Published pipelines

CellProfiler enables reproducible research because a saved pipeline includes all the modules and settings. Here, we provide links to pipelines used in some published studies, as well as the version of CellProfiler used to create them. You can instead download the most current version of CellProfiler; older pipelines should automatically update to the current version when loaded.

If you used CellProfiler in a publication and would like to post your pipelines here, please contact us; we would be happy to host them. Please remember to give CellProfiler the proper citation in your paper.

Please note that each download link contains a compressed ZIP file with the following:

• The CellProfiler pipelines.
• Supplemental notes describing the pipelines.

List of publications

• Elkabets M, Gifford AM, Scheel C, Nilsson B, Reinhardt F, Bray MA, Carpenter AE, Jirström K, Magnuson K, Ebert BL, Ponten F, Weinberg RA, McAllister SS (2011). Human tumors instigate granulin-expressing hematopoietic cells that promote malignancy by activating stromal fibroblasts in mice. J Clin Invest 121(2):784-99/doi. PMID: 21266779 PMCID: PMC3026724
• [Download] (CellProfiler version 9978)
• Bray MA, Fraser AN, Hasaka TP, Carpenter AE (2012). Workflow and metrics for image quality control in large-scale high-content screens. J Biomol Screening 17(2):135-143/doi. PMID: 21956170
• [Download] (CellProfiler version 10997)
• González JE, Barquinero JF, Lee M, García O, Casacó A (2012). Radiosensitization induced by the anti-epidermal growth factor receptor monoclonal antibodies cetuximab and nimotuzumab in A431 cells. Cancer Biol Ther 13(2):1-6/doi. PMID: 22231391
• [Download] (CellProfiler version 10997)
• Kitami T, Logan DJ, Negri J, Hasaka T, Tolliday NJ, et al. (2012) A chemical screen probing the relationship between mitochondrial content and cell size. PLoS ONE 7(3):e33755. doi. PMID: 22479437
• [Download] (CellProfiler version 10997)
• González JE, Romero I, Barquinero JF, Garcia O. (2012) Automatic analysis of silver-stained comets by CellProfiler software. Mutation Research 748(1-2):60-4/doi. PMID: 22771502
• [Download] (CellProfiler version 11710)

Pre-publication pipelines and data

• Chudnovsky J, et al. [Download] (CellProfiler version 11710)
• Hartwell K, et al. [Download] (Note:CellProfiler version 7807 for Windows7 64bit included in download) (CellProfiler Analyst version 11710)