title: CellProfiler: image analysis software for identifying and quantifying cell phenotypes.
abstract: Biologists can now prepare and image thousands of samples per day using automation, enabling chemical screens and functional genomics (for example, using RNA interference). Here we describe the first free, open-source system designed for flexible, high-throughput cell image analysis, CellProfiler. CellProfiler can address a variety of biological questions quantitatively, including standard assays (for example, cell count, size, per-cell protein levels) and complex morphological assays (for example, cell/organelle shape or subcellular patterns of DNA or protein staining).
authors.affiliation: Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA.
authors.forename: Anne E
authors.initials: AE
authors.lastname: Carpenter
authors.forename: Thouis R
authors.initials: TR
authors.lastname: Jones
authors.forename: Michael R
authors.initials: MR
authors.lastname: Lamprecht
authors.forename: Colin
authors.initials: C
authors.lastname: Clarke
authors.forename: In Han
authors.initials: IH
authors.lastname: Kang
authors.forename: Ola
authors.initials: O
authors.lastname: Friman
authors.forename: David A
authors.initials: DA
authors.lastname: Guertin
authors.forename: Joo Han
authors.initials: JH
authors.lastname: Chang
authors.forename: Robert A
authors.initials: RA
authors.lastname: Lindquist
authors.forename: Jason
authors.initials: J
authors.lastname: Moffat
authors.forename: Polina
authors.initials: P
authors.lastname: Golland
authors.forename: David M
authors.initials: DM
authors.lastname: Sabatini
mesh_terms: D004305:Dose-Response Relationship, Drug; D020869:Gene Expression Profiling; D007091:Image Processing, Computer-Assisted; D008957:Models, Genetic; D009154:Mutation; D010641:Phenotype; D015203:Reproducibility of Results; D012984:Software