# Simulation-Based Segmentation of Blood Vessels in Cerebral 3D OCTA Images

arXiv: https://arxiv.org/abs/2403.07116 · HTML: https://mlsanity.com/paper/2403.07116/

## Key facts

- Cited by 4 papers in the map (data through 14 Oct 2026).
- Builds on 10 of its 32 references that are in the map.
- First posted on arXiv 11 Mar 2024.

## Builds on (most cited first, 10 of 10)

- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [OCTA-500: A Retinal Dataset for Optical Coherence Tomography Angiography Study](https://mlsanity.com/paper/2012.07261/) (2020)
- [Synthetic optical coherence tomography angiographs for detailed retinal vessel segmentation without human annotations](https://mlsanity.com/paper/2306.10941/) (2023)
- [Physiology-based simulation of the retinal vasculature enables annotation-free segmentation of OCT angiographs](https://mlsanity.com/paper/2207.11102/) (2022)
- [LIFE: A Generalizable Autodidactic Pipeline for 3D OCT-A Vessel Segmentation](https://mlsanity.com/paper/2107.04282/) (2021)
- [PAENet: A Progressive Attention-Enhanced Network for 3D to 2D Retinal Vessel Segmentation](https://mlsanity.com/paper/2108.11695/) (2021)
- [3D Vessel Reconstruction in OCT-Angiography via Depth Map Estimation](https://mlsanity.com/paper/2102.13588/) (2021)
- [Link Prediction for Flow-Driven Spatial Networks](https://mlsanity.com/paper/2303.14501/) (2023)
- [FreeCOS: Self-Supervised Learning from Fractals and Unlabeled Images for Curvilinear Object Segmentation](https://mlsanity.com/paper/2307.07245/) (2023)
- [Dynamic contrast in scanning microscopic OCT](https://mlsanity.com/paper/2003.00006/) (2020)

## Built on by (most cited first, 4 of 4)

- [vesselFM: A Foundation Model for Universal 3D Blood Vessel Segmentation](https://mlsanity.com/paper/2411.17386/) (2024)
- [VessShape: Few-shot 2D blood vessel segmentation by leveraging shape priors from synthetic images](https://mlsanity.com/paper/2510.27646/) (2025)
- [Synthetic Vasculature and Pathology Enhance Vision-Language Model Reasoning](https://mlsanity.com/paper/2512.11060/) (2025)
- [vesselFM-CT: Segmenting All Blood Vessels in CT Images for System-Level Cardiovascular Analysis](https://mlsanity.com/paper/2606.09400/) (2026)

## Abstract (arXiv)

Segmentation of blood vessels in murine cerebral 3D OCTA images is foundational for in vivo quantitative analysis of the effects of neurovascular disorders, such as stroke or Alzheimer's, on the vascular network. However, to accurately segment blood vessels with state-of-the-art deep learning methods, a vast amount of voxel-level annotations is required. Since cerebral 3D OCTA images are typically plagued by artifacts and generally have a low signal-to-noise ratio, acquiring manual annotations poses an especially cumbersome and time-consuming task. To alleviate the need for manual annotations, we propose utilizing synthetic data to supervise segmentation algorithms. To this end, we extract patches from vessel graphs and transform them into synthetic cerebral 3D OCTA images paired with their matching ground truth labels by simulating the most dominant 3D OCTA artifacts. In extensive experiments, we demonstrate that our approach achieves competitive results, enabling annotation-free blood vessel segmentation in cerebral 3D OCTA images.