The clustering method by the self-organizing map algorithm of chromosome profiles measured by slit-scan flowcytometer is proposed. Moreover, the physical models of chromosomes have been introduced in order to take into account the rotation of chromosomes in the flowcytometer. The self-organizing map algorithm has been improved so that it can modify the characteristic parameters of chromosome physical models. By this modification, the lengths of chromosomes and the intensity distribution of chromosome fluorescence can be estimated from chromosome profile data measured by the flowcytometer. But the distribution of the rotation angles was unnatural and the numerical evaluations of clustering results were much worse than conventional method. In this paper, we changed the physical models and the geometry of maps, and evaluated the clustering results more precisely considering the rotation of the chromosomes.
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