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 (by date)



  • Sokolov, A. M., Aurich, M., & Bordey, A. (2023). In Utero Electroporated Neurons for Medium-Throughput Screening of Compounds Regulating Neuron Morphology. eNeuro, 10(8) / doi
    • [Download] (CellProfiler version 4.2.1)
  • Schiller, H., Kouassi, J., Hong, Y., Rados, T., Kwak, J., DiLucido, A., Safer, D., Marchfelder, A., Pfeiffer, F., Bisson-Filho, A., Schulze, S., and Pohlschroder, M. (2023). Identification and characterization of structural and regulatory cell-shape determinants in Haloferax volcanii. bioRxiv / doi
  • Choudhury, Q. J., Ambati, S., Link, C. D., Lin, X., Lewis, Z. A., & Meagher, R. B. (2023). Dectin‐3‐targeted antifungal liposomes efficiently bind and kill diverse fungal pathogens. Molecular Microbiology / doi 
    • [Download] (CellProfiler version 4.2.4)
  • Pellegrini F, Martino S, Fianco G, Ventura I, Valente D, Fiore M, Trisciuoglio D, Degrassi F (2023) Blockage of autophagosome-lysosome fusion through SNAP29 O-GlcNAcylation promotes apoptosis via ROS production. Autophagy / doi
    • [Download] (CellProfiler version 4.2.5)
  • Upender I, Yoshida O, Schrecengost A, Ranson H, Wu Q, Rowley D, Kishore S, Cywes C, Miller E, Whalen K (2023) A Marine Derived Fatty Acid Targets the Cell Membrane of Gram-Positive Bacteria. Journal of Antimicrobial Agents and Chemotherapy 
    • [Download] (CellProfiler version 4.2.5)
  • Schrenk S, Bischoff L, Goines J, Cai Y, Vemaraju S, Odaka Y, Good S, Palumbo J, Szabo S, Reynaud D, Van Raamsdonk C, Lang R, Boscolo E (2023) MEK inhibition reduced vascular tumor growth and coagulopathy in a mouse model with hyperactive GNAQ. Nature Communications 
    • [Download] (CellProfiler version 4.2.1) 
  • Davies SP, Ronca V, Wootton GE, Krajewska NM, Bozward AG, Fiancette R, Patten DA, Yankouskaya K, Reynolds GM, Pat S, Osei-Bordom DC, Richardson N, Grover LM, Weston CJ, Oo YH. Expression of E-cadherin by CD8+ T cells promotes their invasion into biliary epithelial cells. Nature Communications 
    • [Download] (CellProfiler version 4.1.3)


  • Jang W, Puchkov D, Samsó P, Liang Y, Nadler-Holly M, Sigrist S, Kintscher U, Liu F, Mamchaoui K, Mouly V, Haucke V (2022) Endosomal lipid signaling reshapes the endoplasmic reticulum to control mitochondrial function. Science, 378, 6625, (1173-1174) / doi 
    • [Download] (CellProfiler version 4.1.3)
  • Zhao, L.; Fonseca, A.; Meschichi, A.; Sicard, A.; Rosa, S. (2022) Whole-mount smFISH allows combining RNA and protein quantification at cellular and subcellular resolution. bioRxiv (2022).10.05.510616; doi.
    • [Download] (CellProfiler version 4.2.1)
  • Janssen, A.F.J.; Breusegem, S.Y.; Larrieu, D. Current Methods and Pipelines for Image-Based Quantitation of Nuclear Shape and Nuclear Envelope Abnormalities. Cells 2022, 11, 347 doi.
    • [Download] (CellProfiler version 4.1.3)
  • Campana, C., Van Koetsveld, P. M., Feelders, R. A., de Herder, W. W., Iyer, A. M., van Velthuysen, M.-L. F., Veenstra, M. J., van den Dungen, E. S. r., Franck, S. E., Ferone, D., Gatto, F., & Hofland, L. J. (2022). Digital quantification of somatostatin receptor subtype 2a immunostaining: a validation study. European Journal of Endocrinology / European Federation of Endocrine Societies. doi.
    • [Download] (CellProfiler version 4.0.7)
  • Sánchez-Jaramillo EA, Gasca-Lozano LE, Vera-Cruz JM, Hernández-Ortega LD, Gurrola-Díaz CM, Bastidas-Ramírez BE, Vargas-Guerrero B, Mena-Enríquez M, Martínez-Limón FJ, Salazar-Montes AM. Nanoparticles Formulation Improves the Antifibrogenic Effect of Quercetin on an Adenine-Induced Model of Chronic Kidney Disease. Int J Mol Sci. 2022 May 12;23(10):5392. doi.
    • [Download] (CellProfiler version 3.1.9)



