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Image analysis research aimed at analyzing images of banded, human chromosomes is described. An experimental automated karyotyping system (AKS) has been assembled. The goal of the system is to label the chromosomes from a metaphase image with minimal human intervention. The AKS is unique in that it is designed to automatically process cells containing overlapping chromosomes. It also has four novel algorithmic features: the use of cross section sequence graphs, an over-segmentation-based segmentation strategy, the use of the `pale path' concept for banded chromosomes and the application of mathematical programming for cell-level chromosome classification in cells with overlapping chromosomes. System performance was analyzed using a variety of metaphase images exhibiting various levels of overlapping chromosomes.