iCLOTS: open-source, artificial intelligence-enabled software for analyses of blood cells in microfluidic and microscopy-based assays
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Published:2023-08-18
Issue:1
Volume:14
Page:
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ISSN:2041-1723
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Container-title:Nature Communications
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language:en
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Short-container-title:Nat Commun
Author:
Fay Meredith E., Oshinowo Oluwamayokun, Iffrig Elizabeth, Fibben Kirby S., Caruso Christina, Hansen Scott, Musick Jamie O., Valdez José M., Azer Sally S., Mannino Robert G., Choi HyoannORCID, Zhang Dan Y.ORCID, Williams Evelyn K., Evans Erica N., Kanne Celeste K., Kemp Melissa L.ORCID, Sheehan Vivien A., Carden Marcus A., Bennett Carolyn M., Wood David K.ORCID, Lam Wilbur A.ORCID
Abstract
AbstractWhile 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.
Funder
Foundation for the National Institutes of Health U.S. Department of Health & Human Services | NIH | National Institute of Allergy and Infectious Diseases All funders indicated as "Foundation for the National Institutes of Health" are specifically within the Institute of Heart, Lung, and Blood division.
Publisher
Springer Science and Business Media LLC
Subject
General Physics and Astronomy,General Biochemistry, Genetics and Molecular Biology,General Chemistry,Multidisciplinary
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