Population-Scale Segmentation of Penile Tissue in DIXON MRI using Deep Learning for Quantitative Phenotyping in Male Reproductive Health

Penile measurement is clinically relevant across male reproductive and urogenital health, including conditions such as micropenis, congenital and endocrine disorders, and sexual or urinary dysfunction. However, quantitative assessment of penile size has relied mainly on external length or circumference measurements, which are difficult to standardize, sensitive to measurement conditions, and unable to capture the internal portion of the penis. MRI enables volumetric assessment of the whole penis in vivo, but automated segmentation has not previously been established at population scale. Automated whole-organ volumetry would enable high-throughput phenotyping for multi-omics and clinical studies of male reproductive disease. Here, we present a deep learning framework for whole-penis segmentation in multi-channel DIXON MRI. Using a newly curated expert-annotated training dataset ($n = 145$ subjects; $13,050$ annotated slices) and a double-annotated independent test benchmark ($n = 24$ subjects; $2,160$ double-annotated slices), we optimized a 3D nnU-Net architecture. The model achieved a 5-fold cross-validation Dice score of $0.90$ and performed at observer-level accuracy on the independent test set (Dice: $0.92$; Hausdorff distance: $3.58$). We deployed the model in $34,412$ UK Biobank participants, enabling automated quantification of total penile tissue, including both external and internal components. Longitudinal evaluation in 2,282 men demonstrated high inter-session reproducibility ($r = 0.87$). This framework establishes a reproducible and population-scalable method for MRI-based assessment of penile anatomy and provides an open technical resource for future studies in urological imaging and male reproductive health. The trained model weights will be publicly released.

Towards Population Scale Testis Volume Segmentation in DIXON MRI

Testis size is known to be one of the main predictors of male fertility, usually assessed in clinical workup via palpation or imaging. Despite its potential, population-level evaluation of testicular volume using imaging remains underexplored. Previous studies, limited by small and biased datasets, have demonstrated the feasibility of machine learning for testis volume segmentation. This paper presents an evaluation of segmentation methods for testicular volume using Magnet Resonance Imaging data from the UKBiobank. The best model achieves a median dice score of $0.87$, compared to median dice score of $0.83$ for human interrater reliability on the same dataset, enabling large-scale annotation on a population scale for the first time. Our overall aim is to provide a trained model, comparative baseline methods, and annotated training data to enhance accessibility and reproducibility in testis MRI segmentation research.