Multi-Organ Segmentation

Abdominal organ segmentation is essential in modern medical applications. While existing deep learning approaches demonstrate promising performance, their heavy reliance on large-scale image data raises concerns over generalization capability and privacy risks. This motivates the development of generalizable segmentation training paradigms based on domain-randomized image synthesis, facilitating generalization across unseen real image domains. However, existing paradigms either suffer from limited segmentation performance when applied to abdominal organs, or require dataset-specific finetuning. To address these limitations, we propose ReSeg, a novel two-stage retraining-free framework for domain-agnostic zero-shot abdominal organ segmentation. At the first stage, our organ-agnostic synthetic data-driven pretraining approach exploits semantically and visually diverse synthetic images generated by a dedicated data engine to optimize a Generalizable Semantic Representation Network (GSRNet). The network is thereby capable of learning semantic features robust against variations in anatomical structure, imaging contrast, resolution and spatial context, which provide universal representation capabilities that serve as a foundation for segmentation learning. Subsequently, in the second stage, we continue to train an Organ-specific Encoder-decoder Segmentation Network (OESNet), whose encoder is initialized with the pretrained weights. This training process is facilitated by another dedicated data engine, which generates diversified visual images while strictly retaining the inherent spatial layout of abdominal organs. Comprehensive evaluation on seven abdominal organ segmentation datasets across three different modalities including CT, MRI, and PET demonstrates that ReSeg consistently outperforms existing state-of-the-art (SOTA) methods while eliminating the need for real training images.

Multi-cancer segmentation in computed tomography (CT) is fundamentally limited by the scarcity of tumor masks across different organs. We present Merlin Plus, the first large-scale CT dataset with radiologist-created tumor masks across 9 organs. Merlin Plus extends the Merlin dataset by adding 1,153 per-voxel tumor masks and longitudinal metadata. To create these tumor masks, we developed a report-based active-learning framework in which radiology reports identify tumor cases for annotation and support training of a tumor segmentation model. The model generates initial masks, which radiologists review and correct to produce the final masks, reducing annotation burden while maintaining high-quality annotations. Besides tumor masks, the longitudinal metadata in Merlin Plus enables temporal modeling of cancer progression. By directly addressing the major bottleneck of limited multi-cancer segmentation masks, Merlin Plus supports scalable multi-organ cancer detection, segmentation, and longitudinal analysis in CT. Dataset is available at: https://github.com/MrGiovanni/MerlinPlus

Multi-organ segmentation using deep learning requires large amounts of annotated patient data; however, institutions often lack sufficiently large and diverse annotated datasets. Privacy constraints further prevent institutions from sharing patient data to overcome this limitation. Moreover, due to the labor-intensive nature of annotation and the scarcity of diverse expertise, institutions typically have labels for only a small portion of their local data, leaving the larger unlabeled portion unused. In this work, we propose a flexible semi-supervised federated multi-task student-teacher framework that leverages federated learning (FL) to improve multi-organ segmentation using both labeled and unlabeled data across participating sites. At each communication round, the proposed framework initiates local training, where clients with labels for the same task form a federation to produce an aggregated teacher model. The resulting teachers generate task-specific features for all data at each client. Subsequently, all clients form a second federation to train a multi-task student model with a shared encoder and task-specific decoders that replicate the teacher-generated features across all segmentation tasks. The aggregated student model is then used to update the local teachers and initiate the next training round. Extensive experiments demonstrated the effectiveness of the proposed method compared with local and federated single-organ models, yielding an average performance gain of 13 percent across clients. The experiments also demonstrated the impact of multi-task learning and unlabeled data and the applicability of the framework in relaxing labeled-data requirements for client participation. The code is available at https://github.com/AshknMrd/FedMust.

