Background: Oxygen glucose deprivation (OGD) presents the most used model to study ischemic stroke in vitro. Since mitochondria play the key role in cell metabolism, they are very sensitive to reduction in glucose and oxygen levels which indicates the change of their network. Constant fusion and fission cycles regulate their shape which could be divided into tubular, intermediate and fragmented mitochondria. Aim: The main goal of this study was to establish the adequate tool for automatic morphological analysis of mitochondria and analyse the influence of OGD on mitochondrial shapes of differentiating cells. Materials and Methods: Neural stem cells (NSC) isolated from the telencephalic wall of 14.5 days old mouse embryos were cultivated in differentiation medium. On days 1, 7 and 14 of differentiation they were exposed to 24 hours long OGD treatment. Immunocytochemistry was performed using Tomm20, mitochondrial outer membrane marker. Our in-house made tool, LUSCA, was used to analyse mitochondrial morphology. Experiments were repeated 3 times and statistical analysis were performed in GraphPad Prism using T-test and ANOVA. Results: Image analysis algorithms which are automated and require less user input are preferred because they are less biassed. LUSCA, running in the open access software platform FIJI (ImageJ), provides a reliable, accurate and fully automated analysis of mitochondrial shapes implementing machine learning. We successfully segmented tubular, intermediate, and fragmented shapes of mitochondria due to their configuration differences. Our analysis revealed OGD treatment decreases the total Tomm20 positive area in maturating NSC compared to the control group. Moreover, the control group manifested more tubular filaments while the OGD group had an increase of intermediate and fragmented mitochondria. Conclusion: So far, we successfully applied LUSCA for mitochondria, vessel, and neuron analysis. The changes of mitochondrial shape reported here indicate that OGD stimulates fission cycles while fusion cycles were more present in the control group. [ABSTRACT FROM AUTHOR]