Dravet Syndrome (DS) is a severe developmental and epileptic encephalopathy that emerges in infancy and exhibits significant resistance to pharmacological intervention. Despite ongoing efforts to comprehend the mechanistic processes underlying this disorder, regrettably, neither animal models nor cellular models fully replicate the characteristic features of DS. Brain organoids are increasingly recognized as a potent tool for studying neurodevelopment since they partially mimic natural processes occurring in the human brain. However, the in vitro model is constrained by the inherent variability in the differentiation process. In this context, we have developed an AI-based technology capable of discerning, amid this variability, the intrinsic phenotypic differences among cell lines. This has allowed us to delve deeper into the molecular mechanisms triggering the excitatory-inhibitory balance of DS.