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Robust and generalizable segmentation of human functional tissue units

View ORCID ProfileLeah L. Godwin, View ORCID ProfileYingnan Ju, View ORCID ProfileNaveksha Sood, View ORCID ProfileYashvardhan Jain, View ORCID ProfileEllen M. Quardokus, View ORCID ProfileAndreas Bueckle, View ORCID ProfileTeri Longacre, View ORCID ProfileAaron Horning, View ORCID ProfileYiing Lin, View ORCID ProfileEdward D. Esplin, View ORCID ProfileJohn W. Hickey, View ORCID ProfileMichael P. Snyder, View ORCID ProfileN. Heath Patterson, View ORCID ProfileJeffrey M. Spraggins, View ORCID ProfileKaty Börner
doi: https://doi.org/10.1101/2021.11.09.467810
Leah L. Godwin
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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  • For correspondence: llschers@iu.edu katy@indiana.edu
Yingnan Ju
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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Naveksha Sood
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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Yashvardhan Jain
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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Ellen M. Quardokus
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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Andreas Bueckle
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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Teri Longacre
2Department of Pathology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Aaron Horning
3Thermo Fisher Scientific, South San Francisco, CA 94080, USA
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Yiing Lin
4Department of Surgery, Washington University School of Medicine, St. Louis, MO 63110, USA
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Edward D. Esplin
5Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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John W. Hickey
6Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Michael P. Snyder
5Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
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N. Heath Patterson
7Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
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Jeffrey M. Spraggins
7Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN 37232, USA
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Katy Börner
1Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN 47408, USA
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  • For correspondence: llschers@iu.edu katy@indiana.edu
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Abstract

The Human BioMolecular Atlas Program aims to compile a reference atlas for the healthy human adult body at the cellular level. Functional tissue units (FTU, e.g., renal glomeruli and colonic crypts) are of pathobiological significance and relevant for modeling and understanding disease progression. Yet, annotation of FTUs is time consuming and expensive when done manually and existing algorithms achieve low accuracy and do not generalize well. This paper compares the five winning algorithms from the “Hacking the Kidney” Kaggle competition to which more than a thousand teams from sixty countries contributed. We compare the accuracy and performance of the algorithms on a large-scale renal glomerulus Periodic acid-Schiff stain dataset and their generalizability to a colonic crypts hematoxylin and eosin stain dataset. Results help to characterize how the number of FTUs per unit area differs in relationship to their position in kidney and colon with respect to age, sex, body mass index (BMI), and other clinical data and are relevant for advancing pathology, anatomy, and surgery.

Competing Interest Statement

Michael P. Snyder is cofounder and a member of the scientific advisory board of Personalis, Qbio, January AI, SensOmics, Protos, Mirvie, NiMo and Oralome. He is on the scientific advisory board of Danaher, GenapSys and Jupiter.

Footnotes

  • https://cns-iu.github.io/ccf-research-kaggle-2021/

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Robust and generalizable segmentation of human functional tissue units
Leah L. Godwin, Yingnan Ju, Naveksha Sood, Yashvardhan Jain, Ellen M. Quardokus, Andreas Bueckle, Teri Longacre, Aaron Horning, Yiing Lin, Edward D. Esplin, John W. Hickey, Michael P. Snyder, N. Heath Patterson, Jeffrey M. Spraggins, Katy Börner
bioRxiv 2021.11.09.467810; doi: https://doi.org/10.1101/2021.11.09.467810
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Robust and generalizable segmentation of human functional tissue units
Leah L. Godwin, Yingnan Ju, Naveksha Sood, Yashvardhan Jain, Ellen M. Quardokus, Andreas Bueckle, Teri Longacre, Aaron Horning, Yiing Lin, Edward D. Esplin, John W. Hickey, Michael P. Snyder, N. Heath Patterson, Jeffrey M. Spraggins, Katy Börner
bioRxiv 2021.11.09.467810; doi: https://doi.org/10.1101/2021.11.09.467810

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