citations.html

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    <div style="float:right; width: 40%; margin-left:10px;">
      <br />

      <h1>
        CellProfiler's impact
      </h1>

      <h2>
      </h2>

      <ul>
        <li>Impact on human health [<a href="impact.html">details here</a>]
        </li>

        <li>Citations (3,340 as of May 9, 2016) [<a href=
        "https://scholar.google.com/scholar?q=%22www+cellprofiler+org%22+OR+CellProfiler+OR+%22cellprofiler%22&hl=en&as_sdt=0,22">list</a>]
        <br />
          <img alt="CellProfiler citation publication" height="350" src=
          "http://d1zymp9ayga15t.cloudfront.net/images/CP_Cite_2016_May.png" width="330" /><br />
        </li>
      </ul>
    </div>

    <div style="float:left; width: 58%; margin-right:10px;">
      <center>
        <h1>
          How to cite CellProfiler in publications<span style=
          "font-size:75%"><br />
          (the project's survival depends on it!)</span>
        </h1>
      </center>

      <ul>
        <li class="li_ul">
          <span style="font-size:75%"><span style=
          "font-weight:bold">CellProfiler for cells:</span></span>
        </li>

        <li class="li_ul" style="list-style:none">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 [<a href=
        "http://genomebiology.com/2006/7/10/R100" title=
        "Genome biology image analysis paper">link to paper at Genome
        Biology</a>]
        </li>

        <li style="list-style: none; display: inline">
          <p style="font-style:italic">
            or
          </p>
        </li>

        <li class="li_ul" style="list-style:none">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/<a href=
        "http://bioinformatics.oxfordjournals.org/content/27/8/1179.full.pdf?keytype=ref&ijkey=ujLFUXwONdtX58c">doi</a>.
        PMID: 21349861 PMCID: PMC3072555
        </li>

        <li class="li_ul">
          <span style="font-weight:bold">CellProfiler for the Worm
          Toolbox:</span>
        </li>

        <li class="li_ul" style="list-style:none">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 [<a href=
        "http://d1zymp9ayga15t.cloudfront.net/content/papers/59-Wahlby_NatMeth_2012.pdf">PDF</a>]
        </li>

        <li class="li_ul">
          <span style="font-weight:bold">CellProfiler for other biological
          images:</span>
        </li>

        <li class="li_ul" style="list-style:none">Lamprecht MR, Sabatini DM,
        Carpenter AE (2007) CellProfiler: free, versatile software for
        automated biological image analysis. Biotechniques 42(1):71-75. PMID:
        17269487 [<a href=
        "http://d1zymp9ayga15t.cloudfront.net/content/papers/26-Lamprecht_Biotech_2007.pdf">PDF</a>]
        </li>

        <li class="li_ul">
          <span style="font-weight:bold">CellProfiler Analyst software in
          general:</span>
        </li>

        <li class="li_ul" style="list-style:none">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 [<a href=
        "http://www.biomedcentral.com/1471-2105/9/482">link to paper at BioMed
        Central</a>].
        </li>

        <li class="li_ul">
          <span style="font-weight:bold">CellProfiler Analyst for scoring
          phenotypes by machine learning</span>:
        </li>

        <li class="li_ul" style="list-style:none">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 [<a href="http://www.pnas.org/content/106/6/1826.full">link
        to paper at PNAS</a>]
          <p>
          </p>
        </li>

        <li>
          <p style="font-style:italic">
            It's also nice if you cite the website (<a href=
            "http://www.cellprofiler.org" title=
            "CellProfiler free image analysis software">www.cellprofiler.org</a>)
            and <a href="mailto:imagingadmin@broadinstitute.org">email us</a>
            so that we are aware of your publication, but this is much less
            critical than citing the publications.
          </p>
        </li>

        <li>
          <p style="font-style:italic">
            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 <a href="published_pipelines.html">here</a>.
            Please <a href="mailto:imagingadmin@broadinstitute.org">contact
            us</a> for more information.
          </p>
        </li>
      </ul>
    </div>