How to cite CellProfiler in publications
(the project's survival depends on it!)
CellProfiler for cells (feel free to cite the most recent):
- Stirling DR, Swain-Bowden MJ, Lucas AM, Carpenter AE, Cimini BA, Goodman A (2021). CellProfiler 4: improvements in speed, utility and usability. BMC Bioinformatics, 22 (1), 433. . PMID: 34507520 PMCID: PMC8431850. doi. pdf.
- McQuin C, Goodman A, Chernyshev V, Kamentsky L, Cimini BA, Karhohs KW, Doan M, Ding L, Rafelski SM, Thirstrup D, Wiegraebe W, Singh S, Becker T, Caicedo JC, Carpenter AE (2018). CellProfiler 3.0: Next-generation image processing for biology. PLoS Biol. 16(7):e2005970. PMID: 29969450. doi.
- 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. PMID: 21349861 PMCID: PMC3072555. doi.
- 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
CellProfiler for the Worm Toolbox: Wählby C, Kamentsky L, Liu ZH, Riklin-Raviv T, Conery AL, O’Rourke EJ, Sokolnicki KL, Visvikis O, Ljosa V, Irazoqui JE, Golland P, Ruvkun G, Ausubel FM, Carpenter AE (2012). An image analysis toolbox for high-throughput C. elegans assays. Nature Methods 9(7):714-716/doi: 10.1038/nmeth.1984. PMID: 22522656 PMCID: PMC3433711 [PDF]
CellProfiler for non-cell 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:
- Stirling DR, Carpenter AE, Cimini BA (2021). CellProfiler Analyst 3.0: Accessible data exploration and machine learning for image analysis. Bioinformatics. PMID: 34478488. doi. pdf (Research article)
- 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]
- 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].
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.
