Project Imaging-X: A Survey of 1000+ Open-Access Medical Imaging Datasets for Foundation Model Development

Foundation models have demonstrated remarkable success across diverse domains and tasks, primarily due to the thrive of large-scale, diverse, and high-quality datasets. However, in the field of medical imaging, the curation and assembling of such medical datasets are highly challenging due to the reliance on clinical expertise and strict ethical and privacy constraints, resulting in a scarcity of large-scale unified medical datasets and hindering the development of powerful medical foundation models. In this work, we present the largest survey to date of medical image datasets, covering over 1,000 open-access datasets with a systematic catalog of their modalities, tasks, anatomies, annotations, limitations, and potential for integration. Our analysis exposes a landscape that is modest in scale, fragmented across narrowly scoped tasks, and unevenly distributed across organs and modalities, which in turn limits the utility of existing medical image datasets for developing versatile and robust medical foundation models. To turn fragmentation into scale, we propose a metadata-driven fusion paradigm (MDFP) that integrates public datasets with shared modalities or tasks, thereby transforming multiple small data silos into larger, more coherent resources. Building on MDFP, we release an interactive discovery portal that enables end-to-end, automated medical image dataset integration, and compile all surveyed datasets into a unified, structured table that clearly summarizes their key characteristics and provides reference links, offering the community an accessible and comprehensive repository. By charting the current terrain and offering a principled path to dataset consolidation, our survey provides a practical roadmap for scaling medical imaging corpora, supporting faster data discovery, more principled dataset creation, and more capable medical foundation models.

TopoVST: Toward Topology-fidelitous Vessel Skeleton Tracking

Automatic extraction of vessel skeletons is crucial for many clinical applications. However, achieving topologically faithful delineation of thin vessel skeletons remains highly challenging, primarily due to frequent discontinuities and the presence of spurious skeleton segments. To address these difficulties, we propose TopoVST, a topology-fidelitious vessel skeleton tracker. TopoVST constructs multi-scale sphere graphs to sample the input image and employs graph neural networks to jointly estimate tracking directions and vessel radii. The utilization of multi-scale representations is enhanced through a gating-based feature fusion mechanism, while the issue of class imbalance during training is mitigated by embedding a geometry-aware weighting scheme into the directional loss. In addition, we design a wave-propagation-based skeleton tracking algorithm that explicitly mitigates the generation of spurious skeletons through space-occupancy filtering. We evaluate TopoVST on two vessel datasets with different geometries. Extensive comparisons with state-of-the-art baselines demonstrate that TopoVST achieves competitive performance in both overlapping and topological metrics. Our source code is available at: https://github.com/EndoluminalSurgicalVision-IMR/TopoVST.

TubeMLLM: A Foundation Model for Topology Knowledge Exploration in Vessel-like Anatomy

Modeling medical vessel-like anatomy is challenging due to its intricate topology and sensitivity to dataset shifts. Consequently, task-specific models often suffer from topological inconsistencies, including artificial disconnections and spurious merges. Motivated by the promise of multimodal large language models (MLLMs) for zero-shot generalization, we propose TubeMLLM, a unified foundation model that couples structured understanding with controllable generation for medical vessel-like anatomy. By integrating topological priors through explicit natural language prompting and aligning them with visual representations in a shared-attention architecture, TubeMLLM significantly enhances topology-aware perception. Furthermore, we construct TubeMData, a pionner multimodal benchmark comprising comprehensive topology-centric tasks, and introduce an adaptive loss weighting strategy to emphasize topology-critical regions during training. Extensive experiments on fifteen diverse datasets demonstrate our superiority. Quantitatively, TubeMLLM achieves state-of-the-art out-of-distribution performance, substantially reducing global topological discrepancies on color fundus photography (decreasing the $β_{0}$ number error from 37.42 to 8.58 compared to baselines). Notably, TubeMLLM exhibits exceptional zero-shot cross-modality transferring ability on unseen X-ray angiography, achieving a Dice score of 67.50% while significantly reducing the $β_{0}$ error to 1.21. TubeMLLM also maintains robustness against degradations such as blur, noise, and low resolution. Furthermore, in topology-aware understanding tasks, the model achieves 97.38% accuracy in evaluating mask topological quality, significantly outperforming standard vision-language baselines.

