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J Pathol Inform. 2011;2:S4. doi: 10.4103/2153-3539.92031. Epub 2012 Jan 19.

Automatic annotation of histopathological images using a latent topic model based on non-negative matrix factorization.

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  • 1BioIngenium Research Group, Faculty of Engineering and School of Medicine, Universidad Nacional de Colombia, Carrera 30 45-03 Ed 471 1er Piso, Bogotá D.C., 11001000, Colombia.


Histopathological images are an important resource for clinical diagnosis and biomedical research. From an image understanding point of view, the automatic annotation of these images is a challenging problem. This paper presents a new method for automatic histopathological image annotation based on three complementary strategies, first, a part-based image representation, called the bag of features, which takes advantage of the natural redundancy of histopathological images for capturing the fundamental patterns of biological structures, second, a latent topic model, based on non-negative matrix factorization, which captures the high-level visual patterns hidden in the image, and, third, a probabilistic annotation model that links visual appearance of morphological and architectural features associated to 10 histopathological image annotations. The method was evaluated using 1,604 annotated images of skin tissues, which included normal and pathological architectural and morphological features, obtaining a recall of 74% and a precision of 50%, which improved a baseline annotation method based on support vector machines in a 64% and 24%, respectively.


Automatic Annotation; Bag of Features; Basal Cell Carcinoma; Histopathology Images; Non-negative Matrix Factorization; Visual Latent Semantic Analysis

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