BACKGROUND Confocal laser scanning microscopy (CLSM) is the method of choice to study interfacial biofilms and acquires time-resolved three-dimensional data of the biofilm structure. CLSM can be used in a multi-channel modus where the different channels map individual biofilm components. This communication presents a novel image quantification tool, PHLIP, for the quantitative analysis of large amounts of multichannel CLSM data in an automated way. PHLIP can be freely downloaded from http://phlip.sourceforge.net. RESULTS PHLIP is an open source public license Matlab toolbox that includes functions for CLSM imaging data handling and ten image analysis operations describing various aspects of biofilm morphology. The use of PHLIP is here demonstrated by a study of the development of a natural marine phototrophic biofilm. It is shown how the examination of the individual biofilm components using the multi-channel capability of PHLIP allowed the description of the dynamic spatial and temporal separation of diatoms, bacteria and organic and inorganic matter during the shift from a bacteria-dominated to a diatom-dominated phototrophic biofilm. Reflection images and weight measurements complementing the PHLIP analyses suggest that a large part of the biofilm mass consisted of inorganic mineral material. CONCLUSION The presented case study reveals new insight into the temporal development of a phototrophic biofilm where multi-channel imaging allowed to parallel monitor the dynamics of the individual biofilm components over time. This application of PHLIP presents the power of biofilm image analysis by multi-channel CLSM software and demonstrates the importance of PHLIP for the scientific community as a flexible and extendable image analysis platform for automated image processing.

中文翻译：

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使用新的图像定量软件PHLIP，通过共聚焦激光扫描显微镜对海洋光化生物膜进行分析。

背景技术共聚焦激光扫描显微镜（CLSM）是研究界面生物膜并获取生物膜结构的时间分辨三维数据的首选方法。CLSM可用于多通道方式，其中不同的通道映射各个生物膜成分。此次交流提出了一种新颖的图像量化工具PHLIP，用于以自动化方式对大量多通道CLSM数据进行定量分析。可以从http://phlip.sourceforge.net免费下载PHLIP。结果PHLIP是一个开源的公共许可证Matlab工具箱，其中包括CLSM成像数据处理功能和十个描述生物膜形态各方面的图像分析操作。在这里，通过对天然海洋光养生物膜的研究，证明了PHLIP的使用。它显示了使用PHLIP的多通道功能对单个生物膜成分的检查如何描述硅藻，细菌以及有机和无机物从细菌占主导地位向硅藻转变的动态时空分离。主导的营养生物膜。反射图像和重量测量补充了PHLIP分析，表明生物膜质量的很大一部分由无机矿物材料组成。结论所提出的案例研究揭示了对光养生物膜的时间发展的新见解，其中多通道成像允许平行监测各个生物膜组分随时间的动态。