Using Cell-ID-1.4 with R for microscope-based cytometry

ARIEL CHERNOMORETZ; ALAN BUSH; RICHARD YU; ANDREW GORDON; ALEJANDRO COLMAN-LERNER

Current protocols in molecular biology

Wiley-Interscience

Año: 2008 vol. 14 p. 1 - 27

1934-3639

This unit describes a method for quantifying various cellular parameters (e.g., volume, total and subcellular fluorescence localization) from sets of microscope images of individ- ual cells. It includes procedures for tracking cells over time. One purposefully defocused transmission image (sometimes referred to as bright-field or BF) is acquired to locate each cell. Fluorescent images (one for each of the color channels to be analyzed) are then ac- quired by conventional wide-field epifluorescence or confocal microscopy. This method uses the image processing capabilities of Cell-ID (Gordon et al., 2007) and data analysis by the statistical programming framework R (R-Development-Team, 2008), which we have supplemented with a package tailored to analyze Cell-ID output. Both programs are open-source software packages. Curr. Protoc. Mol. Biol. 84:14.18.1-14.18.27. ⃝C 2008 by John Wiley & Sons, Inc.