
==== Front
bioRxiv
BIORXIV
bioRxiv
2692-8205
Cold Spring Harbor Laboratory

10.1101/2024.08.25.609595
preprint
1
Article
Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys
Jain Yashvardhan http://orcid.org/0000-0002-6300-5568

Walsh Claire L. http://orcid.org/0000-0003-3769-3392

Yagis Ekin http://orcid.org/0000-0003-3510-3141

Aslani Shahab http://orcid.org/0009-0007-6298-7874

Nandanwar Sonal
Zhou Yang http://orcid.org/0000-0001-5474-9605

Ha Juhyung http://orcid.org/0000-0002-6596-5116

Gustilo Katherine S. http://orcid.org/0000-0002-5574-4272

Brunet Joseph http://orcid.org/0000-0002-8424-9510

Rahmani Shahrokh http://orcid.org/0000-0002-5773-7076

Tafforeau Paul http://orcid.org/0000-0002-5962-1683

Bellier Alexandre http://orcid.org/0000-0003-0907-0315

Weber Griffin M. http://orcid.org/0000-0002-2597-881X

Lee Peter D. http://orcid.org/0000-0002-3898-8881

Börner Katy http://orcid.org/0000-0002-3321-6137

26 8 2024
2024.08.25.609595https://creativecommons.org/licenses/by/4.0/ This work is licensed under a Creative Commons Attribution 4.0 International License, which allows reusers to distribute, remix, adapt, and build upon the material in any medium or format, so long as attribution is given to the creator. The license allows for commercial use.
http://biorxiv.org/lookup/doi/10.1101/2024.08.25.609595
nihpp-2024.08.25.609595.pdf
Abstract

Efficient algorithms are needed to segment vasculature in new three-dimensional (3D) medical imaging datasets at scale for a wide range of research and clinical applications. Manual segmentation of vessels in images is time-consuming and expensive. Computational approaches are more scalable but have limitations in accuracy. We organized a global machine learning competition, engaging 1,401 participants, to help develop new deep learning methods for 3D blood vessel segmentation. This paper presents a detailed analysis of the top-performing solutions using manually curated 3D Hierarchical Phase-Contrast Tomography datasets of the human kidney, focusing on the segmentation accuracy and morphological analysis, thereby establishing a benchmark for future studies in blood vessel segmentation within phase-contrast tomography imaging.
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