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Autoimmune diseases are proven to be connected with the occurrence of autoantibodies in patient serum. Antinuclear autoantibodies (ANAs) identification can be accomplished in a laboratory using indirect immunofluorescence (IIF) imaging. ANAs are characterized by specific "visual" patterns on a humane epithelial cell line (HEp-2). The identification stage is usually done by trained and highly qualified physicians through visual inspection of slides using a fluorescence microscope. The presence of subjectivity in the identification process, the interobserver variability, the increasing demand of highly specialized personnel, suggest that a realization of an automatic classification system is of great significance for the field of autoimmune diseases diagnosis. Moreover CAD systems can be used in a collaborative scheme in order to augment the physicians' capabilities. In this paper a system for automatic classification of staining patterns on single-cell fluorescence images is proposed. Our method utilizes morphological features extracted from a set of binary images derived via multi-level thresholding of fluorescence images. Furthermore, a modified version of Uniform Local Binary Patterns descriptor is incorporated in order to capture local textural information. The classification is performed using a non-linear SVM Classifier. The proposed method is evaluated using a publicly available dataset, recently released for the purposes of HEP-2 Cells classification competition at ICPR 2012, achieving up to 95.9% overall classification accuracy.