Adaptive Segmentation of DAPI-stained, C-banded, Aggregated and Overlapping Chromosomes

Existing algorithms for automated segmentation of chromosomes and centromeres do not work well for condensed, C-banded and DAPI-stained chromosomes and centromeres. Overlapping and aggregation, which frequently occur in metaphase spreads, introduce additional challenges to the counting of chromosomes and centromeres in the Dicentrics Chromosome Assay (DCA). In this paper, we introduce adaptive algorithms, for segmentation of difficult metaphase spreads that include overlapping and aggregated chromosomes. In order to enhance and segment chromosomes, two optimizations are done: (1) the best algorithm among several options is automatically chosen based on predefined figures of merit, (2) the algorithm is automatically optimized with a binary search to modify its parameters to achieve predefined thresholds. These algorithms are designed to separate mildly or moderately aggregated chromosomal clusters. The clusters are segmented by skeleton junctions, reduction of the overall object thickness, and the watershed algorithm. The chromosomes are characterized by rules we establish, using minimal assumptions. Centromeres are detected by detecting bright spots on the surface of the chromosomes, and then using cluster analysis and shape and intensity profiles to identify them as centromeres. High sensitivity and specificity for chromosome and centromere detection were achieved.