# Deep Learning for Vascular Segmentation and Applications in Phase Contrast Tomography Imaging

arXiv: https://arxiv.org/abs/2311.13319 · HTML: https://mlsanity.com/paper/2311.13319/

## Key facts

- Cited by 2 papers in the map (data through 14 Oct 2026).
- Builds on 33 of its 134 references that are in the map.
- First posted on arXiv 22 Nov 2023.

## Builds on (most cited first, 30 of 33)

- [Attention Is All You Need](https://mlsanity.com/paper/1706.03762/) (2017)
- [U-Net: Convolutional Networks for Biomedical Image Segmentation](https://mlsanity.com/paper/1505.04597/) (2015)
- [Fully Convolutional Networks for Semantic Segmentation](https://mlsanity.com/paper/1411.4038/) (2014)
- [Neural Machine Translation by Jointly Learning to Align and Translate](https://mlsanity.com/paper/1409.0473/) (2014)
- [DeepLab: Semantic Image Segmentation with Deep Convolutional Nets, Atrous Convolution, and Fully Connected CRFs](https://mlsanity.com/paper/1606.00915/) (2016)
- [Pyramid Scene Parsing Network](https://mlsanity.com/paper/1612.01105/) (2016)
- [V-Net: Fully Convolutional Neural Networks for Volumetric Medical Image Segmentation](https://mlsanity.com/paper/1606.04797/) (2016)
- [TransUNet: Transformers Make Strong Encoders for Medical Image Segmentation](https://mlsanity.com/paper/2102.04306/) (2021)
- [UNet++: A Nested U-Net Architecture for Medical Image Segmentation](https://mlsanity.com/paper/1807.10165/) (2018)
- [SegNet: A Deep Convolutional Encoder-Decoder Architecture for Image Segmentation](https://mlsanity.com/paper/1511.00561/) (2015)
- [3D U-Net: Learning Dense Volumetric Segmentation from Sparse Annotation](https://mlsanity.com/paper/1606.06650/) (2016)
- [Attention U-Net: Learning Where to Look for the Pancreas](https://mlsanity.com/paper/1804.03999/) (2018)
- [The Medical Segmentation Decathlon](https://mlsanity.com/paper/2106.05735/) (2021)
- [MONAI: An open-source framework for deep learning in healthcare](https://mlsanity.com/paper/2211.02701/) (2022)
- [clDice -- A Novel Topology-Preserving Loss Function for Tubular Structure Segmentation](https://mlsanity.com/paper/2003.07311/) (2020)
- [Transformers in Medical Imaging: A Survey](https://mlsanity.com/paper/2201.09873/) (2022)
- [Deep learning for cardiac image segmentation: A review](https://mlsanity.com/paper/1911.03723/) (2019)
- [The Importance of Skip Connections in Biomedical Image Segmentation](https://mlsanity.com/paper/1608.04117/) (2016)
- [Semantic Segmentation using Adversarial Networks](https://mlsanity.com/paper/1611.08408/) (2016)
- [DeepVesselNet: Vessel Segmentation, Centerline Prediction, and Bifurcation Detection in 3-D Angiographic Volumes](https://mlsanity.com/paper/1803.09340/) (2018)
- [ImageCAS: A Large-Scale Dataset and Benchmark for Coronary Artery Segmentation based on Computed Tomography Angiography Images](https://mlsanity.com/paper/2211.01607/) (2022)
- [An application of cascaded 3D fully convolutional networks for medical image segmentation](https://mlsanity.com/paper/1803.05431/) (2018)
- [Graph Convolutional Networks for Coronary Artery Segmentation in Cardiac CT Angiography](https://mlsanity.com/paper/1908.05343/) (2019)
- [RC-Net: A Convolutional Neural Network for Retinal Vessel Segmentation](https://mlsanity.com/paper/2112.11078/) (2021)
- [Hepatic vessel segmentation based on 3D swin-transformer with inductive biased multi-head self-attention](https://mlsanity.com/paper/2111.03368/) (2021)
- [Automatic Segmentation, Feature Extraction and Comparison of Healthy and Stroke Cerebral Vasculature](https://mlsanity.com/paper/2002.11208/) (2020)
- [Kid-Net: Convolution Networks for Kidney Vessels Segmentation from CT-Volumes](https://mlsanity.com/paper/1806.06769/) (2018)
- [Cerebrovascular Network Segmentation on MRA Images with Deep Learning](https://mlsanity.com/paper/1812.01752/) (2018)
- [Deep 3D Vessel Segmentation based on Cross Transformer Network](https://mlsanity.com/paper/2208.10148/) (2022)
- [Extremely weakly-supervised blood vessel segmentation with physiologically based synthesis and domain adaptation](https://mlsanity.com/paper/2305.17054/) (2023)

## Built on by (most cited first, 2 of 2)

- [vesselFM: A Foundation Model for Universal 3D Blood Vessel Segmentation](https://mlsanity.com/paper/2411.17386/) (2024)
- [VesselTok: Tokenizing Vessel-like 3D Biomedical Graph Representations for Reconstruction and Generation](https://mlsanity.com/paper/2603.18797/) (2026)

## Abstract (arXiv)

Automated blood vessel segmentation is vital for biomedical imaging, as vessel changes indicate many pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. We present a thorough literature review, highlighting the state of machine learning techniques across diverse organs. Our goal is to provide a foundation on the topic and identify a robust baseline model for application to vascular segmentation in a new imaging modality, Hierarchical Phase Contrast Tomography (HiP CT). Introduced in 2020 at the European Synchrotron Radiation Facility, HiP CT enables 3D imaging of complete organs at an unprecedented resolution of ca. 20mm per voxel, with the capability for localized zooms in selected regions down to 1mm per voxel without sectioning. We have created a training dataset with double annotator validated vascular data from three kidneys imaged with HiP CT in the context of the Human Organ Atlas Project. Finally, utilising the nnU Net model, we conduct experiments to assess the models performance on both familiar and unseen samples, employing vessel specific metrics. Our results show that while segmentations yielded reasonably high scores such as clDice values ranging from 0.82 to 0.88, certain errors persisted. Large vessels that collapsed due to the lack of hydrostatic pressure (HiP CT is an ex vivo technique) were segmented poorly. Moreover, decreased connectivity in finer vessels and higher segmentation errors at vessel boundaries were observed. Such errors obstruct the understanding of the structures by interrupting vascular tree connectivity. Through our review and outputs, we aim to set a benchmark for subsequent model evaluations using various modalities, especially with the HiP CT imaging database.