How to cite this software in publications
Other papers describing the software
Papers using CellProfiler and/or CellProfiler Analyst

How to cite this software in publications- the project's survival depends on it!

• CellProfiler for cells:
• 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 other biological 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 software in general:
• Jones TR, Kang IH, Wheeler DB, Lindquist RA, Papallo A, Sabatini DM, Golland P, Carpenter AE (submitted) CellProfiler Analyst: data exploration and analysis software for complex image-based screens.
• 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 (submitted) Automated scoring of diverse cellular morphologies in image-based screens.

It's also nice if you cite the website (www.cellprofiler.org) and email us so that we are aware of your publication, but these are much less critical than citing the publications.

Other papers describing the software and/or its methods:

• Overview of process of high-throughput screening with CellProfiler

Jones TR, Carpenter AE, Golland P, Sabatini DM (2006) Methods for high-content, high-throughput image-based cell screening. Proceedings of the Workshop on Microscopic Image Analysis with Applications in Biology (MIAAB). Metaxas DN, Whitaker RT, Rittcher J, Sebastian T (Eds). Copenhagen, Denmark, October 5, pp 65-72. [PDF]

• Step-by-step CellProfiler tutorial, using human cell cytoplasm-to-nucleus translocation as an example

Carpenter AE (2007) Data analysis: Extracting rich information from images. Methods in Molecular Biology. In press. (Book chapter) Contact imagingadmin(at) broad(dot)mit(dot)edu for a preprint.

• Step-by-step CellProfiler tutorial, using yeast colonies as an example

Vokes, MS and Carpenter, AE (2008) Using CellProfiler for automatic identification and measurement of biological objects in images. Current Protocols in Molecular Biology 82:14.17.1-14.17.12. (Book chapter) PMID: 18425761 [PDF]

• Propagate algorithm in CellProfiler's IdentifySecondary module

Jones TR, Carpenter AE, Golland P (2005) Voronoi-based segmentation of cells on image manifolds. Proceedings of the ICCV Workshop on Computer Vision for Biomedical Image Applications (CVBIA). Yanxi Liu, Tianzi Jiang, Changshui Zhang (Eds.). Beijing, China, October 21. Lecture Notes in Computer Science 3765. Published by Springer-Verlag, Berlin, p. 535-543, ISBN 3-540-29411-2. [PDF] [poster] [hand traced images]

