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's illumination correction modules correct these anomalies (right). Images were contrast-enhanced to display this effect. (d) These corrections reduce noise in quantitative measurements, demonstrated here in DNA content measures (middle) from images of Drosophila Kc167 cells that are improved over the raw images (left). The results are comparable to those produced by white referenced images (right), but they do not require the error prone and often omitted step of collecting a white reference image immediately before image acquisition. (e) Outlines show the identification of nuclei and identification of cell edges made by CellProfiler in human HT29 (left) and Drosophila Kc167 (right) cells. Cells touching the border are intentionally excluded from analysis and images were contrast stretched for display. Scale bars = 15 μm.