Evidence map›Paper›PMID 39253466›Full record

ArticlebioRxiv : the preprint server for biology2024

Vasculature segmentation in 3D hierarchical phase-contrast tomography images of human kidneys.

Yashvardhan Jain, Claire L Walsh, Ekin Yagis, Shahab Aslani, Sonal Nandanwar, Yang Zhou, Juhyung Ha, Katherine S Gustilo, Joseph Brunet, Shahrokh Rahmani and 5 more

Abstract readPreprint
PubMed Full text at PMC Publisher
In one paragraph

Article in bioRxiv : the preprint server for biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Not yet cited in PubMed.

0numbers the graph read from it
0cells of the map it votes in
0citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

0 citing papers in PubMed.

No citing paper in PubMed yet.

4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

15 authors.

Yashvardhan JainDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0002-6300-5568
Claire L WalshDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0000-0003-3769-3392
Ekin YagisDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0000-0003-3510-3141
Shahab AslaniDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0009-0007-6298-7874
Sonal NandanwarDepartment of Mechanical Engineering, University College London, London, UK.
Yang ZhouDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0000-0001-5474-9605
Juhyung HaDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0002-6596-5116
Katherine S GustiloDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0002-5574-4272
Joseph BrunetDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0000-0002-8424-9510
Shahrokh RahmaniDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0000-0002-5773-7076
Paul TafforeauEuropean Synchrotron Radiation Facility, Grenoble, France.ORCID 0000-0002-5962-1683
Alexandre BellierUniv. Grenoble Alpes, Department of Anatomy (LADAF), Grenoble, France.ORCID 0000-0003-0907-0315
Griffin M WeberDepartment of Biomedical Informatics, Harvard Medical School, Boston, MA, United States.ORCID 0000-0002-2597-881X
Peter D LeeDepartment of Mechanical Engineering, University College London, London, UK.ORCID 0000-0002-3898-8881
Katy BörnerDepartment of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA.ORCID 0000-0002-3321-6137

Funding

SenNet Supplement - Consortium BenchmarkingU24CA268108 · NCI · UNIVERSITY OF PITTSBURGH AT PITTSBURGH · PI Philip D. Blood, JONATHAN C. SILVERSTEIN · 2021 to 2026
$22.1M
ConProject-002U2CDK114886 · NIDDK · UNIVERSITY OF WASHINGTON · PI KRETZLER, MATTHIAS · 2017 to 2021
$21.0M
BRAIN CONNECTS: The center for Large-scale Imaging of Neural Circuits (LINC)UM1NS132358 · NINDS · MASSACHUSETTS GENERAL HOSPITAL · PI Suzanne N Haber, Elizabeth M. C. Hillman · 2023 to 2026
$17.5M
KPMP Kidney Mapping and Atlas Project (KMAP)U01DK133090 · NIDDK · UNIVERSITY OF MICHIGAN AT ANN ARBOR · PI Jonathan Himmelfarb, Matthias Kretzler · 2022 to 2026
$10.4M
3D Multiscale Biomolecular Human Reference Atlas Construction, Visualization and Usage [4 of 5]OT2OD033756 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2022 to 2025
$7.4M
The Human Body Atlas: High-Resolution, Functional Mapping of Voxel, Vector, and Meta DatasetsOT2OD026671 · OD · TRUSTEES OF INDIANA UNIVERSITY · PI BORNER, KATY · 2018 to 2021
$3.5M
National Institute of Diabetes and Digestive and Kidney Diseases ATLAS (D2K-ATLAS) Center as an accessible, comprehensive data portfolio for renal and genitourinary development and diseaseU24DK135157 · NIDDK · BRIGHAM AND WOMEN'S HOSPITAL · PI JAIN, SANJAY, VALERIUS, MICHAEL TODD · 2022 to 2023
$3.4M
NCI NIH HHS U24 CA268108NIDDK NIH HHS U01 DK133090NIDDK NIH HHS U24 DK135157NIDDK NIH HHS U2C DK114886NIH HHS OT2 OD026671NIH HHS OT2 OD033756NINDS NIH HHS UM1 NS132358
6 · The paper itself

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.

Identifiers

PMID39253466
PMCPMC11383006

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Registered trials

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.