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Analytical Cellular Pathology
Volume 35 (2012), Issue 5-6, Pages 381-393

Microarray Core Detection by Geometric Restoration

Jimmy C. Azar,1 Christer Busch,2 and Ingrid B. Carlbom1

1Centre for Image Analysis, Uppsala University, Uppsala, Sweden
2Rudbeck Laboratory, Department of Genetics and Pathology, Uppsala University, Uppsala, Sweden

Copyright © 2012 Hindawi Publishing Corporation and the authors. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.


Whole-slide imaging of tissue microarrays (TMAs) holds the promise of automated image analysis of a large number of histopathological samples from a single slide. This demands high-throughput image processing to enable analysis of these tissue samples for diagnosis of cancer and other conditions. In this paper, we present a completely automated method for the accurate detection and localization of tissue cores that is based on geometric restoration of the core shapes without placing any assumptions on grid geometry. The method relies on hierarchical clustering in conjunction with the Davies-Bouldin index for cluster validation in order to estimate the number of cores in the image wherefrom we estimate the core radius and refine this estimate using morphological granulometry. The final stage of the algorithm reconstructs circular discs from core sections such that these discs cover the entire region of each core regardless of the precise shape of the core. The results show that the proposed method is able to reconstruct core locations without any evidence of localization. Furthermore, the algorithm is more efficient than existing methods based on the Hough transform for circle detection. The algorithm’s simplicity, accuracy, and computational efficiency allow for automated high-throughput analysis of microarray images.