CellProfiler was published in 2006 and has been cited in 382 articles (last updated September 13, 2011).

How to cite this software in publications (the project's survival depends on it!)

• CellProfiler for cells:
• Carpenter AE, Jones TR, Lamprecht MR, Clarke C, Kang IH, Friman O, Guertin DA, Chang JH, Lindquist RA, Moffat J, Golland P, Sabatini DM (2006) CellProfiler: image analysis software for identifying and quantifying cell phenotypes. Genome Biology 7:R100. PMID: 17076895 [link to paper at Genome Biology]

or

• Kamentsky L, Jones TR, Fraser A, Bray M, Logan D, Madden K, Ljosa V, Rueden C, Harris GB, Eliceiri K, Carpenter AE (2011) Improved structure, function, and compatibility for CellProfiler: modular high-throughput image analysis software. Bioinformatics 2011/doi. PMID: 21349861 PMCID: In process
• CellProfiler for other biological images:
• Lamprecht MR, Sabatini DM, Carpenter AE (2007) CellProfiler: free, versatile software for automated biological image analysis. Biotechniques 42(1):71-75. PMID: 17269487 [PDF]
• CellProfiler Analyst software in general:
• Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (2008) CellProfiler Analyst: data exploration and analysis software for complex image-based screens. BMC Bioinformatics 9(1):482/doi: 10.1186/1471-2105-9-482. PMID: 19014601 PMCID: PMC2614436 [link to paper at BioMed Central].
• CellProfiler Analyst for scoring phenotypes by machine learning:
• Jones TR, Carpenter AE, Lamprecht MR, Moffat J, Silver S, Grenier J, Root D, Golland P, Sabatini DM (2009) Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. PNAS 106(6):1826-1831/doi: 10.1073/pnas.0808843106. PMID: 19188593 PMCID: PMC2634799 [link to paper at PNAS]

• It's also nice if you cite the website (www.cellprofiler.org) and email us so that we are aware of your publication, but this is much less critical than citing the publications.

• If you used CellProfiler in a publication and would like to include your pipelines as online supplemental information, we are willing to host the pipelines here. Please contact us for more information.