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CellGeo specifications

Information


Unique identifier OMICS_28449
Name CellGeo
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Version 2
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Timothy Elston
  • person_outline Mark Peifer

Publication for CellGeo

CellGeo citations

 (7)
library_books

FiloQuant reveals increased filopodia density during breast cancer progression

2017
PMCID: 5626550
PMID: 28765364
DOI: 10.1083/jcb.201704045

[…] availability of dedicated tools, and therefore, filopodia features are often described using manual analyses. To our knowledge, currently available tools to quantify filopodia include FiloDetect (), CellGeo (), and ADAPT (), each with unique strengths and shortcomings (). Limitations of these tools include requirement for proprietary software (i.e., MATLAB and MATLAB Image Processing Toolbox), la […]

library_books

Filopodyan: An open source pipeline for the analysis of filopodia

2017
PMCID: 5626553
PMID: 28760769
DOI: 10.1083/jcb.201705113

[…] fluorescence intensity at membrane-proximal sites during formation and at the tip. Segmentation uses a membrane marker, providing an alternative to the actin signal used by FiloQuant ( Preprint) and CellGeo (). Filopodyan has the flexibility to allow high-throughput (batch) processing or a highly user-interactive mode that enables generation of manually curated datasets. Tip tracking and fragment […]

library_books

L type calcium channels regulate filopodia stability and cancer cell invasion downstream of integrin signalling

2016
Nat Commun
PMCID: 5146291
PMID: 27910855
DOI: 10.1038/ncomms13297

[…] of the compound of interest (or DMSO) before being imaged live, every 10 s at 37 °C on a TIRF microscope using a 100 × objective. Videos were then automatically analysed using the Matlab application CellGeo.To analyse the dynamics of focal adhesions, cells were transfected with mEmerald-Paxillin and plated for at least 6 h on FN in the presence of amlodipine besylate (or DMSO) before being imaged […]

library_books

Formin generated actomyosin arcs propel T cell receptor microcluster movement at the immune synapse

2016
PMCID: 5100289
PMID: 27799367
DOI: 10.1083/jcb.201603080

[…] area within the identified regions was measured using ImageJ (National Institutes of Health). To compare the actin spike morphology in (bottom panels), the Filotracker script from MATLAB application CellGeo was used on max projections of phalloidin-stained 3D-SIM images as previously described (). To qualitatively assess actin arc morphology, maximum projections of 3D-SIM images of phalloidin-sta […]

library_books

A MAPK Driven Feedback Loop Suppresses Rac Activity to Promote RhoA Driven Cancer Cell Invasion

2016
PLoS Comput Biol
PMCID: 4854413
PMID: 27138333
DOI: 10.1371/journal.pcbi.1004909

[…] e cell (i.e. regions of high actin signal) were assigned a value >1 and regions outside the cell (background) were assigned a value of 0. Thresholded images were analysed using the Matlab application CellGeo [] with a critical length = 20.0, critical width = 12.0 to automatically calculate number of filopodia per leading edge and average length of filopodia. […]

library_books

α5β1 integrin recycling promotes Arp2/3 independent cancer cell invasion via the formin FHOD3

2015
PMCID: 4576860
PMID: 26370503
DOI: 10.1083/jcb.201502040

[…] z plane, this patterned illumination was shifted through five phases at each of five rotational angles. Raw data were processed using ZEN software and analyzed using ImageJ and the Matlab application CellGeo () to determine filopodia number and length, respectively.Quantification of actin protrusions in 3D CDM was performed using maximum z projections of cells imaged for 30–60 min. Using custom so […]

Citations

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CellGeo institution(s)
Department of Pharmacology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA; Department of Cell Biology, Emory University, Atlanta, GA, USA
CellGeo funding source(s)
Supported by grants from National Institutes of Health R01 GM47857, R01 GM057464, National Institutes of Health grants GM079271, GM68820, and NCI 200079604, a grant from the Army Research Office, and National Institutes of Health F31 fellowship 5F31NS062487.

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