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
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
Statistics
- Stars: 3
- Watchers: 15
- Forks: 2
- Open Issues: 3
- Releases: 0
Metadata Files
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
- Repositories: 30
- Profile: https://github.com/CellProfiler
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
Top Committers
| Name | 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
- AnimagetableforanexperimentinvolvingcellsimagedforGFPandHoechstwouldhavetwochannelsandwouldlooksomethinglikethis *
- AnobjecttableforanexperimentinvolvingcellsimagedforGFPandHoechstwouldhavetwochannelsandwouldlooksomethinglikethis *
- CPAcurrentlyrequiresimagefilestobemonochromatic *
- CPAcurrentlysupportsthefollowingimagefiletypes *
- CPArequiresaccesstothefollowingdatasources *
- I.AExampleimagetable *
- I.BExampleobjecttable *
- I.Preliminarydatarequirements *
- TheimagetablerequiresonecolumnforauniqueimageIDandapairofcolumnsforeachchannelrepresentedintheimages *
- Theobjecttablerequiresfourcolumns *
- ThesecanbestoredeitherlocallyorremotelyandaccessedviaHTTP.Thedirectorystructuredoesnotmatteraslongasthefilepathsstoredintheimagetablepointtothecorrectimages. *
- ThesemayresideinaMySQLorSQLitedatabaseorinasetofcomma-separatedvalue *
- ThroughoutCPA ,thetermimageismeanttoincludeallimagedataassociatedwithananalyzedfield
- jekyll ~> 3.1, >= 3.1.1
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