Supported Applications


  • Description

    is a cell image analysis software designed to enable biologists without training in computer vision or programming to quantitatively measure phenotypes from thousands of images automatically.

  • Installation

    Use the following command to install this title with the CLI client: $ sbgrid-cli install cellprofiler Copy to clipboard
  • Primary Citation*

    A. E. Carpenter, T. R. Jones, M. R. Lamprecht, C. Clarke, I. H. Kang, O. Friman, D. A. Guertin, J. H. Chang, R. A. Lindquist, J. Moffat, P. Golland, and D. M. Sabatini. 2006. CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology. 7(10): R100.
    (Note: Cite this publication for CellProfiler for cells.)

    C. McQuin, A. Goodman, Chernyshev V, L. Kamentsky, B. A. Cimini, K. W. Karhohs, M. Doan, L. Ding, S. M. Rafelski, D. Thirstrup, W. Wiegraebe, S. Singh, T. Becker, J. C. Caicedo, and A. E. Carpenter. 2018. CellProfiler 3.0: Next-generation image processing for biology. PLoS biology. 16(7): e2005970.
    (Note: Cite this publication for CellProfiler for cells.)

    • *Full citation information available through

  • Citation Note

    Please visit https://cellprofiler.org/citations for full citation guidance.

    Although not required, it is requested that you cite the following url: http://cellprofiler.org/ in addition to the publications and that an email be sent to imagingadmin@broadinstitute.org to notify them of your publication.

  • Keywords


  • Default Versions

    Linux 64:  3.1.5
    OS X INTEL:  4.2.1

  • Other Versions

      Linux 64:

      4.2.1, 3.1.3, 2.1.1-2
    • OS X INTEL:

      4.1.3, 3.1.5, 3.1.3, 3.0.0
  • Developers

    Anne E Carpenter, Lee Kamentsky, Mark-Anthony Bray, Thouis Raymond Jones