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published_pipelines.html
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---
layout: default
redirect_from: "/published_pipelines.shtml"
---
<h1>
<a id="PublishedPipelines" name="PublishedPipelines"></a>Published
pipelines
</h1>
<p>
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
<a href="download.html">current version</a> of CellProfiler; older
pipelines should automatically update to the current version when
loaded.
</p>
<p>
If you used CellProfiler in a publication and would like to post your
pipelines here, please <a href=
"mailto:[email protected]">contact us</a>; we would be
happy to host them. Please remember to give CellProfiler the proper
<a href="citations.html">citation</a> in your paper.
</p>
<p>
Please note that each download link contains a compressed ZIP file
with the following:
</p>
<ul>
<li>The CellProfiler pipelines.
</li>
<li>Supplemental notes describing the pipelines.
</li>
</ul>
<p>
</p>
<h2>
List of publications
</h2>
<ul>
<li class="li_ul">
<a name="Jones_2008"></a>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. <span style="font-style:italic">PNAS</span> 106(6):1826–1831 /
<a href="http://dx.doi.org/10.1073/pnas.0808843106">doi</a>. PMID: 19188593. PMCID: PMC2634799
</li>
<li class="li_ul" style="list-style:none">
<a href="http://d1zymp9ayga15t.cloudfront.net/Jones_PNAS_2009_training_sets.zip">[Download]</a>
</li>
<li class="li_ul">
<a name="Logan_2010"></a>Logan DJ, Carpenter AE (2010). Screening
cellular feature measurements for image-based assay development.
<span style="font-style:italic">J Biomol Screen</span> 15(7):
840–846 /<a href=
"http://dx.doi.org/10.1177/1087057110370895">doi</a>. PMID:
20516293
</li>
<li class="li_ul" style="list-style:none">
<a href="http://www.broadinstitute.org/bbbc/BBBC013/">[Broad
Bioimage Benchmark Collection entry]</a> (CellProfiler version
<a href="previousReleases.html#v10997">2.0.10997</a>)
</li>
<li class="li_ul">
<a name="Cataldo_2010"></a>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. <span style="font-style:italic">Am. J. Pathol.</span> 177(2):
575–585/<a href="http://dx.doi.org/10.2353/ajpath.2010.081068">doi</a>. PMID: 20566748 PMCID:
PMC2913344
</li>
<li class="li_ul" style="list-style:none">
<a href="http://d1zymp9ayga15t.cloudfront.net/small_files/Cataldo_2010.cp.zip">[Download]</a>
(CellProfiler version <a href="http://http://cellprofiler.org/previousReleases#v11710">2.0.11710</a>)
<li class="li_ul">
<a name="Elkabets_2010"></a>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.
<span style="font-style:italic">J Clin Invest</span>
121(2):784-99/<a href="http://dx.doi.org/10.1172/JCI43757">doi</a>.
PMID: 21266779 PMCID: PMC3026724
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Elkabets_2010.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#v9978">2.0.9978</a>)
</li>
<li class="li_ul">
<a name="Bray_2011"></a>Bray MA, Fraser AN, Hasaka TP, Carpenter AE
(2012). Workflow and metrics for image quality control in
large-scale high-content screens. <span style="font-style:italic">J
Biomol Screening</span> 17(2):135-143 / <a href=
"http://dx.doi.org/10.1177/1087057111420292">doi</a>. PMID:
21956170
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Bray_2011_SupplementalMaterial.zip">
[Download]</a> (CellProfiler version <a href=
"previousReleases.html#v10997">2.0.10997</a>)
</li>
<li class="li_ul">
<a name="Gonzalez_2012"></a>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. <i>Cancer Biol
Ther</i> 13(2):1-6 / <a href=
"http://dx.doi.org/10.4161/cbt.13.2.18439">doi</a>. PMID: 22231391
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/CancerBiolTher_Gonzalez_2012.zip">
[Download]</a> (CellProfiler version <a href=
"previousReleases.html#v10997">2.0.10997</a>)
</li>
<li class="li_ul">
<a name="Kitami_2012"></a>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. <span style="font-style:italic">PLoS
ONE</span> 7(3):e33755 / <a href=
"http://dx.doi.org/10.1371/journal.pone.0033755">doi</a>. PMID:
22479437
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/PIPE_main_batch_InformerBigRun_Threshold_CP10997.cp">
[Download]</a> (CellProfiler version <a href=
"previousReleases.html#v10997">2.0.10997</a>)
</li>
<li class="li_ul">
<a name="Gonzalez_2012b"></a>González JE, Romero I, Barquinero JF,
Garcia O. (2012). Automatic analysis of silver-stained comets by
CellProfiler software. <span style="font-style:italic">Mutation
