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Segmentation of human functional tissue units in support of a Human Reference Atlas.
Jain, Yashvardhan; Godwin, Leah L; Ju, Yingnan; Sood, Naveksha; Quardokus, Ellen M; Bueckle, Andreas; Longacre, Teri; Horning, Aaron; Lin, Yiing; Esplin, Edward D; Hickey, John W; Snyder, Michael P; Patterson, Nathan Heath; Spraggins, Jeffrey M; Börner, Katy.
Afiliación
  • Jain Y; Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA. yashjain@iu.edu.
  • Godwin LL; Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
  • Ju Y; Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
  • Sood N; Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
  • Quardokus EM; Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
  • Bueckle A; Department of Intelligent Systems Engineering, Luddy School of Informatics, Computing, and Engineering, Indiana University, Bloomington, IN, 47408, USA.
  • Longacre T; Department of Pathology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
  • Horning A; Thermo Fisher Scientific, South San Francisco, CA, 94080, USA.
  • Lin Y; Department of Surgery, Washington University School of Medicine, St. Louis, MO, 63110, USA.
  • Esplin ED; Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
  • Hickey JW; Department of Microbiology & Immunology, Stanford University School of Medicine, Stanford, CA, 94305, USA.
  • Snyder MP; Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
  • Patterson NH; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA.
  • Spraggins JM; Mass Spectrometry Research Center, Vanderbilt University, Nashville, TN, 37232, USA.
  • Börner K; Department of Cell and Developmental Biology, Vanderbilt University, Nashville, TN, 37232, USA.
Commun Biol ; 6(1): 717, 2023 07 19.
Article en En | MEDLINE | ID: mdl-37468557
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.
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Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Algoritmos / Imagen por Resonancia Magnética Límite: Adult / Humans Idioma: En Revista: Commun Biol Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos
Texto completo
Imprimir
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PubMed Links
Buscar en Google

Texto completo: 1 Banco de datos: MEDLINE Asunto principal: Algoritmos / Imagen por Resonancia Magnética Límite: Adult / Humans Idioma: En Revista: Commun Biol Año: 2023 Tipo del documento: Article País de afiliación: Estados Unidos