Segmentation of human functional tissue units in support of a Human Reference Atlas

Yashvardhan Jain; Leah L. Godwin; Yingnan Ju; Naveksha Sood; Ellen M. Quardokus; Andreas Bueckle; Teri Longacre; Aaron Horning; Yiing Lin; Edward D. Esplin; John W. Hickey; Michael P. Snyder; Nathan Heath Patterson; Jeffrey M. Spraggins; Katy Börner

doi:10.1038/s42003-023-04848-5

Communications Biology (Jul 2023)

Segmentation of human functional tissue units in support of a Human Reference Atlas

Yashvardhan Jain,
Leah L. Godwin,
Yingnan Ju,
Naveksha Sood,
Ellen M. Quardokus,
Andreas Bueckle,
Teri Longacre,
Aaron Horning,
Yiing Lin,
Edward D. Esplin,
John W. Hickey,
Michael P. Snyder,
Nathan Heath Patterson,
Jeffrey M. Spraggins,
Katy Börner

Affiliations

Yashvardhan Jain: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University
Leah L. Godwin: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University
Yingnan Ju: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University
Naveksha Sood: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University
Ellen M. Quardokus: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University
Andreas Bueckle: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University
Teri Longacre: Department of Pathology, Stanford University School of Medicine
Aaron Horning: Thermo Fisher Scientific
Yiing Lin: Department of Surgery, Washington University School of Medicine
Edward D. Esplin: Department of Genetics, Stanford University School of Medicine
John W. Hickey: Department of Microbiology & Immunology, Stanford University School of Medicine
Michael P. Snyder: Department of Genetics, Stanford University School of Medicine
Nathan Heath Patterson: Mass Spectrometry Research Center, Vanderbilt University
Jeffrey M. Spraggins: Mass Spectrometry Research Center, Vanderbilt University
Katy Börner: Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University

DOI: https://doi.org/10.1038/s42003-023-04848-5
Journal volume & issue: Vol. 6, no. 1
pp. 1 – 13

Abstract

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Abstract The Human BioMolecular Atlas Program (HuBMAP) aims to compile a Human Reference Atlas (HRA) for the healthy adult body at the cellular level. Functional tissue units (FTUs), relevant for HRA construction, are of pathobiological significance. Manual segmentation of FTUs does not scale; highly accurate and performant, open-source machine-learning algorithms are needed. We designed and hosted a Kaggle competition that focused on development of such algorithms and 1200 teams from 60 countries participated. We present the competition outcomes and an expanded analysis of the winning algorithms on additional kidney and colon tissue data, and conduct a pilot study to understand spatial location and density of FTUs across the kidney. The top algorithm from the competition, Tom, outperforms other algorithms in the expanded study, while using fewer computational resources. Tom was added to the HuBMAP infrastructure to run kidney FTU segmentation at scale—showcasing the value of Kaggle competitions for advancing research.

Published in Communications Biology

ISSN: 2399-3642 (Online)
Publisher: Nature Portfolio
Country of publisher: United Kingdom
LCC subjects: Science: Biology (General)
Website: https://www.nature.com/commsbio/

About the journal