BrAIn: A comprehensive artificial intelligence-based morphology analysis system for brain organoids and neuroscience

We introduce BrAIn, a DL-based application for analyzing the developmental progression of BOs. BrAIn tracks their evolution from embryoid bodies (EBs) and quantifies parameters including area, Feret diameter, perimeter, roundness, and circularity. It also classifies budding and abnormal morphologies of 3D organoids and detects monolayer neural rosette structures, key features of neuronal differentiation. Designed with accessibility in mind, BrAIn provides a no-code interface, enabling researchers of all technical backgrounds to conduct advanced morphological analyses with ease. 📒 Citation If you use BrAIn in your work, please cite: Kahveci B., et al. BrAIn: A comprehensive artificial intelligence-based morphology analysis system for brain organoids and neuroscience. (2025)