Multi-organ segmentation is often challenged by partially annotated datasets and domain shifts across different imaging sources. To address these limitations, we propose a two-stage learning framework that efficiently leverages partial supervision. In the first stage, the model learns from available annotations to produce accurate segmentations of annotated organs, establishing robust feature representations. In the second stage, we introduce learnable organ prototypes and a Sinkhorn-triplet loss to enforce organ-wise feature consistency across datasets. This encourages latent embeddings of the same organ to remain close, while increasing separation between different organs, even when annotations are missing. Our approach achieves performance comparable to state-of-the-art methods on the BTCV dataset, while remaining computationally efficient. By explicitly aligning feature distributions rather than relying solely on pseudo-labels, the framework effectively mitigates domain shift, making it particularly suitable for medical image segmentation tasks with limited annotation resources.

Pseudo-labeling is a strong paradigm for semi-supervised medical image segmentation, yet its effectiveness is highly sensitive to confidence thresholding. In abdominal multi-organ segmentation, a fixed global threshold is particularly suboptimal because organ classes differ substantially in size, appearance, and learning difficulty. In this work, we propose ThreshGuide, a class-aware threshold adaptation framework that uses labeled data to guide pseudo-label selection on unlabeled data. Built upon a standard teacher-student architecture, the teacher model evaluates labeled samples during training to estimate class-aware threshold targets by maximizing an error-aware F\b{eta} criterion that balances precision and coverage. These targets are then smoothed with an exponential moving average (EMA) and used to filter unlabeled voxels in a class-dependent manner. Experiments on FLARE2022 and AMOS2022 show that ThreshGuide performs competitively overall, yielding clear improvements specifically on hard-to-learn organs.

Distribution-free risk control adds organ-specific recall guarantees to frozen segmentation. We calibrate per-organ thresholds for an AMOS-trained nnU-Net, audit transfer to RAOS, and estimate local re-certification cost using case-level voxel false-negative rate (FNR). The AMOS control passes, but $7/12$ organs exceed $α{=}0.10$ after transfer; smaller calibration sets can mask exceedances with conservative or vacuous thresholds. Risk-Controlling Prediction Sets (RCPS) give high-probability control of population-mean risk, whereas Conformal Risk Control (CRC) gives weaker expectation control. Both require exchangeability; fixed and global thresholds give no per-organ guarantee. The Waudby--Smith--Ramdas (WSR) betting bound re-certifies six Tier-1 organs with 25 local cases, versus 30--40 for Hoeffding--Bentkus (HB). CRC needs 10--15 but has a heavier individual-case tail. No Tier-2 organ meets our illustrative precision criterion with 25 cases.

Dense voxel-level annotation remains a major bottleneck in 3D medical image segmentation. Single-slice propagation methods such as Sli2Vol reduce this burden by propagating one annotated seed slice through a volume using label-free registration. However, axial-only propagation accumulates errors with distance from the seed, especially in surface-distance metrics, because it ignores coronal and sagittal evidence and therefore underuses the 3D information available in CT/MRI volumes. To better leverage volumetric geometry, we study how key training and inference choices affect slice-propagation models, including single-axis versus multi-axis label-free registration, single-seed versus multi-seed propagation, and orthogonal seed configurations. Instead of propagating from a single axial seed, we use three orthogonal seeds---one axial, one coronal, and one sagittal---and fuse their propagated labels with a simple label-free rule. Our results show that the training paradigm has limited impact: an axially trained network applied to off-axis seeds captures nearly all the improvement, while explicit three-axis training adds little. Instead, performance is driven by inference-time seed geometry, especially orthogonality rather than the number of annotated slices, as a budget-matched three-axial control provides no benefit and can even degrade performance. On a multi-organ CT cohort, orthogonal seeding with the axial Sli2Vol backbone improves Dice by 21.9%, Normalized Surface Dice by 25.5%, and reduces Average Hausdorff Distance by 53.5% over the single-axis baseline.

