• 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

    • Jones, TR, Carpenter AE, Lamprecht MR, Moffat J, Silver SJ, Grenier JK, Castoreno AB, Eggert US, Root DE, Golland P, Sabatini DM (2008). Scoring diverse cellular morphologies in image-based screens with iterative feedback and machine learning. PNAS 106(6):1826–1831 / doi. PMID: 19188593. PMCID: PMC2634799
    • [Download]
    • Logan DJ, Carpenter AE (2010). Screening cellular feature measurements for image-based assay development. J Biomol Screen 15(7): 840–846 / doi. PMID: 20516293
    • [Broad Bioimage Benchmark Collection entry] (CellProfiler version 2.0.10997)
    • Cataldo, Anne M; McPhie, Donna L; Lange, Nicholas T; Punzell, Steven; Elmiligy, Sarah; Ye, Nancy Z; Froimowitz, Michael P; Hassinger, Linda C; Menesale, Emily B; Sargent, Laura W; Logan, David J; Carpenter, Anne E; Cohen, Bruce M (2010). Abnormalities in Mitochondrial Structure in Cells from Patients with Bipolar Disorder. Am. J. Pathol. 177(2): 575–585 / doi. PMID: 20566748 PMCID: PMC2913344
    • [Download] (CellProfiler version 2.0.11710)
    • 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 2.0.9978)
    • 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 2.0.10997)
    • 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 2.0.10997)
    • Kitami T, Logan DJ, Negri J, Hasaka T, Tolliday NJ, Carpenter AE, Spiegelman BM, Mootha VK (2012). A chemical screen probing the relationship between mitochondrial content and cell size. PLoS ONE 7(3):e33755 / doi. PMID: 22479437
    • [Download] (CellProfiler version 2.0.10997)
    • 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 2.0.10997)
    • Hartwell KA, Miller PG, Mukherjee S, Kahn AR, Stewart AL, Logan DJ, Negri JM, Duvet M, Järås M, Puram R, Dancik V, Al-Shahrour F, Kindler T, Tothova Z, Chattopadhyay S, Hasaka T, Narayan R, Dai M, Huang C, Shterental S, Chu LP, Haydu JE, Shieh JH, Steensma DP, Munoz B, Bittker JA, Shamji AF, Clemons PA, Tolliday NJ, Carpenter AE, Gilliland DG, Stern AM, Moore MA, Scadden DT, Schreiber SL, Ebert BL, Golub TR (2013). Niche-based screening identifies small-molecule inhibitors of leukemia stem cells. Nat Chem Biol 9(12):840-8 / doi. PMID: 24161946
    • [Download] (Note:CellProfiler version 7807 for Windows7 64bit included in download) (CellProfiler Analyst version 11710)
    • Chudnovsky Y, Kim D, Zheng S, Whyte WA, Bansal M, Bray MA, Gopal S, Theisen MA, Bilodeau S, Thiru P, Muffat J, Yilmaz OH, Mitalipova M, Woolard K, Lee J, Nishimura R, Sakata N, Fine HA, Carpenter AE, Silver SJ, Verhaak RGW, Califano A, Young RA, Ligon KL, Mellinghoff IK, Root DE, Sabatini DM, Hahn WC, Chheda MG (2014). ZFHX4 interacts with the NuRD core member CHD4 and regulates the glioblastoma tumor-initiating cell state. Cell Reports 6(2):313-24 / doi. PMID: 24440720
    • [Download] (CellProfiler version 2.0.11710)
    • Nieland, TJF; Logan, DJ; Saulnier, J; Lam, D; Johnson, C; Root, DE; Carpenter, AE; Sabatini, BL (2014). High Content Image Analysis Identifies Novel Regulators of Synaptogenesis in a High-Throughput RNAi Screen of Primary Neurons PLoS ONE 9(3).e91744 / doi. PMID: 24633176
    • [Download] (CellProfiler version 2.0.11710)
    • Moldovan L, Anghelina M, Kantor T, Jones D, Ramadan E, Xiang Y, Huang K, Kolipaka A, Malarkey W, Ghasemzadeh N, Mohler PJ, Quyyumi A, Moldovan NI (2014). A module of human peripheral blood mononuclear cell rranscriptional network containing primitive and differentiation markers is related to specific cardiovascular health variables. PLoS ONE 9(4):e95124 / doi. PMID: 24759906
    • [Download] (CellProfiler version 2.0.11710)
    • Sheik-Khalil E, Bray MA, Ozkaya Şahin G, Scarlatti G, Jansson M, Carpenter AE, Fenyö EM (2014). Automated image-based assay for evaluation of HIV neutralization and cell-to-cell fusion inhibition. BMC Infect Dis 14:472 / doi. PMID: 25176034
