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Identification of microorganisms by Fourier transform infrared (FT-IR) spectroscopy is known as a promising alternative to conventional identification techniques in clinical, food, and environmental microbiology. In this study we demonstrate the application of FT-IR hyperspectral imaging for rapid, objective, and cost-effective diagnosis of pathogenic bacteria. The proposed method involves a relatively short cultivation step under standardized conditions, transfer of the microbial material onto suitable IR windows by a replica method, FT-IR hyperspectral imaging measurements, and image segmentation by machine learning classifiers, a hierarchy of specifically optimized artificial neural networks (ANN). For cultivation, aliquots of the initial microbial cell suspension were diluted to guarantee single-colony growth on solid agar plates. After a short incubation period when microbial microcolonies achieved diameters between 50 and 300 μm, microcolony imprints were produced by using a specifically developed stamping device which allowed spatially accurate transfer of the microcolonies' upper cell layers onto IR-transparent CaF windows. Dry microcolony imprints were subsequently characterized using a mid-IR microspectroscopic imaging system equipped with a focal plane array (FPA) detector. Spectral data analysis involved preprocessing, quality tests, and the application of supervised modular ANN classifiers for hyperspectral image segmentation. The resulting easily interpretable segmentation maps suggest a taxonomic resolution below the species level.

Previous 2D saliency detection methods extract salient cues from a single view and directly predict the expected results. Both traditional and deep-learning-based 2D methods do not consider geometric information of 3D scenes. Therefore the relationship between scene understanding and salient objects cannot be effectively established. This limits the performance of 2D saliency detection in challenging scenes. In this paper, we show for the first time that saliency detection problem can be reformulated as two sub-problems: light field synthesis from a single view and light-field-driven saliency detection. We propose a high-quality light field synthesis network to produce reliable 4D light field information. Then we propose a novel light-field-driven saliency detection network with two purposes, that is, i) richer saliency features can be produced for effective saliency detection; ii) geometric information can be considered for integration of multi-view saliency maps in a view-wise attention fashion. The whole pipeline can be trained in an end-to-end fashion. For training our network, we introduce the largest light field dataset for saliency detection, containing 1580 light fields that cover a wide variety of challenging scenes. With this new formulation, our method is able to achieve state-of-the-art performance.

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