Research</span> 748(1-2):60-4 / <a href=
"http://dx.doi.org/10.1016/j.mrgentox.2012.06.007">doi</a>. PMID:
22771502
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/MutationResearch_Gonzalez_2012.zip">
[Download]</a> (CellProfiler version <a href=
"previousReleases.html#v10997">2.0.10997</a>)
</li>
<li class="li_ul">
<a name="Hartwell_2012"></a>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. <span style="font-style:italic">Nat Chem
Biol</span> 9(12):840-8 / <a href=
"http://dx.doi.org/10.1038/nchembio.1367">doi</a>. PMID: 24161946
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Hartwell_2012.zip">[Download]</a>
(Note:CellProfiler version 7807 for Windows7 64bit included in
download) (CellProfiler Analyst version <a href=
"http://cellprofiler.org/releases/">11710</a>)
</li>
<li class="li_ul">
<a name="Chudnovsky_2012"></a>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.
<span style="font-style:italic">Cell Reports</span> 6(2):313-24 /
<a href="http://dx.doi.org/10.1016/j.celrep.2013.12.032">doi</a>.
PMID: 24440720
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/CellReports_Chudnovsky_2012.zip">
[Download]</a> (CellProfiler version <a href=
"previousReleases.html#v11710">2.0.11710</a>)
</li>
<li class="li_ul">
<a name="Nieland_2014"></a>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
<span style="font-style:italic">PLoS ONE</span> 9(3).e91744 /
<a href="http://dx.doi:10.1371/journal.pone.0091744">doi</a>. PMID:
24633176
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/PLoSOne_Nieland_2014.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#v11710">2.0.11710</a>)
</li>
<li class="li_ul">
<a name="Moldovan_2014"></a>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. <span style=
"font-style:italic">PLoS ONE</span> 9(4):e95124 / <a href=
"http://dx.doi.org/10.1371/journal.pone.0095124">doi</a>. PMID:
24759906
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/PLoSOne_Moldovan_2014.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#v11710">2.0.11710</a>)
</li>
<li class="li_ul">
<a name="SheikKhalil_2014"></a>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. <span style=
"font-style:italic">BMC Infect Dis</span> 14:472 / <a href=
"http://dx.doi.org/10.1186/1471-2334-14-472">doi</a>. PMID:
25176034
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/SheikKhalil_2014.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#v11710">2.0.11710</a>)
</li>
<li class="li_ul">
<a name="Singh_2014"></a>Singh S, Bray MA, Jones TR, Carpenter AE
(2014). Pipeline for illumination correction of images for
high-throughput microscopy. <span style="font-style:italic">Journal
of Microscopy</span> 256(3):231-6 / <a href=
"http://dx.doi.org/10.1111/jmi.12178">doi</a>. PMID: 25228240
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/JMicroscopy_Singh_2014.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#2.1.0">2.1.0</a>)
</li>
<li class="li_ul">
<a name="Metelo_2013"></a>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. <span style="font-style:italic">Journal of Clinical
Investigation</span> 25(5): 1987-97 / <a href=
"http://dx.doi.org/10.1172/JCI73665">doi</a>. PMID: 25866969
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Metelo_2013.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#v11710">2.0.11710</a>)
</li>
<li class="li_ul">
<a name="Du_2014"></a>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. <span style="font-style:italic">Oncotarget</span>
10;6(7):4704-16. PMID: 25609200
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Du_2014.zip">[Download]</a>
(CellProfiler version <a href=
"previousReleases.html#2.1.0">2.1.0</a>)
</li>
<li class="li_ul">
<a name="Leavesley_2015"></a>Leavesley SJ, Nakhmani A, Gao Y, Rich
TC (2015). Automated Image Analysis of FRET Signals for Subcellular
cAMP Quantification. <span style="font-style:italic">Methods in
Molecular Biology</span> 1294:59-70 / <a href=
"http://dx.doi.org/10.1007/978-1-4939-2537-7_5">doi</a>. PMID:
25783877
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Leavesley_2015.zip">[Download]</a>
(CellProfiler version <a href=
"http://cellprofiler.org/download.html">2.1.1</a>)
</li>
<li class="li_ul">
<a name="Logan_2015"></a>Logan DJ, Shan J, Bhatia SN, Carpenter AE
(2015). Quantifying co-cultured cell phenotypes in high-throughput
using pixel-based classification. <span style=
"font-style:italic">Methods</span> 96:6-11 / <a href=
"dx.doi.org/10.1016/j.ymeth.2015.12.002">doi</a>. PMID: 26687239.