    • [Download] (CellProfiler version 2.0.11710)
    • Singh S, Bray MA, Jones TR, Carpenter AE (2014). Pipeline for illumination correction of images for high-throughput microscopy. Journal of Microscopy 256(3):231-6 / doi. PMID: 25228240
    • [Download] (CellProfiler version 2.1.0)
    • Metelo AM, Noonan HR, Li X, Jin Y, Baker R, Kamentsky L, Zhang Y, van Rooijen E, Shin J, Carpenter AE, Yeh JR, Peterson RT, Iliopoulos O (2015). Pharmacological HIF2α inhibition improves VHL disease-associated phenotypes in zebrafish model. Journal of Clinical Investigation 25(5): 1987-97 / doi. PMID: 25866969
    • [Download] (CellProfiler version 2.0.11710)
    • Du Z, Abedalthagafi M, Aizer AA, McHenry AR, Sun HH, Bray MA, Viramontes O, Machaidze R, Brastianos PK, Reardon DA, Dunn IF, Freeman GJ, Ligon KL, Carpenter AE, Alexander BM, Agar NY, Rodig SJ, Bradshaw EM, Santagata S (2014). Increased expression of the immune modulatory molecule PD-L1 (CD274) in anaplastic meningioma. Oncotarget 10;6(7):4704-16. PMID: 25609200
    • [Download] (CellProfiler version 2.1.0)
    • Leavesley SJ, Nakhmani A, Gao Y, Rich TC (2015). Automated Image Analysis of FRET Signals for Subcellular cAMP Quantification. Methods in Molecular Biology 1294:59-70 / doi. PMID: 25783877
    • [Download] (CellProfiler version 2.1.1)
    • Logan DJ, Shan J, Bhatia SN, Carpenter AE (2015). Quantifying co-cultured cell phenotypes in high-throughput using pixel-based classification. Methods 96:6-11 / doi. PMID: 26687239. PMCID: PMC4766037.
    • [Broad Bioimage Benchmark Collection entry]
    • Jolly AL, Luan CH, Dusel BE, Dunne SF, Winding MJ, Dixit VJ, Robins C, Saluk JL, Logan DJ, Carpenter AE, Cohen, AR, Gelfand VI (2015). A Genome-wide RNAi screen for microtubule network formation and lysosome motility regulation in Drosophila S2 cells. Cell Reports 14(3):611-20 / doi. PMID: 26774481.
    • [Download] (CellProfiler version 2.0.10997)
    • Ricci F, Subramanian A, Wade M (2015). Open access to high-content clonogenic analysis. Journal of Biomolecular Screening 20(3): 391-401 / doi. PMID: 25381257.
    • [Download] (CellProfiler version version 2.1.1 (revision 6c2d896; for Windows 64-bit).)
    • Grenfell A, Strzelecka M, Crowder ME, Helmke KJ, Schlaitz AL, Heald R (2016). A versatile multivariate image analysis pipeline reveals features of Xenopus extract spindles. Journal of Cell Biology 213(1): 127-136 / doi. PMID: 27044897.
    • [Download] (CellProfiler version 2.1.1)
    • Dordea AC, Bray MA, Allen K, Fei F, Gregory M, Carpenter AE, Buys ES (2016). An open-source computational tool to automatically quantify immunolabeled retinal ganglion cells. Experimental Eye Research / doi. PMID: 27119563. PMCID: PMC4903927.
    • [Download] (CellProfiler version 2.1.1)
    • Shan J, Logan DJ, Root DE, Carpenter AE, and Bhatia SN (2016). High-throughput platform for the identification of molecular factors involved in phenotypic stabilization of primary human hepatocytes in vitro. Journal of Biomolecular Screening. 21(9):897-911 / doi . PMID: 27650791. PMCID: in process.
    • [Download]
    • Melo-Filho CC, Dantas RF, Braga RC, Neves BJ, Senger MR, Valente WCG, Rezende-Neto JM, Chaves WT, Muratov EN, Paveley RA, Furnham N, Kamentsky L, Carpenter AE, Silva-Junior FP, Andrade CH (2016). QSAR-Driven Discovery of Novel Chemical Scaffolds Active against Schistosoma mansoni. Journal of Chemical Information and Modeling / doi.
    • [Download]
    • Zimmermann-Meisse G, Prévost G, Jover E (2017). Above and beyond C5a Receptor Targeting by Staphylococcal Leucotoxins: Retrograde Transport of Panton-Valentine Leucocidin and γ-Hemolysin. Toxins / doi.
    • [Download]