  • Groiss S, Somvilla I, Daxböck C, Fuchs J, Lang-Olip I, Stiegler P, Leber B, Liegl-Atzwanger B, Brislinger D (2021) Quantification of increased MUC5AC expression in airway mucus of smoker using an automated image-based approach. Microscopy Research & Technique. Epub ahead of print. doi. PMID: 34288207.
    • [Download] (CellProfiler version 3.1.5)


  • Mazzoleni V, Zimmermann‐Meisse G, Smirnova A, Tarassov I, Prévost G (2020) Staphylococcus aureus Panton‐Valentine Leukocidin triggers an alternative NETosis process targeting mitochondria. The FASEB Journal, 00: 1– 22. / doi. PMID: 33241563. 
    • [Download] (CellProfiler version 2.1.1)


  • Sanz G, Martínez-Aranda LM, Tesch PA, Fernandez-Gonzalo R, Lundberg TR (2019) Muscle2View, a CellProfiler pipeline for detection of the capillary-to-muscle fiber interface and high-content quantification of fiber type-specific histology. J Appl Physiol (1985). 127(6):1698-1709. / doi. PMID: 31697593.
  •  Tian R, Gachechiladze MA, Ludwig CH, Laurie MT, Hong, JY, Nathaniel,D, Prabhu AV, Fernandopulle MS, Patel R, Abshari M, Ward ME, Kampmann M (2019) CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons. Neuron, 104(2): 239–255.e12. / doi. PMID: 31422865 PMCID: PMC6813890


  • Tollemar V, Tudzarovski N, Boberg E, Törnqvist Andrén A, Al-Adili A, Le Blanc K, Garming Legert K, Bottai M, Warfvinge G, Sugars RV. Quantitative chromogenic immunohistochemical image analysis in cellprofiler software. Cytometry A. 2018 Oct;93(10):1051-1059. doi. Epub 2018 Aug 8. PMID: 30089197.
  • Bray MA, Carpenter AE (2018). Quality Control for High-Throughput Imaging Experiments Using Machine Learning in Cellprofiler. Methods Mol. Biol. / doi. PMID: 29082489.
  • Zhang H, Ericsson M, Virtanen M, Weström S, Wählby C, Vahlquist A, Törmä H (2018). Quantitative image analysis of protein expression and colocalisation in skin sections. Exp Dermatol. / doi. PMID: 29094393.
  • Bouçanova F, Maia AF, Cruz A, Millar V, Mendes Pinto I, Relvas JB, Domingues HS (2018). Collar occupancy: A new quantitative imaging tool for morphometric analysis of oligodendrocytes. J Neurosci Methods 294:122–135 / doi. PMID: 29174019.
  • Salzmann M, Hoesel B, Haase M, Mussbacher M, Schrottmaier WC, Kral-Pointner JB, Finsterbusch M, Mazharian A, Assinger A, Schmid JA (2018). A novel method for automated assessment of megakaryocyte differentiation and proplatelet formation. Platelets :1–8 / doi. PMID: 29461915.
  • Van Tol N, Rolloos M, van Loon P, van der Zaal B. J. (2018). MeioSeed: a CellProfiler-based program to count fluorescent seeds for crossover frequency analysis in Arabidopsis thaliana. Plant Methods, 14: 32. / doi. PMCID: PMC5905130.
    • [Download] (includes pipeline and classifier files) (CellProfiler version 2.1.1)
  • Gomes-Alves AG, Maia AF, Cruz T, Castro H, Tomás AM (2018) Development of an automated image analysis protocol for quantification of intracellular forms of Leishmania spp. PLoS ONE. / doi. PMID: 30071097 PMCID: PMC6072083.


