Due to the limitations of urine cytology and bladder cystoscopy, molecular biomarker techniques are often utilized as an adjunct in diagnosing urothelial carcinomas. The FDA Cleared oncoFISH bladder application allows scanning and analysis of cells recovered from a voided urine sample that have been fixed on a microscope slide then processed with a panel of four FISH probes that label the centromere of chromosomes 3, 7, and 17, and the 9p21 region of chromosome 9, which are known to be associated with urothelial carcinomas. The hybridized slide is scanned using the Ikoniscope robotic microscope and includes three-dimensional imaging and analysis of the cells and their FISH signals, to determine if the cells within the sample contain aneuploidy for chromosomes 3, 7 and 17 or the homozygous deletion of the 9p21 locus. Since the entire scanning process is efficiently controlled by hardware and imaging algorithms, slides can be scanned quickly while producing high quality, optimally focused and exposed images of cells that appear malignant. Following scanning, the results, including cell images and tabulation of the classes of cells detected, are presented for review and reporting. This automated approach alleviates the limitations of manual analysis, including low throughput, high degree of fluorescence bleaching, and an inability to easily return to a cell of interest on the microscope slide to reassess its FISH signal pattern.