Multi-organ ultrasound segmentation remains challenging when anatomically adjacent structures must be delineated jointly, as localized boundary errors can persist even when Dice scores are high. To address these challenges, we propose Boundary-Adaptive Prompting for Multi-Organ Segmentation (BAP-MOS), a closed-loop adaptive prompting framework. BAP-MOS formulates prompt selection as an organ-specific multi-armed bandit problem over box, point, and combined prompts. An outer Tree-structured Parzen Estimator (TPE) loop selects the prompt-selection parameter vector, while an inner UCB-Tuned loop adapts per-organ prompt preferences during fine-tuning using a bounded Dice--MSD--HD95 validation-probe reward. The framework further introduces an organ-scaled negative prompt ring to adapt sparse prompt geometry across anatomical scales, while keeping the image and prompt encoders frozen and updating only the mask decoder. We evaluate BAP-MOS on pooled prostate-region TRUS cohorts against U-Net, nnU-Net, MedSAM, fixed-prompt SAM/MedSAM, and adaptive policy variants. On this benchmark, BAP-MOS achieves Dice 0.982, HD95 0.482, and MSD 0.204, reducing HD95 by approximately 48% and MSD by 45% relative to the strongest conventional baseline. To verify the generalization ability of the framework, we tested it on the external PFUS1 pelvic-floor ultrasound corpus using MedSAM and its adaptive strategy variants, and the results were good. These results support adaptive prompt allocation as an effective mechanism for improving boundary-sensitive multi-organ ultrasound segmentation without modifying the foundation-model backbone. Source Code is available at: https://github.com/SatvikPraveen/BAP-MOS

Effective multi-organ segmentation in surgical data requires learning the intricate anatomical features and alleviating the challenge of class imbalance, which results from relatively lower proportions of small and limitedly exposed structures. Recent works on laparoscopic multi-organ segmentation focus on learning structure-specific features through class-specific decoder architectures and report favorable results. This work extends the decoder-focused architectures to investigate knowledge sharing in the cross-surgical domain. We utilize two datasets representing different surgical domains, rectal and cholecystectomy surgeries, to explore how surgical conceptual knowledge transfers under partially common anatomical representations. Additionally, we compare the feature adaptation for the encoder and decoder at different training stages to analyse the knowledge adaptation and retention in the network. Our results corroborate previous findings on decoder-specific architectures and demonstrate that the organ-specific decoder model (CEMD), fully fine-tuned after cross-domain pre-training, achieves the highest segmentation performance (62.4% dice) while converging substantially faster than training from scratch. However, we also find that class imbalance in surgical data remains a persistent challenge that transfer learning does not fully resolve for underrepresented anatomical structures.

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.

Deep learning has been widely applied to 3D medical image segmentation tasks. However, due to the diversity of imaging modalities, the high-dimensional nature of the data, and the heterogeneity of anatomical structures, achieving both segmentation accuracy and computational efficiency in multi-organ segmentation remains a challenge. This study proposed GPAFormer, a lightweight network architecture specifically designed for 3D medical image segmentation, emphasizing efficiency while keeping high accuracy. GPAFormer incorporated two core modules: the multi-scale attention-guided stacked aggregation (MASA) and the mutual-aware patch graph aggregator (MPGA). MASA utilized three parallel paths with different receptive fields, combined through planar aggregation, to enhance the network's capability in handling structures of varying sizes. MPGA employed a graph-guided approach to dynamically aggregate regions with similar feature distributions based on inter-patch feature similarity and spatial adjacency, thereby improving the discrimination of both internal and boundary structures of organs. Experiments were performed on public whole-body CT and MRI datasets including BTCV, Synapse, ACDC, and BraTS. Compared to the existed 3D segmentation networkd, GPAFormer using only 1.81 M parameters achieved overall highest DSC on BTCV (75.70%), Synapse (81.20%), ACDC (89.32%), and BraTS (82.74%). Using consumer level GPU, the inference time for one validation case of BTCV spent less than one second. The results demonstrated that GPAFormer balanced accuracy and efficiency in multi-organ, multi-modality 3D segmentation tasks across various clinical scenarios especially for resource-constrained and time-sensitive clinical environments.

