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CellProfiler: image analysis software for identifying and quantifying cell phenotypes.

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).

Pubmed ID: 17076895


  • Carpenter AE
  • Jones TR
  • Lamprecht MR
  • Clarke C
  • Kang IH
  • Friman O
  • Guertin DA
  • Chang JH
  • Lindquist RA
  • Moffat J
  • Golland P
  • Sabatini DM


Genome biology

Publication Data

January 18, 2006

Associated Grants

  • Agency: NIDDK NIH HHS, Id: DK070069-01
  • Agency: NIGMS NIH HHS, Id: R01 GM072555
  • Agency: NIGMS NIH HHS, Id: R01 GM072555-01
  • Agency: NIDDK NIH HHS, Id: T90 DK070069

Mesh Terms

  • Dose-Response Relationship, Drug
  • Gene Expression Profiling
  • Image Processing, Computer-Assisted
  • Models, Genetic
  • Mutation
  • Phenotype
  • Reproducibility of Results
  • Software