PMCID: PMC4766037.
</li>
<li class="li_ul" style="list-style:none">
<a href="http://www.broadinstitute.org/bbbc/BBBC026/">[Broad
Bioimage Benchmark Collection entry]</a>
</li>
<li class="li_ul">
<a name="Jolly_2015"></a>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. <span style="font-style:italic">Cell Reports</span>
14(3):611-20 / <a href="dx.doi.org/10.1016/j.celrep.2015.12.051">doi</a>.
PMID: 26774481.
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Jolly_Lysomsome_Motility_2015.zip">
[Download]</a> (CellProfiler version <a href=
"previousReleases.html#v10997">2.0.10997</a>)
</li>
<li class="li_ul">
<a name="Ricci_2015"></a>Ricci F, Subramanian A, Wade M (2015).
Open access to high-content clonogenic analysis. <span style="font-style:italic">Journal
of Biomolecular Screening</span> 20(3): 391-401 / <a href="http://www.dx.doi.org/10.1177/1087057114557775">
doi</a>. PMID: 25381257.
</li>
<li class="li_ul" style="list-style:none">
<a href="http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Ricci_2015.zip">
[Download]</a> (CellProfiler version <a href="http://d1zymp9ayga15t.cloudfront.net/releases/2.1.1/CellProfiler_2.1.1_win64_r20140723174500.exe">
version 2.1.1 (revision 6c2d896; for Windows 64-bit).</a>)
</li>
<li class="li_ul">
<a name="Grenfell_2016"></a>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. <span style="font-style:italic">
Journal of Cell Biology</span> 213(1): 127-136 / <a href="http://www.dx.doi.org/10.1083/jcb.201509079">
doi</a>. PMID: 27044897.
</li>
<li class="li_ul" style="list-style:none">
<a href="http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Grenfell_2016.zip">
[Download]</a> (CellProfiler version <a href="http://cellprofiler.org/download.html">2.1.1</a>)
</li>
</ul>
<h2>
Pre-publication pipelines and data
</h2>
<ul>
<li class="li_ul">
<a name="Buys_2015"></a>Dordea AC, Bray MA, Allen K, Fei F, Gregory
M, Carpenter AE, Buys ES. An open-source computational tool to
automatically quantify immunolabeled retinal ganglion cells.
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Buys_2015.zip">[Download]</a>
(CellProfiler version <a href="download.html">2.1.1</a>)
</li>
<li class="li_ul">
<a name="Shan_2016"></a>Shan J, Logan DJ, Root DE, Carpenter AE, and Bhatia SN (Under review).
High-throughput platform for the identification of molecular factors involved in phenotypic
stabilization of primary human hepatocytes in vitro.
</li>
<li class="li_ul" style="list-style:none">
<a href=
"http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Shan_et_al_2016.zip">[Download]</a>
</li>
<li class-"li_ul">
<a name="Melo_Filho_2016"></a>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 <i>Schistosoma mansoni</i>. <span style="font-style:italic">
Journal of Chemical Information and Modeling</span> / <a href="http://dx.doi.org/10.1021/acs.jcim.6b00055">doi</a>.
</li>
<li class="li_ul" style="list-style:none">
<a href="http://d1zymp9ayga15t.cloudfront.net/PublishedPipelines/Melo_Filho_2016.zip">
[Download]</a>
</ul>