  • 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.
  • Bray MA, Gustafsdottir SM, Ljosa V, Singh S, Sokolnicki KL, Bittker JA, Bodycombe NE, Dancík V, Hasaka TP, Hon CS, Kemp MM, Li K, Walpita D, Wawer MJ, Golub TR, Schreiber SL, Clemons PA, Shamji AF, Carpenter AE (2017). A dataset of images and morphological profiles of 30,000 small-molecule treatments using the Cell Painting assay. Gigascience / doi.
  • Barczak A, Avraham R, Singh S, Luo SS, Zhang WR, Bray MA, Hinman AE, Thompson M, Nietupski RM, Golas A, Montgomery P, Fitzgerald M, Smith RS, White DW, Tischler AD, Carpenter AE, and Hung DT (2017). Systematic, multiparametric analysis of Mycobacterium tuberculosis intracellular infection offers insight into coordinated virulence. PLoS ONE.
  • Sucic L, Galati-Fournier V, Kym U, Pfeifle V, Gros S, Schäfer KH, Holland-Cunz S, Keck S (2017). Increased regulatory T cells in pediatric acute appendicitis. Pediatr Allergy Immunol. doi. PMID: 28881058.
  • Erben L, He M-X, Laeremans A, Park E, Buonanno A (2017). QA Novel Ultrasensitive In Situ Hybridization Approach to Detect Short Sequences and Splice Variants with Cellular Resolution. Mol Neurobiol. / doi. PMID: 29264769.


  • 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.
  • Dordea AC, Bray MA, Allen K, Logan D, 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.
  • 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.
  • 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 mansoniJournal of Chemical Information and Modeling / doi.


  • 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
  • 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 / doi. PMID: 25609200
  • 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
  • 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.
  • 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.
  • 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.


  • 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
  • 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
  • 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
  • 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
  • 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
  • Wählby C, Conery AL, Bray MA, Kamentsky L, Larkins-Ford J, Sokolnicki KL, Veneskey M, Michaels K, Carpenter AE, O'Rourke EJ (2014). High- and low-throughput scoring of fat mass and body fat distribution in C. elegans. Methods 68(3):492-499. / doi. PMID: 24784529. This publication includes four example pipelines, described below: 
    • Untangle worms: In this pipeline, we identify individual worms and extract shape and intensity measurements. Worm untangling requires a worm model, which is provided together with the pipeline. If adjusting the pipeline to fit your own data, worm detection will likely improve by creating a new worm model based on your own image data. [Download (1.4 MB)]
    • Straighten worms and extract intensity measurements using a low-resolution atlas: Once worms are untangled, this pipeline shows how they can be straightened and aligned with a low-resolution worm atlas to extract localized intensity measurements and compare patterns of reporter signals. Included are steps for identifying secondary objects (fluorescent marker signals) and relating these objects to individual worms, enabling count of signals on a per-worm basis. [Download (1 MB)]
    • Create your own worm model: The UntangleWorms module has an "Untangle" mode and a "Train" mode. This pipeline describes how the "Train" mode is used to create a worm model. Training consists of providing a large number of images of worms that are representative of the worm variation within the population, and that do not touch or overlap. Note that this example download includes only two images and will not result in a good model, as it will not be representative of all possible variations of the worm shapes. We recommend using at least 60 worms to create a model. [Download (1.6 MB)]
    • Untangle worms and make measurements bright-field staining pattern phenotype: This pipeline detects individual worms by worm untangling and finds sub-objects (fatty regions stained with oil red O) within the worms. Using bright-field data only, it detects fatty regions by intensity thresholding in a single image channel and relates the fatty regions to individual worms. This enables detection of rare phenotypes in heterogeneous populations, phenotypes that would be missed if population averages were observed. More data can be found on the BBBC. [Download (1.7 MB)]


  • 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 2.0.11710)


  • 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
  • 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
  • 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
  • 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


  • 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


  • Logan DJ, Carpenter AE (2010). Screening cellular feature measurements for image-based assay development. J Biomol Screen 15(7): 840–846 / doi. PMID: 20516293
  • 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



  • 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