Improving PET/CT-Based Whole-Body Lesion Segmentation Using Prediction Uncertainty-Augmented Models

Accurate lesion segmentation from whole-body Positron Emission Tomography (PET)/Computed Tomography (CT) scans is essential for cancer staging and treatment planning. PET provides functional metabolic information with different radiotracers, while CT offers anatomical localization. Lesion delineation from PET/CT imaging is clinically challenging due to subtle imaging features, confounders, and inter-reader variability. Existing deep learning approaches suffer from training-related stochasticity, inconsistent predictions, missed lesions in high tumor-burden cases, and lack uncertainty quantification, limiting their clinical reliability. Using nnU-Net as a baseline, we propose an uncertainty-aware framework for whole-body PET/CT lesion segmentation that integrates (1) Bayesian ensembling to reduce training stochasticity, (2) voxel-wise uncertainty quantification with epistemic and aleatoric decomposition, and (3) epistemic uncertainty-augmented training to improve lesion detection. Two public datasets, AutoPET-III (1,611 scans) and Deep-PSMA (200 scans), comprising FDG and PSMA studies across multiple cancer types, are used for training and evaluation. Bayesian ensembling improves robustness and performance over deterministic nnU-Net models on the unseen AutoPET-III test set. Uncertainty maps highlight regions of model disagreement and correlate with misclassifications, particularly false positives. Uncertainty-augmented training improves lesion recovery at the cost of increased FPVol, reflecting a precision-recall trade-off. A case-adaptive routing strategy further improves Dice by selecting between the base and augmented models. To our knowledge, this is the first study to systematically investigate uncertainty quantification in multi-tracer, pan-cancer PET/CT segmentation and to combine Bayesian ensembling with uncertainty-aware modeling for this task.

Multi-planar 2D-U-Net Segmentation of 3D-CT Abdominal Organs augmented by Spatial Occurrence Maps

This work proposes a lightweight 2D-U-Net-based framework for segmenting five abdominal organs in large field-of-view 3D CT scans. The method combines coarse-to-fine segmentation, predictions from multiple anatomical planes, and additional fuzzy 3D spatial maps that provide anatomical location cues to improve segmentation accuracy. We combine multi-planar 2D-U-Net models augmented by a spatial occurrence map. The approach involves two main stages. First, the abdominal volume of interest region is detected by traversing the whole scan axially with a 2D-U-Net and determining the x-y-z-minimum and -maximum extents of the 5 abdominal organs of interest. Second, we use spatial occurrence maps to enhance our multi-planar 2D-U-net architecture inside the bounds from the former stage. The method is evaluated on 80 CT scans from various public sources. The results show Dice improvements of about 4% at maximum compared to the same model trained without spatial occurrence maps.

ORACLE-CT: Anatomy-Aware Support Pooling for CT Classification

Abdominal CT disease classification is challenging because each scan is a large 3D volume with many possible findings, while diagnostic evidence is often confined to specific organs or anatomical compartments. Most study-level classifiers aggregate encoder features using anatomy-agnostic pooling or attention, creating a mismatch between localized disease evidence and global evidence aggregation. We propose ORACLE--CT, an encoder-agnostic anatomy-aware aggregation framework that uses multi-organ segmentation to define label-specific anatomical supports and restrict attention pooling to relevant regions. The framework supports single-organ, multi-organ union, comparative, localized, and global support strategies. We evaluate ORACLE--CT with three encoder families: DINOv3, I3D--ResNet-121, and the radiology-native Pillar--0 encoder. Models are trained end-to-end on MERLIN and evaluated internally and under frozen external transfer to Duke--Abdomen and AMOS. Compared with global average pooling, support-masked pooling improved MERLIN macro-AUROC/AUPRC from 0.838/0.638 to 0.858/0.676 for DINOv3 and from 0.829/0.617 to 0.848/0.659 for I3D--ResNet-121. On harmonized 10-label external evaluation, DINOv3 improved on Duke--Abdomen from 0.802/0.628 to 0.835/0.683 and on AMOS from 0.742/0.313 to 0.762/0.350, with similar gains for I3D--ResNet-121. For Pillar--0, most gains came from learned attention, with smaller additional benefit from anatomical masking. ORACLE--CT improves discrimination and external robustness while preserving an auditable link between predictions and anatomical evidence.

