Myotubes are multinucleated muscle fibers serving as key model systems for studying muscle physiology, disease mechanisms, and drug responses. Mechanistic studies and drug screening thereby rely on quantitative morphological readouts such as diameter, length, and branching degree, which in turn require precise three-dimensional instance segmentation. Yet established pretrained biomedical segmentation models fail to generalize to this domain due to the absence of large annotated myotube datasets. We introduce a geometry-driven synthesis pipeline that models individual myotubes via polynomial centerlines, locally varying radii, branching structures, and ellipsoidal end caps derived from real microscopy observations. Synthetic volumes are rendered with realistic noise, optical artifacts, and CycleGAN-based Domain Adaptation (DA). A compact 3D U-Net with self-supervised encoder pretraining, trained exclusively on synthetic data, achieves a mean IPQ of 0.22 on real data, significantly outperforming three established zero-shot segmentation models, demonstrating that biophysics-driven synthesis enables effective instance segmentation in annotation-scarce biomedical domains.
Deformable linear objects such as wires and cables are difficult to segment because they are thin, highly deformable, and frequently self-occluded, while large-scale instance-level annotations are expensive to obtain in real scenes. Existing resources either focus on cable tracing or semantic segmentation under constrained settings, or generate visually plausible images without physically grounded wire deformation. We present WireSeg-32k, a synthetic dataset for wire instance segmentation with 32,000 RGB images, instance masks, depth maps, and a complementary real-world test set with annotations. To generate this dataset, we develop DeformX, a co-simulation pipeline that couples Cosserat-rod dynamics with photorealistic Isaac Sim rendering, enabling physically plausible, contact-consistent wire shapes, CAD-based wire assets, and diverse visually grounded scenes. As a simple baseline, LoRA fine-tuning SAM3 on WireSeg-32k alone improves real-world mAP@75 by 10.2% over the off-the-shelf model, showing that physically grounded synthetic data can transfer to real wire perception.
The morphological analysis of mitochondria in fluorescence microscopy (FM) is crucial for understanding cellular health, energy production, and metabolic regulation. While foundation models like the Segment Anything Model (SAM) have revolutionized natural image segmentation, their direct application to FM is hindered by a significant domain shift characterized by diffraction-limited resolution, low contrast, and complex overlapping organelle networks. Furthermore, the development of robust models is bottlenecked by a severe lack of high-quality, manually annotated instance segmentation datasets for mitochondria. In this paper, we propose a scalable solution to this data scarcity by finetuning SAM exclusively on synthetically generated FM data. We simulate realistic mitochondria data and emulate the optical properties of fluorescence microscopes to create a large-scale annotated dataset. We evaluate our fine-tuned model on a curated dataset of real, manually annotated FM images. Qualitative and quantitative analyses demonstrate that our synthetically fine-tuned model improves precision and average dice score over strong baselines. This work establishes the potential of simulation-assisted training for FM instance segmentation.
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.