EndoSERV: A Vision-based Endoluminal Robot Navigation System

Robot-assisted endoluminal procedures are increasingly used for early cancer intervention. However, the intricate, narrow and tortuous pathways within the luminal anatomy pose substantial difficulties for robot navigation. Vision-based navigation offers a promising solution, but existing localization approaches are error-prone due to tissue deformation, in vivo artifacts and a lack of distinctive landmarks for consistent localization. This paper presents a novel EndoSERV localization method to address these challenges. It includes two main parts, \textit{i.e.}, \textbf{SE}gment-to-structure and \textbf{R}eal-to-\textbf{V}irtual mapping, and hence the name. For long-range and complex luminal structures, we divide them into smaller sub-segments and estimate the odometry independently. To cater for label insufficiency, an efficient transfer technique maps real image features to the virtual domain to use virtual pose ground truth. The training phases of EndoSERV include an offline pretraining to extract texture-agnostic features, and an online phase that adapts to real-world conditions. Extensive experiments based on both public and clinical datasets have been performed to demonstrate the effectiveness of the method even without any real pose labels.

Long-Short Term Agents for Pure-Vision Bronchoscopy Robotic Autonomy

Accurate intraoperative navigation is essential for robot-assisted endoluminal intervention, but remains difficult because of limited endoscopic field of view and dynamic artifacts. Existing navigation platforms often rely on external localization technologies, such as electromagnetic tracking or shape sensing, which increase hardware complexity and remain vulnerable to intraoperative anatomical mismatch. We present a vision-only autonomy framework that performs long-horizon bronchoscopic navigation using preoperative CT-derived virtual targets and live endoscopic video, without external tracking during navigation. The framework uses hierarchical long-short agents: a short-term reactive agent for continuous low-latency motion control, and a long-term strategic agent for decision support at anatomically ambiguous points. When their recommendations conflict, a world-model critic predicts future visual states for candidate actions and selects the action whose predicted state best matches the target view. We evaluated the system in a high-fidelity airway phantom, three ex vivo porcine lungs, and a live porcine model. The system reached all planned segmental targets in the phantom, maintained 80\% success to the eighth generation ex vivo, and achieved in vivo navigation performance comparable to the expert bronchoscopist. These results support the preclinical feasibility of sensor-free autonomous bronchoscopic navigation.

U-VLM: Hierarchical Vision Language Modeling for Report Generation

Automated radiology report generation is key for reducing radiologist workload and improving diagnostic consistency, yet generating accurate reports for 3D medical imaging remains challenging. Existing vision-language models face two limitations: they do not leverage segmentation-pretrained encoders, and they inject visual features only at the input layer of language models, losing multi-scale information. We propose U-VLM, which enables hierarchical vision-language modeling in both training and architecture: (1) progressive training from segmentation to classification to report generation, and (2) multi-layer visual injection that routes U-Net encoder features to corresponding language model layers. Each training stage can leverage different datasets without unified annotations. U-VLM achieves state-of-the-art performance on CT-RATE (F1: 0.414 vs 0.258, BLEU-mean: 0.349 vs 0.305) and AbdomenAtlas 3.0 (F1: 0.624 vs 0.518 for segmentation-based detection) using only a 0.1B decoder trained from scratch, demonstrating that well-designed vision encoder pretraining outweighs the benefits of 7B+ pre-trained language models. Ablation studies show that progressive pretraining significantly improves F1, while multi-layer injection improves BLEU-mean. Code is available at https://github.com/yinghemedical/U-VLM.

TopoSculpt: Betti-Steered Topological Sculpting of 3D Fine-grained Tubular Shapes

Medical tubular anatomical structures are inherently three-dimensional conduits with lumens, enclosing walls, and complex branching topologies. Accurate reconstruction of their geometry and topology is crucial for applications such as bronchoscopic navigation and cerebral arterial connectivity assessment. Existing methods often rely on voxel-wise overlap measures, which fail to capture topological correctness and completeness. Although topology-aware losses and persistent homology constraints have shown promise, they are usually applied patch-wise and cannot guarantee global preservation or correct geometric errors at inference. To address these limitations, we propose a novel TopoSculpt, a framework for topological refinement of 3D fine-grained tubular structures. TopoSculpt (i) adopts a holistic whole-region modeling strategy to capture full spatial context, (ii) first introduces a Topological Integrity Betti (TIB) constraint that jointly enforces Betti number priors and global integrity, and (iii) employs a curriculum refinement scheme with persistent homology to progressively correct errors from coarse to fine scales. Extensive experiments on challenging pulmonary airway and Circle of Willis datasets demonstrate substantial improvements in both geometry and topology. For instance, $\beta_{0}$ errors are reduced from 69.00 to 3.40 on the airway dataset and from 1.65 to 0.30 on the CoW dataset, with Tree length detected and branch detected rates improving by nearly 10\%. These results highlight the effectiveness of TopoSculpt in correcting critical topological errors and advancing the high-fidelity modeling of complex 3D tubular anatomy. The project homepage is available at: https://github.com/Puzzled-Hui/TopoSculpt.

