Challenges in Deep Learning-Based Small Organ Segmentation: A Benchmarking Perspective for Medical Research with Limited Datasets

Accurate segmentation of carotid artery structures in histopathological images is vital for advancing cardiovascular disease research and diagnosis. However, deep learning model development in this domain is constrained by the scarcity of annotated cardiovascular histopathological data. This study investigates a systematic evaluation of state-of-the-art deep learning segmentation models, including convolutional neural networks (U-Net, DeepLabV3+), a Vision Transformer (SegFormer), and recent foundation models (SAM, MedSAM, MedSAM+UNet), on a limited dataset of cardiovascular histology images. Despite employing an extensive hyperparameter optimization strategy with Bayesian search, our findings reveal that model performance is highly sensitive to data splits, with minor differences driven more by statistical noise than by true algorithmic superiority. This instability exposes the limitations of standard benchmarking practices in low-data clinical settings and challenges the assumption that performance rankings reflect meaningful clinical utility.