Multi-organ segmentation in medical imaging remains challenging due to large anatomical variability, complex inter-organ dependencies, and diverse organ scales and shapes. Conventional encoder-decoder architectures often struggle to capture both fine-grained local details and long-range context, which are crucial for accurate delineation - especially for small or deformable organs. To address these limitations, we propose MD-RWKV-UNet, a dynamic encoder network that enables scale-aware representation and spatially adaptive context modeling. At its core is the MD-RWKV block, a dual-path module that integrates deformable spatial shifts with the Receptance Weighted Key Value mechanism, allowing the receptive field to adapt dynamically to local structural cues. We further incorporate Selective Kernel Attention to enable adaptive selection of convolutional kernels with varying receptive fields, enhancing multi-scale interaction and improving robustness to organ size and shape variation. In parallel, a cross-stage dual-attention fusion strategy aggregates multi-level features across the encoder, preserving low-level structure while enhancing semantic consistency. Unlike methods that stack static convolutions or rely heavily on global attention, our approach provides a lightweight yet expressive solution for dynamic organ modeling. Experiments on Synapse and ACDC demonstrate state-of-the-art performance, particularly in boundary precision and small-organ segmentation.

Recently Mamba-based methods have shown promise in abdominal organ segmentation. However, existing approaches neglect cross-channel anatomical semantic collaboration and lack explicit boundary-aware feature fusion mechanisms. To address these limitations, we propose CS-MUNet with two purpose-built modules. The Boundary-Aware State Mamba module employs a Bayesian-attention framework to generate pixel-level boundary posterior maps, injected directly into Mamba's core scan parameters to embed boundary awareness into the SSM state transition mechanism, while dual-branch weight allocation enables complementary modulation between global and local structural representations. The Channel Mamba State Aggregation module redefines the channel dimension as the SSM sequence dimension to explicitly model cross-channel anatomical semantic collaboration in a data-driven manner. Experiments on two public benchmarks demonstrate that CS-MUNet consistently outperforms state-of-the-art methods across multiple metrics, establishing a new SSM modeling paradigm that jointly addresses channel semantic collaboration and boundary-aware feature fusion for abdominal multi-organ segmentation.

State-of-the-art models for medical image segmentation achieve excellent accuracy but require substantial computational resources, limiting deployment in resource-constrained clinical settings. We present SegMate, an efficient 2.5D framework that achieves state-of-the-art accuracy, while considerably reducing computational requirements. Our efficient design is the result of meticulously integrating asymmetric architectures, attention mechanisms, multi-scale feature fusion, slice-based positional conditioning, and multi-task optimization. We demonstrate the efficiency-accuracy trade-off of our framework across three modern backbones (EfficientNetV2-M, MambaOut-Tiny, FastViT-T12). We perform experiments on three datasets: TotalSegmentator, SegTHOR and AMOS22. Compared with the vanilla models, SegMate reduces computation (GFLOPs) by up to 2.5x and memory footprint (VRAM) by up to 2.1x, while generally registering performance gains of around 1%. On TotalSegmentator, we achieve a Dice score of 93.51% with only 295MB peak GPU memory. Zero-shot cross-dataset evaluations on SegTHOR and AMOS22 demonstrate strong generalization, with Dice scores of up to 86.85% and 89.35%, respectively. We release our open-source code at https://github.com/andreibunea99/SegMate.

The Segment Anything Model (SAM) is a promising foundation model for medical image segmentation, but its prompt-driven design is not directly suitable for fully automatic multi-class anatomical segmentation. Without manual point, box, or mask prompts, SAM faces a dual over-smoothing problem: deep image features may lose fine local structural evidence, while mask tokens may become semantically ambiguous. We propose SAM-DCE, a decoupled context enhancement framework for prompt-free medical image segmentation. SAM-DCE introduces Spatial Representation Compensation (SRC) to recover anatomical evidence from intermediate ViT features and Semantic Token Calibration (STC) to improve the category consistency of foreground mask tokens. Rather than replacing the pretrained decoder or fusing output masks, SAM-DCE refines the spatial and semantic representations before recombining them through SAM's original token-to-mask mechanism. On the Synapse multi-organ CT segmentation dataset, SAM-DCE achieved a mean Dice score of 83.86% and an HD95 of 16.04 mm, outperforming the representative CNN-, Transformer-, and SAM-based baselines evaluated here. Ablation experiments further showed that SRC and STC provide complementary improvements, supporting the proposed spatial--semantic factorization for prompt-free SAM adaptation.