Temporally Consistent Graph Extraction and Matching for Longitudinal Angiographic Images

Blood vessel segmentation and -tracing are essential tasks in many medical imaging applications. Although numerous methods exist, the prevailing segment-then-fix paradigm is fundamentally limited regarding its suitability for modeling the task of complete and topologically accurate vascular network reconstruction. Here, we propose an approach to extract topologically more accurate vascular graphs from 3D image data, building upon highly successful ideas from the related biomedical tasks of cell segmentation and -tracking. Our approach first predicts voxel-wise vessel direction vectors joint with standard vessel segmentation masks. Second, to extract the vascular graph from these predictions, we introduce a direction-vector-guided extension of the TEASAR algorithm. Our approach achieves state-of-the-art performance on three benchmark datasets, spanning both synthetic and real imagery. We further demonstrate the applicability of our approach to challenging 3D micro-CT scans of rat heart vasculature. Finally, we propose meaningful and interpretable measures of topological error, namely false splits and false merges for graphs. Overall, our approach substantially improves the topological accuracy of reconstructed vascular graphs, being able to separate closely apposed vessel segments and handle multiple vascular trees within a single volume.

Automatic extraction of retinal vascular biomarkers from color fundus images (CFI) is crucial for large-scale studies of the retinal vasculature. We present VascX, an open-source Python toolbox that extracts biomarkers from CFI artery-vein segmentations. VascX starts from vessel segmentation masks, extracts their skeletons, builds undirected and directed vessel graphs, and resolves vessel segments into longer vessels. A comprehensive set of biomarkers is derived, including vascular density, central retinal equivalents (CREs), and tortuosity. Spatially localized biomarkers may be calculated over grids placed relative to the fovea and optic disc. VascX is released via GitHub and PyPI with comprehensive documentation and examples. Our test-retest reproducibility analysis on repeat imaging of the same eye by different devices shows that most VascX biomarkers have moderate to excellent agreement (ICC > 0.5), with important differences in the level of robustness of different biomarkers. Our analyses of biomarker sensitivity to image perturbations and heuristic parameter values support these differences and further characterize VascX biomarkers. Ultimately, VascX provides an explainable and easily modifiable feature-extraction toolbox that complements segmentation to produce reliable retinal vascular biomarkers. Our graph-based biomarker computation stages support reproducible, region-aware measurements suited for large-scale clinical and epidemiological research. By enabling easy extraction of existing biomarkers and rapid experimentation with new ones, VascX supports oculomics research. Its robustness and computational efficiency facilitate scalable deployment in large databases, while open-source distribution lowers barriers to adoption for ophthalmic researchers and clinicians.

Accurate segmentation of vascular structures in digital subtraction angiography (DSA) images remains challenging due to the thin, elongated, and branching nature of blood vessels. Pixel-wise deep learning approaches such as U-Net achieve strong general-purpose segmentation performance but often produce fragmented or discontinuous predictions in fine vascular regions, since they do not explicitly enforce structural connectivity. Region growing algorithms preserve spatial context and topological continuity, but are highly sensitive to seed point initialization and can be computationally expensive. We propose UI-VISA (U-Net Initialized Vascular Image Segmentation Architecture), a hybrid pipeline that combines the complementary strengths of both approaches. UI-VISA uses U-Net's foreground predictions as informed seed points for a CNN-guided region growing algorithm, which then iteratively refines the segmentation by enforcing local connectivity and recovering fine vessel details that U-Net alone tends to miss or over-predict. We evaluate UI-VISA against standalone U-Net and a prior region-growing-based method (VISA) using 5-fold cross-validation on 26 DSA images. UI-VISA achieves the highest mean Dice and clDice scores across folds, and a paired Wilcoxon signed-rank test shows the improvement in clDice is statistically significant ($p=0.023$), consistent with the method's design goal of preserving vascular connectivity, while the improvement in Dice does not reach significance ($p=0.104$).