Papers using CellProfiler and/or CellProfiler Analyst

1. Wheeler DB, Bailey SN, Guertin DA, Carpenter AE, Higgins CO, Sabatini DM (2004) RNAi living-cell microarrays for loss-of-function screens in Drosophila melanogaster cells. Nature Methods, 1(2):1-6. PMID 15782175 [PDF]
2. Bailey SN, Ali SM, Carpenter AE, Higgins CO, Sabatini DM (2006) Microarrays of lentiviruses for gene function screens in immortalized and primary cells. Nature Methods, 3(2):117-22. PMID 16432521 [PDF]
3. Moffat J, Grueneberg DA, Yang X, Kim SY, Kloepfer AM, Hinkle G, Piqani B, Eisenhaure TM, Luo B, Grenier JK, Carpenter AE, Foo SY, Stewart SA, Stockwell BR, Hacohen N, Hahn WC, Lander ES, Sabatini DM, Root DE (2006) A lentiviral RNAi library for human and mouse genes applied to an arrayed viral high-content screen. Cell, 124(6):1283-98. PMID 16564017 [PDF]
4. Sigal A, Milo M, Cohen A, Geva-Zatorsky N, Klein Y, Alaluf I, Swerdlin N, Perzov N, Danon T, Liron Y, Raveh T, Carpenter AE, Lahav G, Alon U (2006) Dynamic proteomics in individual human cells uncovers widespread cell-cycle dependence of nuclear proteins. Nature Methods, 3(7):525-31. PMID 16791210. [PDF]
5. Baltus AE, Menke DB, Hu YC, Goodheart ML, Carpenter AE, de Rooij DG, Page DC (2006) In germ cells of mouse embryonic ovaries, the decision to enter meiosis precedes premeiotic DNA replication. Nature Genetics. 38(12):1430_1434. PMID: 17115059 [PDF]
6. Cowen LE, Carpenter AE, Matangkasombut O, Fink GR, Lindquist S (2006) Genetic architecture of Hsp90-dependent drug resistance. Eukaryotic Cell. 5(12):2184-8. PMID 17056742 [PDF]
7. Hartwell KH, Muir B, Reinhardt F, Carpenter AE, Sgroi DC, Weinberg RA (2006) The Spemann Organizer gene, Goosecoid, promotes tumor metastasis. PNAS. 103(50):18969-74 PMID: 17142318. [PDF]
8. Buth H, Buttigieg PL, Ostafe R, Rehders M, Dannenmann SR, Schaschke N, Stark HJ, Boukamp P, Brix K: Cathepsin B is essential for regeneration of scratch-wounded normal human epidermal keratinocytes. European Journal of Cell Biology 2007, 86:747-761. PMID: 17651862
9. Dai C, Whitesell L, Rogers AB, Lindquist S: Heat shock factor 1 is a powerful multifaceted modifier of carcinogenesis. Cell 2007, 130:1005-1018. PMID: 17889646
10. Kuijl C, Savage NDL, Marsman M, Tuin AW, Janssen L, Egan DA, Ketema M, van den Nieuwendijk R, van den Eeden SJF, Geluk A et al: Intracellular bacterial growth is controlled by a kinase network around PKB/AKT1. Nature 2007, 450:725-U710. PMID-none
11. Li DD, Shao ZH, Vanden Hoek TL, Brorson JR: Reperfusion accelerates acute neuronal death induced by simulated ischemia. Experimental Neurology 2007, 206:280-287. PMID: 17599834
12. Lian S, Fritzler MJ, Katz J, Hamazaki T, Terada N, Satoh M, Chan EKL: Small interfering RNA-mediated silencing induces target-dependent assembly of GW/P bodies. Molecular Biology of the Cell 2007, 18:3375-3387. PMID: 17596515
13. Mu JJ, Wang Y, Luo H, Leng M, Zhang JL, Yang T, Besusso D, Jung SY, Qin J: A proteomic analysis of ataxia telangiectasia-mutated (ATM)/ATM-Rad3-related (ATR) substrates identifies the ubiquitin-proteasome system as a regulator for DNA damage checkpoints. Journal of Biological Chemistry 2007, 282:17330-17334. PMID: 17478428
14. Oh TI, Sung JH, Tatosian DA, Shuler ML, Kim D: Real-time fluorescence detection of multiple microscale cell culture analog devices In situ. Cytometry Part A 2007, 71A:857-865. PMID: 17559134
15. Pincus Z, Theriott JA: Comparison of quantitative methods for cell-shape analysis. Journal of Microscopy-Oxford 2007, 227:140-156. PMID: 17845709
16. Schlumberger MC, Kappeli R, Wetter M, Muller AJ, Misselwitz B, Dilling S, Kremer M, Hardt WD: Two newly identified SipA domains (F1, F2) steer effector protein localization and contribute to Salmonella host cell manipulation. Molecular Microbiology 2007, 65:741-760. PMID: 17635190
17. Togriarini I, Sorace S, Zonefrati R, Galli G, Gozzini A, Sala SC, Thyrion GDZ, Carossino AM, Tanini A, Mavilia C et al: In vitro differentiation of human mesenchymal stem cells on Ti6Al4V surfaces. Biomaterials 2008, 29:809-824. PMID: 18022689
18. Wiley DJ, Rosqvist R, Schesser K: Induction of the Yersinia type 3 secretion system as an all-or-none phenomenon. Journal of molecular biology 2007, 373:27-37. PMID: 17825321
19. Sumiyoshi M, Ricciuto J, Tisdale A, Gipson IK, Mantelli F, Argueso P: Antiadhesive character of mucin O-glycans at the apical surface of corneal epithelial cells. Investigative ophthalmology & visual science 2008, 49:197-203. PMID: 18172093
20. Hasegawa Y, Murph M, Yu S, Tigyi G, Mills GB: Lysophosphatidic acid (LPA)-induced vasodilator-stimulated phosphoprotein mediates lamellipodia formation to initiate motility in PC-3 prostate cancer cells. Molecular Oncology 2008, 2(1): 54-69. PMID-none