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.