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(Semi-) Automatic Recognition of Microorganisms in Water K. Rodenacker, P. Gais 2, U. Jütting and B. A. Hense GSF-IBB, 2 GSF-Patho, Neuherberg, Germany
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Karsten Rodenacker GSF-IBB AG2 2 Content Introduction Material Methods Results Summary and Discussion
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Karsten Rodenacker GSF-IBB AG2 3 Introduction Studies on the effects of toxicants on the biocenosis of aquatic model ecosystem Characterization of plankton commun. (identification, counting of phyto- plankton)
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Karsten Rodenacker GSF-IBB AG2 4 Material Preparation Container of semi- permeable LDPE tubes containing the test substance Water column
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Karsten Rodenacker GSF-IBB AG2 5 Material Data gathering Sedimentation Slide preparation Microscopy
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Karsten Rodenacker GSF-IBB AG2 6 Material Data processing with QWin, QUIPS Scan path and autofocus Digitization and storage ~45 sec/image
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Karsten Rodenacker GSF-IBB AG2 7 Material Some organisms to be classified GYLAPEUMMIPUCRER HUKUOOMACHACCRMA QULAKICOZIGAACMX CLSAPLGEZIGA
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Karsten Rodenacker GSF-IBB AG2 8 Methods Data processing with IDL Image segmentation Feature extraction Classification Re-classification and training
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Karsten Rodenacker GSF-IBB AG2 9 Methods Image segmentation: (two-step method) Rough segmentation image threshold Fine segmentation object threshold (RATS) Unbiased count (forbidden line)
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Karsten Rodenacker GSF-IBB AG2 10 Methods Feature extraction Shape geometrical analytical (Fourier, curvature) topological (convex hull, distance map) algebraic (moments, PCA)
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Karsten Rodenacker GSF-IBB AG2 11 Methods Feature extraction Extinction (optical density) histogram features mean (M1), SD (M2), skewness (M3) etc. moments (algebraic) transmitted light optical density Histogram of values of transmitted light
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Karsten Rodenacker GSF-IBB AG2 12 Methods Classification Hierarchical tree classifier based on stepwise linear discriminance analysis ALL GYLA KICO OOMA CLSA CHAC CRER PEUM Artefacts
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Karsten Rodenacker GSF-IBB AG2 13 Methods Re-Classification Interaction Control Correction Training
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Karsten Rodenacker GSF-IBB AG2 14 Preliminary Results Comparison of manual and automatic procedure
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Karsten Rodenacker GSF-IBB AG2 15 Preliminary Results Comparison of manual and automatic procedure
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Karsten Rodenacker GSF-IBB AG2 16 Summary and Discussion Difficulties or failures Separate softwares (Qwin, IDL) Autofocus automized microscope Segmentation Unlimited number of organism groups
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Karsten Rodenacker GSF-IBB AG2 17 Summary and Discussion Successes Effective training system for biologists AND computer scientists Very good collaboration between the different faculties
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Karsten Rodenacker GSF-IBB AG2 18 Summary and Discussion Outlook Fluorescence Multiple focal depth Type specific object shape features (dominant feature points) Texture object features
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