PanGuide3D: Cohort-Robust Pancreas Tumor Segmentation via Probabilistic Pancreas Conditioning and a Transformer Bottleneck
Authors: Sunny Joy Ma, Xiang Ma
Organizations: Trailridge School, Waukee, IA, 50263, USA · Department of Biochemistry, Grand View University, Des Moines, IA 50316, USA · Department of Computer Science, Iowa State University, Ames, IA 50011, USA
Pancreatic tumor segmentation in contrast-enhanced computed tomography (CT) is clinically important yet technically challenging: lesions are often small, heterogeneous, and easily confused with surrounding soft tissue, and models that perform well on one cohort frequently degrade under cohort shift. Our goal is to improve cross-cohort generalization while keeping the model architecture simple, efficient, and practical for 3D CT segmentation. We introduce PanGuide3D, a cohort-robust architecture with a shared 3D encoder, a pancreas decoder that predicts a probabilistic pancreas map, and a tumor decoder that is explicitly conditioned on this pancreas probability at multiple scales via differentiable soft gating. To capture long-range context under distribution shift, we further add a lightweight Transformer bottleneck in the U-Net bottleneck representation. We evaluate cohort transfer by training on the PanTS (Pancreatic Tumor Segmentation) cohort and testing both in-cohort (PanTS) and out-of-cohort on MSD (Medical Segmentation Decathlon) Task07 Pancreas, using matched preprocessing and training protocols across strong baselines. We collect voxel-level segmentation metrics, patient-level tumor detection, subgroup analyses by tumor size and anatomical location, volume-conditioned performance analyses, and calibration measurements to assess reliability. Across the evaluated models, PanGuide3D achieves the best overall tumor performance and shows improved cross-cohort generalization, particularly for small tumors and challenging anatomical locations, while reducing anatomically implausible false positives. These findings support probabilistic anatomical conditioning as a practical strategy for improving cross-cohort robustness in an end-to-end model and suggest potential utility for contouring support, treatment planning, and multi-institutional studies.
Pancreatic tumor segmentation in 3D CT volumes is challenged by extreme scale variability across both the pancreas and tumor, and highly irregular tumor morphology. While recent advances have pushed segmentation performance, existing methods do not explicitly address these challenges and come at the cost of excessive computational complexity, limiting their practicality in resource-constrained clinical environments. We propose TRIUNE-Net, a lightweight unified architecture that harmonizes scale, shape, and efficiency through three synergistic innovations. A multi-scale context aggregation module with stage-adaptive dilated convolutions enables the model to reason across the broad range of anatomical scales present in both organs. A serial linear-deformable attention mechanism combines large effective receptive fields with shapeadaptive deformable convolutions to capture irregular, non-convex tumor morphologies. Finally, an information-preserving downsampling module replaces conventional max pooling entirely, retaining all spatial information while adding negligible parameters, preventing small tumors from being discarded before they can be recognized. On both the MSD Pancreas and NVD Pancreas datasets, TRIUNE-Net achieves state-of-theart results with only 5.86 M parameters and no external pre-training, outperforming all baselines across all key tumor metrics. Specifically, it surpasses the next-best model by 0.45% in tumor Dice, 6.0 points in F1 score, 6.6 points in sensitivity, and 3.4 points in precision, simultaneously reflecting its ability to suppress both missed tumors and false alarms in clinically realistic conditions. Our code is available at: https://github.com/abdora-ai/TRIUNE-Net
Amir Hossein Saleknia, Alireza Kheyrkhah, Sanaz Karimijafarbigloo +5
Robust medical image segmentation across imaging modalities is challenging because of large differences in appearance and intensity distributions. Models trained on a single modality often show substantial performance drops when applied to unseen domains. In this work, we develop a unified 3D pancreas segmentation framework that applies domain-adversarial learning to 4,604 heterogeneous CT and MRI scans to learn anatomical representations. A shared nnU-Net encoder-decoder is trained for whole-pancreas segmentation, with a latent domain discriminator encouraging CT-MRI feature alignment. The learned encoder is subsequently transferred to pancreatic head-body-tail segmentation using limited MRI-only subregion annotations. An average Dice score of 87.31% on the in-distribution test set and Dice scores ranging from 84.20% to 88.09% across external OOD datasets were achieved in whole pancreas segmentation. Dice scores of 80.53% on MRI and 83.05% on CT were achieved for downstream subregion segmentation, without using CT subregion annotations. These results demonstrate that a unified anatomical representation can support both cross-modality pancreas segmentation and label-efficient downstream transfer.
Automatic pancreas segmentation is fundamental to abdominal MRI analysis, yet deep learning models trained on one MRI sequence often fail catastrophically when applied to another-a challenge that has received little systematic investigation. We introduce CrossPan, a multi-institutional benchmark comprising 1,386 3D scans across three routinely acquired sequences (T1-weighted, T2-weighted, and Out-of-Phase) from eight centers. Our experiments reveal three key findings. First, cross-sequence domain shifts are far more severe than cross-center variability: models achieving Dice scores above 0.85 in-domain collapse to near-zero (<0.02) when transferred across sequences. Second, state-of-the-art domain generalization methods provide negligible benefit under these physics-driven contrast inversions, whereas foundation models like MedSAM2 maintain moderate zero-shot performance through contrast-invariant shape priors. Third, semi-supervised learning offers gains only under stable intensity distributions and becomes unstable on sequences with high intra-organ variability. These results establish cross-sequence generalization-not model architecture or center diversity-as the primary barrier to clinically deployable pancreas MRI segmentation. Dataset and code are available at https://crosspan.netlify.app/.