title: Automated profiling of individual cell-cell interactions from high-throughput time-lapse imaging microscopy in nanowell grids (TIMING).
abstract: BACKGROUND
  There is a need for effective automated methods for profiling dynamic cell-cell interactions with single-cell resolution from high-throughput time-lapse imaging data, especially, the interactions between immune effector cells and tumor cells in adoptive immunotherapy.
  
  
  RESULTS
  Fluorescently labeled human T cells, natural killer cells (NK), and various target cells (NALM6, K562, EL4) were co-incubated on polydimethylsiloxane arrays of sub-nanoliter wells (nanowells), and imaged using multi-channel time-lapse microscopy. The proposed cell segmentation and tracking algorithms account for cell variability and exploit the nanowell confinement property to increase the yield of correctly analyzed nanowells from 45% (existing algorithms) to 98% for wells containing one effector and a single target, enabling automated quantification of cell locations, morphologies, movements, interactions, and deaths without the need for manual proofreading. Automated analysis of recordings from 12 different experiments demonstrated automated nanowell delineation accuracy >99%, automated cell segmentation accuracy >95%, and automated cell tracking accuracy of 90%, with default parameters, despite variations in illumination, staining, imaging noise, cell morphology, and cell clustering. An example analysis revealed that NK cells efficiently discriminate between live and dead targets by altering the duration of conjugation. The data also demonstrated that cytotoxic cells display higher motility than non-killers, both before and during contact.
  
  
  BACKGROUND
  broysam@central.uh.edu or nvaradar@central.uh.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Electrical and Computer Engineering and.
authors.forename: Amine
authors.initials: A
authors.lastname: Merouane
authors.affiliation: Department of Electrical and Computer Engineering and.
authors.forename: Nicolas
authors.initials: N
authors.lastname: Rey-Villamizar
authors.affiliation: Department of Electrical and Computer Engineering and.
authors.forename: Yanbin
authors.initials: Y
authors.lastname: Lu
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA and.
authors.forename: Ivan
authors.initials: I
authors.lastname: Liadi
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA and.
authors.forename: Gabrielle
authors.initials: G
authors.lastname: Romain
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA and.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Lu
authors.affiliation: Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Harjeet
authors.initials: H
authors.lastname: Singh
authors.affiliation: Division of Pediatrics, The University of Texas MD Anderson Cancer Center, Houston, TX, USA.
authors.forename: Laurence J N
authors.initials: LJ
authors.lastname: Cooper
authors.affiliation: Department of Chemical and Biomolecular Engineering, University of Houston, Houston, TX, USA and.
authors.forename: Navin
authors.initials: N
authors.lastname: Varadarajan
authors.affiliation: Department of Electrical and Computer Engineering and.
authors.forename: Badrinath
authors.initials: B
authors.lastname: Roysam
mesh_terms: D000465:Algorithms; D002450:Cell Communication; D002465:Cell Movement; D058948:Cell Tracking / Q000379:methods*; D002478:Cells, Cultured; D018920:Coculture Techniques; D057166:High-Throughput Screening Assays / Q000379:methods; D006801:Humans; D007091:Image Processing, Computer-Assisted; D020014:K562 Cells; D007694:Killer Cells, Natural / Q000166:cytology*; D049329:Nanostructures / Q000737:chemistry*; D013601:T-Lymphocytes / Q000166:cytology*; D059008:Time-Lapse Imaging / Q000379:methods*