https://github.com/cellprofiler/cellprofiler.github.com-backup

OLD cp website repo. Current repo is here: https://github.com/CellProfiler/cellprofiler.github.com. We are currently in the process of transferring any remaining and relevant issues to the current Github repo so that this repo can then be deleted.

https://github.com/cellprofiler/cellprofiler.github.com-backup

Science Score: 28.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • CITATION.cff file
    Found CITATION.cff file
  • codemeta.json file
  • .zenodo.json file
  • DOI references
  • Academic publication links
  • Committers with academic emails
    5 of 10 committers (50.0%) from academic institutions
  • Institutional organization owner
  • JOSS paper metadata
  • Scientific vocabulary similarity
    Low similarity (3.2%) to scientific vocabulary

Keywords from Contributors

cellprofiler cellprofiler-analyst image-analysis
Last synced: 11 months ago · JSON representation ·

Repository

OLD cp website repo. Current repo is here: https://github.com/CellProfiler/cellprofiler.github.com. We are currently in the process of transferring any remaining and relevant issues to the current Github repo so that this repo can then be deleted.

Basic Info
  • Host: GitHub
  • Owner: CellProfiler
  • License: other
  • Language: HTML
  • Default Branch: master
  • Homepage:
  • Size: 147 MB
Statistics
  • Stars: 3
  • Watchers: 15
  • Forks: 2
  • Open Issues: 3
  • Releases: 0
Archived
Created over 10 years ago · Last pushed over 9 years ago
Metadata Files
Readme License Citation

README.md

cellprofiler.github.io

THIS REPO IS NO LONGER IN USE AND IS CURRENTLY IN THE PROCESS OF BEING DELETED. Existing issues will be filed in the current repo (https://github.com/CellProfiler/cellprofiler.github.com) if still relevant. Please file any website-related issues in the current repo.

Owner

  • Name: CellProfiler
  • Login: CellProfiler
  • Kind: organization
  • Location: Cambridge, MA

Software for quantitative analysis of biological images

Citation (citations.html)

---
layout: default
redirect_from: "/citations.shtml"
---

    <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>

GitHub Events

Total
Last Year

Committers

Last synced: over 2 years ago

All Time
  • Total Commits: 355
  • Total Committers: 10
  • Avg Commits per committer: 35.5
  • Development Distribution Score (DDS): 0.482
Past Year
  • Commits: 0
  • Committers: 0
  • Avg Commits per committer: 0.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
alisonkozol a****l@b****g 184
David Logan d****n@b****g 69
Allen Goodman a****n@i****m 58
Mario Emmenlauer m****o@e****e 18
David Dao c****o@g****m 16
Shantanu Singh s****h@b****g 5
Holger Hennig h****n@g****m 2
Lee Kamentsky l****k@b****g 1
David Logan D****n@p****m 1
Jeanelle a****n@b****g 1
Committer Domains (Top 20 + Academic)

Dependencies

CPA/sources/1_preliminary_requirements.txt pypi
  • AnimagetableforanexperimentinvolvingcellsimagedforGFPandHoechstwouldhavetwochannelsandwouldlooksomethinglikethis *
  • AnobjecttableforanexperimentinvolvingcellsimagedforGFPandHoechstwouldhavetwochannelsandwouldlooksomethinglikethis *
  • CPAcurrentlyrequiresimagefilestobemonochromatic *
  • CPAcurrentlysupportsthefollowingimagefiletypes *
  • CPArequiresaccesstothefollowingdatasources *
  • I.AExampleimagetable *
  • I.BExampleobjecttable *
  • I.Preliminarydatarequirements *
  • TheimagetablerequiresonecolumnforauniqueimageIDandapairofcolumnsforeachchannelrepresentedintheimages *
  • Theobjecttablerequiresfourcolumns *
  • ThesecanbestoredeitherlocallyorremotelyandaccessedviaHTTP.Thedirectorystructuredoesnotmatteraslongasthefilepathsstoredintheimagetablepointtothecorrectimages. *
  • ThesemayresideinaMySQLorSQLitedatabaseorinasetofcomma-separatedvalue *
  • ThroughoutCPA ,thetermimageismeanttoincludeallimagedataassociatedwithananalyzedfield
Gemfile rubygems
  • jekyll ~> 3.1, >= 3.1.1
  • jekyll-redirect-from ~> 0.9.1
Gemfile.lock rubygems
  • colorator 0.1
  • ffi 1.9.10
  • jekyll 3.1.2
  • jekyll-redirect-from 0.9.1
  • jekyll-sass-converter 1.4.0
  • jekyll-watch 1.3.1
  • kramdown 1.10.0
  • liquid 3.0.6
  • listen 3.0.6
  • mercenary 0.3.6
  • rb-fsevent 0.9.7
  • rb-inotify 0.9.7
  • rouge 1.10.1
  • safe_yaml 1.0.4
  • sass 3.4.22