Software

CellProfiler: image analysis software for identifying and quantifying cell phenotypes

Anne E Carpenter¹ , Thouis R Jones^1,2 , Michael R Lamprecht¹ , Colin Clarke^1,2 , In Han Kang² , Ola Friman³ , David A Guertin¹ , Joo Han Chang¹ , Robert A Lindquist¹ , Jason Moffat¹ , Polina Golland² and David M Sabatini^1,4

¹Whitehead Institute for Biomedical Research, Cambridge, MA 02142, USA

²Computer Sciences and Artificial Intelligence Laboratory, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

³Department of Radiology, Brigham and Women's Hospital, Boston, MA 02115, USA

⁴Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA

author email corresponding author email

Genome Biology 2006, 7:R100doi:10.1186/gb-2006-7-10-r100

Published:	31 October 2006

Subject areas: Bioinformatics, Cell biology

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).