Abstract: Any given cell type has an associated “normal” nuclear morphology, which is im-portant to maintain proper cellular functioning and safeguard genomic integrity. Deviations from this can be indicative of diseases such as cancer or premature aging syndrome. To accurately as-sess nuclear abnormalities, it is important to use quantitative measures of nuclear morphology. Here, we give an overview of several nuclear abnormalities including micronuclei, nuclear enve-lope invaginations, blebs and ruptures and review the current methods used for image-based quantification of these abnormalities. We discuss several parameters that can be used to quantify nuclear shape and compare their outputs using example images. In addition, we present new pipelines for quantitative analysis of nuclear blebs and invaginations. Quantitative analysis of nuclear aberrations and shape will be important in a wide range of applications, from assessment of cancer cells anomalies to studies of nucleus deformability under mechanical or other types of stress.