title: Improved structure, function and compatibility for CellProfiler: modular high-throughput image analysis software.
abstract: 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.
  
  
  METHODS
  CellProfiler 2.0 is free and open source, available at http://www.cellprofiler.org 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.
  
  
  BACKGROUND
  anne@broadinstitute.org
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Imaging Platform, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA.
authors.forename: Lee
authors.initials: L
authors.lastname: Kamentsky
authors.forename: Thouis R
authors.initials: TR
authors.lastname: Jones
authors.forename: Adam
authors.initials: A
authors.lastname: Fraser
authors.forename: Mark-Anthony
authors.initials: MA
authors.lastname: Bray
authors.forename: David J
authors.initials: DJ
authors.lastname: Logan
authors.forename: Katherine L
authors.initials: KL
authors.lastname: Madden
authors.forename: Vebjorn
authors.initials: V
authors.lastname: Ljosa
authors.forename: Curtis
authors.initials: C
authors.lastname: Rueden
authors.forename: Kevin W
authors.initials: KW
authors.lastname: Eliceiri
authors.forename: Anne E
authors.initials: AE
authors.lastname: Carpenter
mesh_terms: D000465:Algorithms; D057166:High-Throughput Screening Assays; D007091:Image Processing, Computer-Assisted / Q000379:methods*; D009474:Neurons / Q000648:ultrastructure; D012984:Software