LegSegNet: A Public Deep Learning System for Lower Extremity CT Tissue Segmentation and Quantification

Lower extremity computed tomography (CT) contains clinically relevant information for body composition analysis, sarcopenia assessment, and musculoskeletal disease monitoring, but extracting these measurements at scale requires accurate tissue segmentation and an automated quantification workflow. Existing public segmentation tools are not designed for comprehensive lower extremity CT analysis, particularly for clinically important inter/intramuscular adipose tissue, and most public methods only provide mask prediction rather than an end-to-end quantification system. To address this problem, we present LegSegNet, a deep learning system for lower extremity CT tissue segmentation and body composition quantification. Given an input CT scan, LegSegNet segments bone, skeletal muscle, subcutaneous adipose tissue, and inter/intramuscular adipose tissue. It then computes quantitative tissue measurements for downstream analysis. We developed the segmentation model using 1,302 manually annotated CT slices and evaluated it on 900 held-out test slices, with all annotations reviewed by radiologists. We benchmark LegSegNet against a broad set of 2D segmentation methods, including CNN-based models, transformer-based models, and finetuned foundation models, and further evaluate its generalization on an external public CT dataset. LegSegNet achieves the best overall segmentation performance, with an average Dice score of 89.31 on the held-out test set. To our knowledge, LegSegNet is the first publicly available end-to-end system for lower extremity CT tissue segmentation and quantification, providing a practical evaluation tool for future computer vision research in medical image analysis. The code and model weights are available at: https://github.com/mazurowski-lab/LegSegNet

Automated Prediction of Postoperative Pancreatic Fistula Using Preoperative Computed Tomography

Postoperative pancreatic fistula (POPF) is a serious complication after pancreatic resection, increasing morbidity, hospital stay, and healthcare costs. We present an automatic, end-to-end deep learning pipeline-from pancreatic segmentation to classification-for preoperative POPF risk estimation and stratification using preoperative CT scans. A data set with auto-segmented pancreas volumes and surgical outcomes was used to evaluate multiple architectures, including a custom lightweight 3D CNN baseline (CNN3D), R(2+1)D ResNet-18, and ResNet-MC3-18 models. Evaluation across multiple 3D architectures demonstrated promising predictive performance. This approach offers a clinically valuable tool and a methodological benchmark for pancreas-specific CT classification, supporting improved preoperative decision-making in pancreatic surgery.

ASAP: Advancing Medical Volumetric Representation Learning with Anatomy-aware Semantically-adaptive Pre-training

Learning transferable and interpretable representations from medical volumetric scans remains challenging due to complex anatomical structures and weak, heterogeneous supervision provided by radiology reports. In this paper, we propose Anatomy-aware Semantically-Adaptive Pre-training (ASAP), a principled vision-language pre-training framework for fine-grained medical volumetric representation learning from large-scale chest CT scans and their corresponding radiology reports. ASAP integrates three key components: (1) an anatomy-aware knowledge injection module that incorporates organ-level structural priors via off-the-shelf segmentation tool to encourage anatomically coherent representations; (2) a semantically-adaptive selective alignment mechanism that dynamically associates sentence-level findings with localized volumetric regions; and (3) a semantically-adaptive fusion module for effective interaction between anatomically informed visual features and grounded textual cues under dual-modal masked modeling paradigm. Beyond methodological contributions, we establish a comprehensive benchmark for medical volumetric vision-language pre-training on chest CT, covering 15 datasets and 22 downstream tasks spanning abnormality classification, segmentation, disease prognosis prediction, report generation, vocabulary classification, cross-modal retrieval and visual question answering. This benchmark provides standardized evaluation protocols to systematically assess representation quality under diverse clinical settings and data regimes. Extensive experiments demonstrate that ASAP consistently achieves state-of-the-art performance across tasks and datasets, with particularly pronounced gains under limited supervision and distribution shift, validating its effectiveness in learning transferable and clinically meaningful volumetric representations.

BiSegMamba: Efficient Bidirectional Tri-Oriented Mamba for 3D Medical Image Segmentation

Accurate 3D medical image segmentation requires both long-range volumetric context and fine boundary preservation. CNN-based methods have limited global dependency modeling, while Transformer-based models are often computationally expensive for dense 3D inputs. Recent Mamba-based methods provide an efficient alternative, but existing volumetric designs still depend on repeated high-resolution scanning, forward-only sequential modeling, and fixed directional summation, causing high cost, scan-order bias, and suboptimal directional aggregation. We propose BiSegMamba, an efficient bidirectional tri-oriented Mamba network for 3D medical image segmentation. BiSegMamba follows a compact-to-detail design, where a progressive compacting stem (PCS) enables efficient latent-space reasoning while retaining shallow high-resolution features for reconstruction. A multi-scale spatial mixer (MSSM) captures local anatomical patterns in early stages, and the proposed bidirectional tri-oriented Ortho Mamba (Bi-ToOM) block models long-range dependencies from multiple orthogonal views using jointly processed forward and backward scan sequences. Adaptive directional fusion (ADF) learns input-dependent channel-wise weights across scan orientations, replacing fixed summation with orientation-aware fusion. Experiments on a collected carotid CTA dataset and three public benchmarks, BraTS2023, ACDC, and AMOS-CT, show that BiSegMamba generalizes well across vascular, cardiac, brain tumor, and abdominal multi-organ segmentation tasks. Compared with SegMamba-V2, BiSegMamba achieves slightly better performance on BraTS2023 and clear improvements on ACDC and the carotid dataset, while reducing computational cost by up to 77.9% FLOPs, demonstrating a strong accuracy-efficiency balance for general 3D medical image segmentation.

