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There are many methods to analyze cell nuclei, but few can detect the presence of DNA damage, without labeling proteins. We have developed a process to detect and classify cell nuclei in the presence of DNA damage. This method uses the morphology of DNA-associated histone proteins, without proteins that specifically label or localize to sites of DNA damage.. We discuss how and why we address this problem, followed by the specifics of the program pipeline, then our results and how it compares to other methods, and concluding about future additions.