Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software

Bioinformatics. 2011 Apr 15;27(8):1179-80. doi: 10.1093/bioinformatics/btr095. Epub 2011 Feb 23.


There is a strong and growing need in the biology research community for accurate, automated image analysis. Here, we describe CellProfiler 2.0, which has been engineered to meet the needs of its growing user base. It is more robust and user friendly, with new algorithms and features to facilitate high-throughput work. ImageJ plugins can now be run within a CellProfiler pipeline.

Availability and implementation: CellProfiler 2.0 is free and open source, available at under the GPL v. 2 license. It is available as a packaged application for Macintosh OS X and Microsoft Windows and can be compiled for Linux.


Supplementary information: Supplementary data are available at Bioinformatics online.

Publication types

  • Research Support, N.I.H., Extramural

MeSH terms

  • Algorithms
  • High-Throughput Screening Assays
  • Image Processing, Computer-Assisted / methods*
  • Neurons / ultrastructure
  • Software*