Abstract
CellProfiler, the first free, open-source system for flexible and high-throughput cell image analysis is described.
Highlights
Examining cells by microscopy has long been a primary method for studying cellular function
In some cases image cytometry is absolutely required to extract the full spectrum of information present in biological images, for reasons we discuss here
To explain some features of CellProfiler, we describe in the subsequent sections the general steps in a typical pipeline
Summary
CFieglluPrreof1iler overview and features CellProfiler overview and features. (a) Main CellProfiler interface, with an analysis pipeline displayed. (b) Schematic of a typical CellProfiler pipeline. (c) Image processing example: uneven illumination from the left to the right within each field of view is noticeable in this three row by five column tiled image (left). CellProfiler measures a large number of features for each identified cell or subcellular compartment, including area, shape, intensity, and texture (each feature is described in Additional data file 4). Unlike whole population-based methods, image cytometry measures individual cell fluorescence intensities so that the DNA content of DNA-stained cells can be determined [46,47] These measurements are very degraded by anomalies in the illumination of the field of view and poor identification algorithms (the most common errors are counting two nearby nuclei as one nucleus with twice the DNA content and incorrectly splitting a nucleus into two half-nuclei). Image analysis with CellProfiler produced the expected DNA content distributions for both human and Drosophila cell populations (Figure 2c).
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