Organizations: Center for Big Data and Intelligent Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China · College of Computer Science, Chongqing University, Chongqing, China · Key Laboratory of Digital Health and Intelligent Medicine, Chongqing Municipal Health Commission, Chongqing, China · Chongqing Translational Medicine Center, Chongqing, China
Curvilinear object segmentation, including vessels and cracks, is challenging due to extreme spatial sparsity and topological fragility, where small local errors can cause severe structural disconnections. Meanwhile, modern segmentation pipelines increasingly rely on strong but hard-to-modify foundation encoders whose heavy downsampling limits fine structural recovery. Motivated by this, we focus on the post-encoder stage and study two recurring and actionable failure modes: a reconstruction bottleneck in high-resolution feature restoration and a decision bottleneck in binarization. We present PEPA, a lightweight Post-Encoder Plug-in Adapter for 2D curvilinear segmentation pipelines with accessible decoder/head features and target, query, or class descriptors. PEPA couples (i) Target-Conditioned Snake Upsampling (TCSU), which uses target-conditioned continuous snake-like sampling to better recover thin and tortuous structures during upsampling, and (ii) Target-Adaptive Differentiable Thresholding (TADT), which predicts target-specific thresholds and optimizes a soft-threshold surrogate with explicit safeguards against trivial bias shifting. Under this post-encoder interface, PEPA can be attached to both prompt-based decoders and conventional dense predictors. Experiments on five medical and industrial benchmarks show that adding PEPA to frozen-encoder baselines yields consistent improvements, with gains in topological connectivity (clDice) typically exceeding those in region overlap (IoU), indicating improved structural continuity. With only ∼0.26M additional parameters, PEPA offers a practical post-encoder enhancement for structure-centric segmentation.
Radiology foundation models learn transferable representations that can be adapted to new tasks by training only small layers on top of a frozen encoder. Dense prediction tasks such as 3D segmentation are, however, underrepresented in their evaluation, and, with the encoder kept frozen, pre-trained models still fall short of nnU-Net, the state-of-the-art reference trained from scratch. To close this gap we extend convolutional MAE pre-training with a robust reconstruction objective, a feature regularizer, and a local-global similarity objective. Using this method, we propose Curia-MAE, a multi-modal, multi-anatomy MAE model pre-trained on 300,000 CT and MRI images covering a large number of anatomical sites. On eight anatomy- and lesion-focused segmentation benchmarks, Curia-MAE improves frozen-encoder performance over a strong MAE baseline, while remaining competitive under full finetuning and superior on lesion tasks, where labeled data is scarce. These results indicate that a single frozen encoder can be reused across diverse segmentation tasks, reducing the cost of adapting and deploying such models in clinical workflows. Curia-MAE pre-trained model weights are made publicly available at https://huggingface.co/raidium/Curia-MAE.
Accurate segmentation of thin, tortuous anatomical structures, such as retinal vessels, cerebral vasculature, and facial wrinkles, remains challenging due to low contrast, frequent discontinuities, and severe class imbalance. Although recent convolutional and Transformer-based models have improved performance, they often yield fragmented predictions and fail to recover fine branches. We propose CSWinUNETR, a general-purpose backbone for 2D and 3D thin-structure segmentation. It employs cross-shaped stripe self-attention to model long-range principal-axis context and incorporates cyclic shifts to enhance information exchange across stripes. To better preserve fine-grained details, we further introduce a detail-enhanced multi-scale self-attention module that aggregates contextual features from multi-resolution representations. In addition, we propose sparse-control dynamic snake convolution, which reconstructs reliable dense curvilinear kernels from sparsely predicted control points to better follow tortuous geometry. Extensive experiments on four benchmarks across ophthalmology, neurovascular imaging, and dermatology demonstrate that CSWinUNETR consistently outperforms state-of-the-art methods without task-specific post-processing or topology-aware losses. The code is available at https://github.com/labhai/CSWinUNETR.
Medical image segmentation remains challenging in low-data regimes, where scarce annotations often yield poor generalization and ambiguous boundaries with missing fine structures. Recent self-supervised pretraining has improved transferability, but it often exhibits a texture bias. In contrast, accurate segmentation is inherently geometry-aware and depends on both topological consistency and precise boundary preservation. To address this problem, we propose a two-stage framework that couples structure-aware encoder pretraining with boundary-oriented decoding. In Stage-1, we aim to learn structure-aware representations for downstream segmentation in low-data regimes. To this end, we propose Mixed-Domain MeanFlow Pretraining, which aligns images and binary masks in a shared latent space through latent transport regression, where masks act as conditional structural guidance rather than prediction targets, making the pretraining task-agnostic. To further improve training stability under scarce supervision, we incorporate a lightweight Dispersive Loss to prevent representation collapse. In Stage-2, we fine-tune the pretrained encoder with a lightweight decoder that combines Direct Attentional Fusion for adaptive cross-scale gating and Frequency-Directional Dynamic Convolution for high-frequency boundary refinement under appearance variation. Experiments on ISIC-2016, Kvasir-SEG, and GlaS demonstrate consistent gains over state-of-the-art methods, with improved robustness in low-data settings and sharper boundary delineation.