CellProfiler: Difference between revisions
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'''CellProfiler''' is free, [[open-source]] cell [[image analysis]] software<ref>{{cite journal |author=Carpenter AE, Jones TR, Lamprecht MR, ''et al'' |title=CellProfiler: image analysis software for identifying and quantifying cell phenotypes |journal=Genome Biol. |volume=7 |issue=10 |pages=R100 |year=2006 |pmid=17076895 |pmc=1794559 |doi=10.1186/gb-2006-7-10-r100 |url=http://genomebiology.com/1465-6906/7/R100}}</ref><ref>{{cite journal |author=Lamprecht MR, Sabatini DM, Carpenter AE |title=CellProfiler: free, versatile software for automated biological image analysis |journal=BioTechniques |volume=42 |issue=1 |pages=71–5 |year=2007 |month=January |pmid=17269487 |doi= |url=}}</ref> |
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. Its strength is in processing large numbers of images, even hundreds of thousands. In theory it can be used on images of any sort. In particular, it has been geared for scientists analyzing images of cells, a type of [[Microscope image processing]]. |
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==Features== |
==Features== |
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==Community== |
==Community== |
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Because CellProfiler is a free, [[open-source]] project, anyone can develop their own image processing [[algorithm]]s as a new module for CellProfiler and contribute it to the project. The CellProfiler Project website contains a forum for discussion where new users can have their questions answered, usually by the creators of the project. |
Because CellProfiler is a free, [[open-source]] project, anyone can develop their own image processing [[algorithm]]s as a new module for CellProfiler and contribute it to the project. The CellProfiler Project website contains a forum for discussion where new users can have their questions answered, usually by the creators of the project. |
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==References== |
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<references/> |
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==External links== |
==External links== |
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Revision as of 19:09, 9 September 2008
CellProfiler is free, open-source cell image analysis software[1][2] . Its strength is in processing large numbers of images, even hundreds of thousands. In theory it can be used on images of any sort. In particular, it has been geared for scientists analyzing images of cells, a type of Microscope image processing.
Features
CellProfiler was designed to bridge the gap between sophisticated computer vision research and the average biologist, so its use does not require advanced computer skills. Users can use standard digital image processing functions on their images (e.g. crop, rotate, rescale intensity, etc.), but the real strength of the software is in its automatic identification of objects in images (usually cells). Once identified, the software measures on the order of 100 different features about the cells, including various measures of area, shape, intensity, texture, location, and count.
CellProfiler is modular, so users can put together a "pipeline" of modules to measure the cells in their images in whatever way they choose. These pipeline files are small and shareable, so colleagues can easily collaborate, and scientists can keep a pipeline as a permanent record of how their images were processed.
History
CellProfiler was released in December 2005 by scientists from the Whitehead Institute for Biomedical Research and Massachusetts Institute of Technology. It is currently developed and maintained by the Imaging Platform[1] of the Broad Institute.
Community
Because CellProfiler is a free, open-source project, anyone can develop their own image processing algorithms as a new module for CellProfiler and contribute it to the project. The CellProfiler Project website contains a forum for discussion where new users can have their questions answered, usually by the creators of the project.
References
- ^ Carpenter AE, Jones TR, Lamprecht MR; et al. (2006). "CellProfiler: image analysis software for identifying and quantifying cell phenotypes". Genome Biol. 7 (10): R100. doi:10.1186/gb-2006-7-10-r100. PMC 1794559. PMID 17076895.
{{cite journal}}: Explicit use of et al. in:|author=(help)CS1 maint: multiple names: authors list (link) CS1 maint: unflagged free DOI (link) - ^ Lamprecht MR, Sabatini DM, Carpenter AE (2007). "CellProfiler: free, versatile software for automated biological image analysis". BioTechniques. 42 (1): 71–5. PMID 17269487.
{{cite journal}}: Unknown parameter|month=ignored (help)CS1 maint: multiple names: authors list (link)
