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Publications

Journal Article Research Support, U.S. Gov't, Non-P.H.S. Research Support, N.I.H., Extramural Epublish 7 citations

PubMed: 37596311 DOI: 10.1038/s41467-023-40522-4

iCLOTS: open-source, artificial intelligence-enabled software for analyses of blood cells in microfluidic and microscopy-based assays.

Nat Commun 14(1):5022

Authors: Meredith E Fay, Oluwamayokun Oshinowo, Elizabeth Iffrig, Kirby S Fibben, Christina Caruso, Scott Hansen, Jamie O Musick, José M Valdez, Sally S Azer, Robert G Mannino, Hyoann Choi, Dan Y Zhang, Evelyn K Williams, Erica N Evans, Celeste K Kanne, Melissa L Kemp, Vivien A Sheehan, Marcus A Carden, Carolyn M Bennett, David K Wood, Wilbur A Lam

Affiliations

  • The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, USA.
  • Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA.
  • Winship Cancer Institute of Emory University, Atlanta, GA, USA.
  • Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
  • Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA.
  • Department of Medicine, Division of Pulmonary, Allergy, Critical Care, and Sleep Medicine, Emory University, Atlanta, GA, USA.
  • Department of Biomedical Engineering, University of Minnesota, Minneapolis, MN, USA.
  • The George W. Woodruff School of Mechanical Engineering, Georgia Institute of Technology, Atlanta, GA, USA.
  • Department of Epidemiology, Gillings School of Public Health, University of North Carolina, Chapel Hill, NC, USA.
  • The Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology & Emory University, Atlanta, GA, USA.
  • Department of Pediatrics, Division of Pediatric Hematology/Oncology, Aflac Cancer Center and Blood Disorders Service of Children's Healthcare of Atlanta, Emory University School of Medicine, Atlanta, GA, USA.
  • Winship Cancer Institute of Emory University, Atlanta, GA, USA.
  • Parker H. Petit Institute of Bioengineering and Bioscience, Georgia Institute of Technology, Atlanta, GA, USA.
  • Institute for Electronics and Nanotechnology, Georgia Institute of Technology, Atlanta, GA, USA.

Abstract

While microscopy-based cellular assays, including microfluidics, have significantly advanced over the last several decades, there has not been concurrent development of widely-accessible techniques to analyze time-dependent microscopy data incorporating phenomena such as fluid flow and dynamic cell adhesion. As such, experimentalists typically rely on error-prone and time-consuming manual analysis, resulting in lost resolution and missed opportunities for innovative metrics. We present a user-adaptable toolkit packaged into the open-source, standalone Interactive Cellular assay Labeled Observation and Tracking Software (iCLOTS). We benchmark cell adhesion, single-cell tracking, velocity profile, and multiscale microfluidic-centric applications with blood samples, the prototypical biofluid specimen. Moreover, machine learning algorithms characterize previously imperceptible data groupings from numerical outputs. Free to download/use, iCLOTS addresses a need for a field stymied by a lack of analytical tools for innovative, physiologically-relevant assays of any design, democratizing use of well-validated algorithms for all end-user biomedical researchers who would benefit from advanced computational methods.

MeSH

Cells, Tissue Adhesions, Intelligence, Blood, Biological Science Disciplines, Microfluidics, Algorithms, Microscopy, Cell Adhesion, Blood Cells, Software, Artificial Intelligence

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