VesselSim: learning 3D blood vessel segmentation without expert annotations

Blood vessel segmentation is a core task in medical image analysis for the care of vascular diseases and surgical planning, yet the challenges of providing expert vascular annotations pose a major obstacle for the progress of related deep learning techniques. To address this, we propose VesselSim, a two-stage framework for universal 3D blood vessel segmentation that eliminates the need for real annotated data during training. First, we introduce a stochastic, geometry-driven vascular simulation framework that models recursive branching, curvature-controlled growth, and collision-aware topology, followed by domain-randomized intensity synthesis to generate 16,500 anatomically plausible 3D angiographic volumes. Second, a 3D U-Net is trained solely on this synthetic data. To bridge the domain gap from synthetic to real images at inference time, we introduce a test-time adaptation strategy via a self-supervised mask reconstruction decoder, enabling adaptation to unseen clinical scans without prior domain knowledge. We evaluate VesselSim in a zero-shot setting on multiple real-world datasets spanning MR and CT across several anatomical regions, including the brain and kidneys. Despite being trained exclusively on synthetic data, VesselSim achieves performance competitive with state-of-the-art vascular segmentation foundation models. These findings suggest that learning vessel geometry from synthetic tubular structures is effective for robust cross-domain generalization, substantially reducing the reliance on acquired medical imaging data and more importantly, expert annotations.

MedVol-R1: Reward-Driven Evidence Grounding for Volumetric Reasoning Segmentation

Volumetric Reasoning Segmentation (VRS) aims to segment a target region in a 3D medical scan from a free-form clinical query, where the referent is often implicit and requires both medical knowledge and volume-grounded reasoning. Existing methods typically rely on specialized segmentation tokens to connect language with mask decoding, but this coupling collapses the decision process into opaque latent representations, limiting interpretability and generalization to diverse narrative expressions. In this paper, we present MedVol-R1, a reinforcement learning-based framework for VRS that explicitly decouples evidence grounding from volumetric delineation: the LVLM grounds clinical reasoning to a verifiable 2D evidence anchor (key axial slice and 2D bounding boxes), which is then propagated into a coherent 3D mask by a frozen MedSAM2 module. We train MedVol-R1 with cold-start supervised fine-tuning followed by GRPO, guided by a multi-component reward that encourages informative evidence selection, accurate 2D spatial grounding, and cross-slice volumetric coherence, without requiring costly chain-of-thought annotations. Experiments on CT-ORG, AbdomenCT-1K, and KiTS23 from the M3D-Seg benchmark demonstrate that MedVol-R1 consistently outperforms strong baselines and achieves state-of-the-art performance, with reinforcement learning providing clear gains over pure supervised fine-tuning.

SpineContextResUNet: A Computationally Efficient Residual UNet for Spine CT Segmentation

Automated segmentation of the vertebral column in Computed Tomography (CT) scans is a prerequisite for pathological assessment and surgical planning. However, state-of-the-art methods, particularly those based on Transformers or large-scale ensembles, demand substantial GPU resources, creating a barrier for clinical adoption in resource-constrained environments or on edge devices. To address this, we introduce SpineContextResUNet, a computationally efficient 3D Residual U-Net designed for rapid spinal localization. Our architecture integrates a lightweight Context Block that employs parallel multi-dilated convolutions to capture long-range anatomical dependencies without the high latency of Recurrent Neural Networks (RNNs) or the memory overhead of Self-Attention mechanisms. Extensive validation on two public benchmarks, VerSe2020 and CTSpine1K, demonstrates that our model achieves a Dice score of 88.17% and 88.13% respectively. To evaluate performance under strict hardware constraints, we compared our model against a bottlenecked SwinUNETR scaled to match our ~1.7M hardware footprint. While the constrained Transformer suffers severe performance degradation due to a lack of spatial inductive biases in a limited-data regime, our CNN-based approach successfully maintains high accuracy. Crucially, heavy baselines like TotalSegmentator fail due to memory exhaustion on commodity hardware (Intel Core i5, 8GB RAM), our model performs robust inference, making it a viable solution for point-of-care diagnostics and deployment on edge platforms like the Nvidia Jetson Orin Nano.