Vesselpose: Vessel Graph Reconstruction from Learned Voxel-wise Direction Vectors in 3D Vascular Images

TL;DR

Vesselpose introduces a novel method for reconstructing topologically accurate vascular graphs from 3D images by predicting voxel-wise vessel directions and extending the TEASAR algorithm, achieving state-of-the-art results.

Contribution

The paper presents a new approach combining vessel direction prediction with a modified TEASAR algorithm for improved vascular graph reconstruction.

Findings

Achieved state-of-the-art performance on three benchmark datasets.

Successfully applied to challenging 3D micro-CT scans of rat heart vasculature.

Proposed interpretable measures of topological error, such as false splits and merges.

Abstract

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.