Automated segmentation of the hypothalamus and associated subunits in brain MRI

•A publicly available deep learning tool to segment the hypothalamus and its subunits.•Our tool outperforms inter-rater accuracy and approaches intra-rater precision level.•It can robustly generalise to unseen heterogeneous datasets.•It yields a rejection rate of less than 1% in a QC analysis performed on 675 scans.•It detects subtle subunit-specific hypothalamic atrophy in Alzheimer’s Disease.