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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


No version available


  • person_outline David Sabatini

Publication for CellProfiler

CellProfiler citations


Factor XIIIA—expressing inflammatory monocytes promote lung squamous cancer through fibrin cross linking

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

[…] ined 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 (p […]


MxB is an interferon induced restriction factor of human herpesviruses

Nat Commun
PMCID: 5958057
PMID: 29773792
DOI: 10.1038/s41467-018-04379-2
call_split See protocol

[…] d 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. […]


The senescence associated secretory phenotype is potentiated by feedforward regulatory mechanisms involving Zscan4 and TAK1

Nat Commun
PMCID: 5928226
PMID: 29712904
DOI: 10.1038/s41467-018-04010-4

[…] foci by following a 4-category counting strategy as formerly reported. Random fields were chosen to show DDR foci and SA-β-gal positivity, while BrdU incorporation and DDR foci were quantified using CellProfiler (http://www.cellprofiler.org) with a minimum of 200 cells counted per sample for above cell-based assays. For clonogenic assays, cells were seeded at 1 × 103 cells/dish in 10 mm dishes fo […]


Concepts in Light Microscopy of Viruses

PMCID: 5923496
PMID: 29670029
DOI: 10.3390/v10040202

[…] LAB/ImageJ compatibility, machine learning or expanded workflow control. Icy (http://icy.bioimageanalysis.org/) combines both image and data analysis. While slightly less intuitive to use compared to CellProfiler/KNIME, Icy provides great segmentation quality even for noisy images and a similar wide array of functionality and compatibility plugins [].Apart from the general solutions for image and […]


MeioSeed: a CellProfiler based program to count fluorescent seeds for crossover frequency analysis in Arabidopsis thaliana

Plant Methods
PMCID: 5905130
PMID: 29692862
DOI: 10.1186/s13007-018-0298-3

[…] t species or for counting any other objects, but the performance of MeioSeed will drop along with increasing differences in shape and size. It might be very worthwhile to consider the combined use of CellProfiler and Ilastik for seed counting purposes in crop species, as we have shown in the present study for rapeseeds and barley grains (Additional files and ). Seed count is considered to be an i […]


The Heteroaryldihydropyrimidine Bay 38 7690 Induces Hepatitis B Virus Core Protein Aggregates Associated with Promyelocytic Leukemia Nuclear Bodies in Infected Cells

PMCID: 5907649
PMID: 29669885
DOI: 10.1128/mSphereDirect.00131-18

[…] ultitile, and MultiTime series 4.0.31 beta software, as previously described (); imaging was carried out using a 40× objective, capturing 9 images per well per experiment. Images were processed using CellProfiler (). […]


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

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