CellProfiler protocols

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CellProfiler specifications


Unique identifier OMICS_06568
Name CellProfiler
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Computer skills Medium
Stability Stable
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/CellProfiler


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  • person_outline David Sabatini <>

Publication for CellProfiler

CellProfiler in pipelines

PMCID: 5844339
PMID: 29487145
DOI: 10.1534/genetics.117.300077

[…] for quality, prior to further feature extraction, and corrected, if needed (). to extract image features describing the cells and connect them to cellular phenotypes, software packages such as cellprofiler or ebimage can be used (; ; ). once features are extracted, they serve as a vector of measurement, which characterizes the phenotype of each cell. multivariate phenotypes acquired […]

PMCID: 5223612
PMID: 27940887
DOI: 10.1083/jcb.201610026

[…] packaged these sets of feature extractors with modular segmentation pipelines into software platforms that are publicly available and widely used (). specific examples of popular platforms include cellprofiler (), cellcognition (), and phenoripper (). outputs from these platforms typically contain hundreds to thousands of different features for each object and image. although these methods […]

PMCID: 5380971
PMID: 28361956
DOI: 10.1038/ncomms14858

[…] (scientific volume imaging) and deconvolved image stacks were transformed into maximum projection images using custom matlab scripts. cell segmentation and ld detection was performed with cellprofiler 1.0.5122 (cellprofiler.org) in a hierarchical manner. first, cell nuclei with a typical diameter between 100 and 250 pixels were detected in dapi images based on the otsu adaptive […]

PMCID: 5438137
PMID: 28542402
DOI: 10.1371/journal.pone.0177921

[…] reconstruction into an image montage. the image stack was processed using standard metamorph filters and segmented into cell nuclei and cytoplasmic features using custom routines created using cellprofiler (broad institute, cambridge, ma, usa). the segmented images from cellprofiler were reconstructed into image montages of the cardiac lobe using fcs express 5 software (de novo software, […]

PMCID: 5645716
PMID: 29062917
DOI: 10.21956/wellcomeopenres.13502.r26508

[…] above and below cells in the image-stack, reducing image size to minimize subsequent processing and computing time., correction for uneven illumination. an illumination function was calculated using cellprofiler v2.2.0 , with a pipeline adapted from roukos et al., 2015 ., images were then analysed with an adapted version of fish-quant, v3 , , run on matlab. the adaptation allowed step number 4, […]

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CellProfiler in publications

PMCID: 5959879
PMID: 29777108
DOI: 10.1038/s41467-018-04355-w

[…] using three representative fields at 200 × magnification for each tumor (5 tumors per group). all ki-67 positive cells per high-powered field were enumerated. ki-67 expression was analyzed using cellprofiler 2.0 software to quantify the number of positively staining cancer cells per high-powered field (200 × magnification). tissue microarray samples for lung squamous cell carcinoma cancers […]

PMCID: 5958057
PMID: 29773792
DOI: 10.1038/s41467-018-04379-2

[…] on a leica tcs sp8 confocal laser scanning microscope (leica microsystems) maintained by the center for microscopy and image analysis, university of zurich. images were analysed using a custom-made cellprofiler version 2.1.1 pipeline and knime version 2.12.2., a549-mxb cells pretreated with sirna were spinoculated with hsv-1 strain macintyre (moi = 500, virus stock produced in 2% fbs medium […]

PMCID: 5945652
PMID: 29749381
DOI: 10.1038/s41598-018-25921-8

[…] isolated at the end of week 3 (after two passages)., proliferation of nscs was measured by disaggregating cells at the end of first or second passage and counting. colony size was quantified using cellprofiler. production of neurons from nscs was measured by plating cells into poly-l-lysine-coated six-well plates (costar) in serum-free culture medium for neurosphere growth but lacking egf, […]

PMCID: 5954971
PMID: 29706521
DOI: 10.1016/j.cub.2018.03.023

[…] control wells were treated with dmso only. live cell imaging was performed using in cell analyzer 2000 (ge healthcare life sciences) 1 hr after addition of the inhibitor. images were analyzed with cellprofiler 2.2.0. and cellprofiler analyst []. in accordance with the results obtained from the cenp-e inhibitor titration, im fibroblasts were treated with 20 nm gsk923295 1 hr before fixation […]

PMCID: 5931751
PMID: 29732401
DOI: 10.1126/sciadv.aao1478

[…] at indicated concentrations. plates were incubated at 37°c for the indicated periods of time. plates were imaged at defined time points following plating, and images were analyzed using a custom cellprofiler pipeline to count and measure the size of colonies., m. tuberculosis h37rv was grown to mid-log phase in supplemented 7h9. the culture was gravity-filtered through a 5-μm syringe filter […]

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CellProfiler institution(s)
Whitehead Institute for Biomedical Research, Cambridge, MA, USA

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