A Survey of Scientific Large Language Models: From Data Foundations to Agent Frontiers

Scientific Large Language Models (Sci-LLMs) are transforming how knowledge is represented, integrated, and applied in scientific research, yet their progress is shaped by the complex nature of scientific data. This survey presents a comprehensive, data-centric synthesis that reframes the development of Sci-LLMs as a co-evolution between models and their underlying data substrate. We formulate a unified taxonomy of scientific data and a hierarchical model of scientific knowledge, emphasizing the multimodal, cross-scale, and domain-specific challenges that differentiate scientific corpora from general natural language processing datasets. We systematically review recent Sci-LLMs, from general-purpose foundations to specialized models across diverse scientific disciplines, alongside an extensive analysis of over 270 pre-/post-training datasets, showing why Sci-LLMs pose distinct demands -- heterogeneous, multi-scale, uncertainty-laden corpora that require representations preserving domain invariance and enabling cross-modal reasoning. On evaluation, we examine over 190 benchmark datasets and trace a shift from static exams toward process- and discovery-oriented assessments with advanced evaluation protocols. These data-centric analyses highlight persistent issues in scientific data development and discuss emerging solutions involving semi-automated annotation pipelines and expert validation. Finally, we outline a paradigm shift toward closed-loop systems where autonomous agents based on Sci-LLMs actively experiment, validate, and contribute to a living, evolving knowledge base. Collectively, this work provides a roadmap for building trustworthy, continually evolving artificial intelligence (AI) systems that function as a true partner in accelerating scientific discovery.

Shape-aware Sampling Matters in the Modeling of Multi-Class Tubular Structures

Accurate multi-class tubular modeling is critical for precise lesion localization and optimal treatment planning. Deep learning methods enable automated shape modeling by prioritizing volumetric overlap accuracy. However, the inherent complexity of fine-grained semantic tubular shapes is not fully emphasized by overlap accuracy, resulting in reduced topological preservation. To address this, we propose the Shapeaware Sampling (SAS), which optimizes patchsize allocation for online sampling and extracts a topology-preserved skeletal representation for the objective function. Fractal Dimension-based Patchsize (FDPS) is first introduced to quantify semantic tubular shape complexity through axis-specific fractal dimension analysis. Axes with higher fractal complexity are then sampled with smaller patchsizes to capture fine-grained features and resolve structural intricacies. In addition, Minimum Path-Cost Skeletonization (MPC-Skel) is employed to sample topologically consistent skeletal representations of semantic tubular shapes for skeleton-weighted objective functions. MPC-Skel reduces artifacts from conventional skeletonization methods and directs the focus to critical topological regions, enhancing tubular topology preservation. SAS is computationally efficient and easily integrable into optimization pipelines. Evaluation on two semantic tubular datasets showed consistent improvements in both volumetric overlap and topological integrity metrics.

Multi-Class Segmentation of Aortic Branches and Zones in Computed Tomography Angiography: The AortaSeg24 Challenge

Multi-class segmentation of the aorta in computed tomography angiography (CTA) scans is essential for diagnosing and planning complex endovascular treatments for patients with aortic dissections. However, existing methods reduce aortic segmentation to a binary problem, limiting their ability to measure diameters across different branches and zones. Furthermore, no open-source dataset is currently available to support the development of multi-class aortic segmentation methods. To address this gap, we organized the AortaSeg24 MICCAI Challenge, introducing the first dataset of 100 CTA volumes annotated for 23 clinically relevant aortic branches and zones. This dataset was designed to facilitate both model development and validation. The challenge attracted 121 teams worldwide, with participants leveraging state-of-the-art frameworks such as nnU-Net and exploring novel techniques, including cascaded models, data augmentation strategies, and custom loss functions. We evaluated the submitted algorithms using the Dice Similarity Coefficient (DSC) and Normalized Surface Distance (NSD), highlighting the approaches adopted by the top five performing teams. This paper presents the challenge design, dataset details, evaluation metrics, and an in-depth analysis of the top-performing algorithms. The annotated dataset, evaluation code, and implementations of the leading methods are publicly available to support further research. All resources can be accessed at https://aortaseg24.grand-challenge.org.