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Fluorescence in situ hybridization (FISH) is a cytogenetic technique used to detect the presence of specific DNA sequences on chromosomes. An application of FISH targets the measurement of the amplification of the HER-2 gene within the chromosomes. This requires computation of the ratio of HER-2 over centromere 17 (CEP-17) markers detected within a representative number of nuclei. Selection of the nuclei that are used to compute this ratio is a crucial step to yield an accurate estimation of HER-2 amplification. In fact, errors deriving from overlapping, clustered and oversegmented nuclei can bias the estimation of the ratio and yield inaccurate evaluation of HER-2 amplification. In this paper, a model is presented to associate a reliability score with each nucleus. The reliability score enables refinement of segmentation results - yielding more accurate identification of the boundary of each nucleus - as well as ranking of detected nuclei so as to use just the most reliable nuclei to compute the ratio. Experimental results demonstrate that the adoption of the proposed model improves the estimation of HER-2 amplification.