title: Using Cell-ID 1.4 with R for microscope-based cytometry.
abstract: This unit describes a method for quantifying various cellular features (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individual cells. It includes procedures for tracking cells over time. One purposely defocused transmission image (sometimes referred to as bright-field or BF) is acquired to segment the image and locate each cell. Fluorescence images (one for each of the color channels to be analyzed) are then acquired by conventional wide-field epifluorescence or confocal microscopy. This method uses the image-processing capabilities of Cell-ID and data analysis by the statistical programming framework R, which is supplemented with a package of routines for analyzing Cell-ID output. Both Cell-ID and the analysis package are open-source.
authors.affiliation: IFIByNE-CONICET and Department of Physiology, Molecular and Cellular Biology, FCEN, University of Buenos Aires, Buenos Aires, Argentina.
authors.forename: Alan
authors.initials: A
authors.lastname: Bush
authors.forename: Ariel
authors.initials: A
authors.lastname: Chernomoretz
authors.forename: Richard
authors.initials: R
authors.lastname: Yu
authors.forename: Andrew
authors.initials: A
authors.lastname: Gordon
authors.forename: Alejandro
authors.initials: A
authors.lastname: Colman-Lerner
mesh_terms: D058948:Cell Tracking / Q000379:methods*; D019295:Computational Biology / Q000295:instrumentation / Q000379:methods; D031541:Fluorescence Resonance Energy Transfer / Q000379:methods; D019044:Image Cytometry / Q000379:methods*; D007091:Image Processing, Computer-Assisted / Q000295:instrumentation / Q000379:methods*; D008856:Microscopy, Fluorescence / Q000295:instrumentation / Q000379:methods*