Sidi Mohamed Sid'El Moctar, Nicolas Vitry, Hélène Bouvraiscs.CV cs.LG q-bio.QM
Segmentation of curvilinear anatomical structures in 3D medical images remains challenging due to complex topology, severe class imbalance, weak contrast, and large variations in structure morphology. While deep learning approaches for 3D curvilinear segmentation have been proposed, they are often tailored to specific anatomies or modalities, limiting generalization across clinical settings and leaving room for improvement. Recent generative models have shown the benefits of iterative prediction for structured segmentation tasks, yet diffusion-based methods suffer from computationally expensive sampling, hindering their use on high-resolution 3D volumes. We present 3D-CurvSegFlow, a flow matching-based model for 3D curvilinear structure segmentation. The model learns a continuous transformation from a simple source distribution to the target vascular representation, enabling progressive refinement of complex curvilinear geometries with efficient inference. We evaluate our method on Three public challenging datasets covering distinct anatomies and modalities: portal vein, cerebral vessel, and coronary arteries. Using a common architecture and training strategy across all tasks, our method outperforms general-purpose and vessel-specific approaches, with strong preservation of thin branches and vascular continuity. This work not only advances the state-of-the-art in 3D curvilinear segmentation but also opens new avenues for efficient, generalizable, and clinically applicable methods in medical image analysis.
Curvilinear structure analysis is an important and fundamental task in multimedia. However, the controllable generation of images with precise curvilinear structure objects remains an open challenge. To address this, we propose CSGen, a hierarchical multimodal diffusion model that synthesizes high-fidelity images precisely aligned with multiple control conditions. The CSGen is built upon three key innovations: 1) We construct a multi-domain and multimodal dataset, including over 24K samples from 5 domains and 7 different types of annotations, to train the unified generation model. 2) We propose a novel hierarchical progressive control strategy that decouples topology clues from visual context by a phased signal injection, mitigating semantic drift while ensuring the topological integrity of sparse structures. 3) We design a sparsity-aware loss re-weighting mechanism to address the extreme sparsity of curvilinear structures, significantly enhancing the attention on thin and fragile structures during optimization. Extensive experiments demonstrate that CSGen generates images with superior structure accuracy and visual realism, significantly improving downstream segmentation performance while maintaining robustness across diverse prompts. Our results confirm CSGen as a scalable, data-centric paradigm for the analysis of complex curvilinear structures in diverse multimedia applications. Code and dataset are available at https://github.com/ShanZard/CSGen.
Youcheng Zong, Runda Jia, Minxuan Hu +2cs.CV eess.SY
Segmenting slender curvilinear structures such as retinal vessels, cracks, and roads demands topological correctness, as even a single-pixel discontinuity can fragment a continuous network and invalidate downstream analysis. Under standard binary-mask supervision, models optimized for pixel-level overlap frequently produce topologically broken predictions. We trace this to a fundamental mismatch: pixel-wise losses distribute gradients uniformly, yet connectivity hinges on a sparse set of bottleneck pixels. These pixels are vastly outnumbered by thick structures and background, rendering their aggregate gradient contribution negligible. We term this phenomenon topological gradient starvation (TGS). To address it, we propose Widest-Path Reachability Fields (WPRF), a differentiable Max-Min reachability objective that redirects gradient flow to connectivity bottlenecks. The module is plug-and-play, backbone-agnostic, and incurs no inference overhead. WPRF implements a differentiable Max-Min objective via dynamic programming on a domain-restricted graph, coupled with a bottleneck-aware observation term that balances gradient contributions across varying structures. Compared to prior topology-aware losses that rely on post-hoc skeletonization or homology computation, WPRF directly optimizes end-to-end reachability via differentiable Max-Min algebra, enabling gradient flow to concentrate on connectivity bottlenecks without auxiliary structures. We introduce OMVIS, a new oral microvessel segmentation dataset. Experiments across nine architectures and six datasets validate the bottleneck-focused gradient routing mechanism. WPRF improves 87\% of experiments with fixed hyperparameters and achieves clDice gains of 7.2 percentage points on structurally fragile datasets.
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 $\sim$0.26M additional parameters, PEPA offers a practical post-encoder enhancement for structure-centric segmentation.
Accurate segmentation of curvilinear structures remains challenging in biomedical imaging due to their thin geometry, complex topology, and sensitivity to noise. This is particularly critical for microscopy images of cytoskeletal network, where low signal-to-noise ratios and dense filament crossings often lead to fragmented or inaccurate segmentation. In this work, we propose CurvSegFlow, a segmentation framework based on time-conditioned flow matching. Instead of predicting a segmentation mask in a single pass, the method models segmentation as a dynamic process that progressively refines a noisy initialization into the target structure through a learned velocity field. The proposed model combines a U-Net backbone with triple-term loss function and temporal embeddings to guide the refinement process across reconstruction stages. This formulation enables gradual error correction and improves the continuity of thin structures. CurvSegFlow is evaluated on multiple synthetic and real microtubule datasets, as well as on public benchmarks of retinal vessels, corneal nerves and coronary arteries. Across datasets, the method achieves competitive or superior performance compared to established segmentation models, with consistent improvements in precision and structural continuity, particularly under low signal-to-noise conditions. These results show that flow-based iterative refinement provides a robust and general framework for curvilinear structure segmentation. Overall, the proposed approach improves segmentation quality in challenging imaging conditions and generalizes effectively across modalities without architectural changes.