA靶向探针，是由数字图像分析程序，从显微照片中提取重要的定量数据扩展。在这里，我们介绍daime（微生物生态学中的数字图像分析），一个新的计算机程序，集成了2-D和3-D图像分析和可视化功能，这是以前没有在一个单一的开源软件包。例如，daime可以自动在图像和共聚焦图像堆栈中查找2-D和3-D对象，并提供用于量化微生物种群和评估新FISH探针的特殊功能。一个新的功能是量化的空间定位模式的微生物在复杂的样品，如生物膜。结合保留样品3-D结构的“3D-FISH”，这种体视学技术被应用于活性污泥原理实验的证明中，并提供了定量证据，表明功能性连接的氨和亚硝酸盐氧化剂在其栖息地聚集在一起。这种图像分析方法补充了最近的分子技术，用于分析微生物群落的结构-功能关系，并将有助于表征微生物之间的共生相互作用。
Combinations of microscopy and molecular techniques to detect, identify and characterize microorganisms in environmental and medical samples are widely used in microbial ecology and biofilm research. The scope of these methods, which include fluorescence in situ hybridization (FISH) with rRNA-targeted probes, is extended by digital image analysis routines that extract from micrographs important quantitative data. Here we introduce daime (digital image analysis in microbial ecology), a new computer program integrating 2-D and 3-D image analysis and visualization functionality, which has previously not been available in a single open-source software package. For example, daime automatically finds 2-D and 3-D objects in images and confocal image stacks, and offers special functions for quantifying microbial populations and evaluating new FISH probes. A novel feature is the quantification of spatial localization patterns of microorganisms in complex samples like biofilms. In combination with '3D-FISH', which preserves the 3-D structure of samples, this stereological technique was applied in a proof of principle experiment on activated sludge and provided quantitative evidence that functionally linked ammonia and nitrite oxidizers cluster together in their habitat. This image analysis method complements recent molecular techniques for analysing structure-function relationships in microbial communities and will help to characterize symbiotic interactions among microorganisms.