The invention relates to a computer implemented method and systems for cell level fish dot counting. FISH (fluorescence in situ hybridization) dot counting is the process of enumerating chromosomal abnormalities in the cells which can be used in areas of diagnosis and cancer research. The method comprises in part overlaying images of a biological sample comprising a nuclear counterstain mask and a FISH binary mask. The FISH binary mask is extracted using a multi-level extended h-maxima or h-minima.