Rodenacker Karsten, Hense Burkhard, Jütting Uta, Gais Peter
Institute of Biomathematics and Biometry, GSF-National Research Center for Environment and Health, Neuherberg 85764, Germany.
Microsc Res Tech. 2006 Sep;69(9):708-20. doi: 10.1002/jemt.20338.
An automatic microscope image acquisition, evaluation, and recognition system was developed for the analysis of Utermöhl plankton chambers in terms of taxonomic algae recognition. The system called PLASA (Plankton Structure Analysis) comprises (1) fully automatic archiving (optical fixation) of aqueous specimens as digital bright field and fluorescence images, (2) phytoplankton analysis and recognition, and (3) training facilities for new taxa. It enables characterization of aqueous specimens by their populations. The system is described in detail with emphasis on image analytical aspects. Plankton chambers are scanned by sizable grids, divers objective(s), and up to four fluorescence spectral bands. Acquisition positions are focused and digitized by a TV camera and archived on disk. The image data sets are evaluated by a large set of quantitative features. Automatic classifications for a number of organisms are developed and embedded in the program. Interactive programs for the design of training sets were additionally implemented. A long-term sampling period of 23 weeks from two ponds at two different locations each was performed to generate a reliable data set for training and testing purposes. These data were used to present this system's results for phytoplankton structure characterization. PLASA represents an automatic system, comprising all steps from specimen processing to algae identification up to species level and quantification.
开发了一种自动显微镜图像采集、评估和识别系统，用于从藻类分类识别的角度分析乌氏浮游生物培养室。该系统称为PLASA（浮游生物结构分析），包括：（1）将水样标本作为数字明场和荧光图像进行全自动存档（光学固定）；（2）浮游植物分析和识别；（3）新分类群的训练设施。它能够根据水样标本中的生物群体对其进行表征。本文详细描述了该系统，重点是图像分析方面。使用大小合适的网格、不同的物镜以及多达四个荧光光谱带对浮游生物培养室进行扫描。采集位置由电视摄像机聚焦并数字化，然后存档到磁盘上。通过大量定量特征对图像数据集进行评估。开发了针对多种生物的自动分类方法并嵌入到程序中。此外，还实现了用于设计训练集的交互式程序。从两个不同地点的两个池塘进行了为期23周的长期采样，以生成用于训练和测试目的的可靠数据集。这些数据用于展示该系统在浮游植物结构表征方面的结果。PLASA是一个自动系统，涵盖了从标本处理到藻类识别直至物种水平及量化的所有步骤。
