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cmeAnalysis specifications


Unique identifier OMICS_26739
Name cmeAnalysis
Alternative name clathrin-mediated endocytosis analysis
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, C++, MATLAB
Computer skills Advanced
Version 1.0.4
Stability Stable
Maintained Yes



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  • person_outline Sandra Schmid <>
  • person_outline Gaudenz Danuser <>

Additional information

Publication for clathrin-mediated endocytosis analysis

cmeAnalysis in publications

PMCID: 5927468
PMID: 29668686
DOI: 10.1371/journal.pbio.2005377

[…] live-cell dual-channel total internal reflection fluorescence microscopy (tirfm) and analyzed ccp dynamics and dyn recruitment using the master–slave (clca–dyn) approach introduced with the cmeanalysis software [,,]., as expected based on previous studies using either overexpressed [,,] or endogenously tagged dyn2 [,,], dyn2-mruby2end was observed, on average, to gradually accumulate […]

PMCID: 5683759
PMID: 28904210
DOI: 10.1091/mbc.E17-05-0282

[…] the triangulated mesh found within the cube. the distance map was generated by determining the average distance of the three closest endocytic clathrin spots for each pixel on the surface., we used cmeanalysis software for 2d single particle tracking (). we used a previously developed trace rejection scheme to filter traces that do not follow a characteristic clathrin coat intensity profile (). […]

PMCID: 5638584
PMID: 28814502
DOI: 10.1091/mbc.E16-12-0871

[…] using a zyla 4.2plus scmos camera (hamamatsu)., the detection, tracking, and analysis of clathrin objects, which allow detection of sclss and ccps, was done as previously described using the cmeanalysis software package (; ). briefly, diffraction-limited clathrin structures were detected using a gaussian-based model method to approximate the point-spread function (), and trajectories […]

PMCID: 5401915
PMID: 28484480
DOI: 10.3389/fpls.2017.00612

[…] for single channel analyses, images were acquired at 1 s intervals, for a duration of 5 min. the time-lapse movies were subjected to only the particle detection and tracking algorithms from the cmeanalysis package () using matlab 2013b (mathworks). using customized homemade matlab scripts (available upon request), the complete raw trajectories were screened so that only tracks […]

PMCID: 4970330
PMID: 27458134
DOI: 10.1083/jcb.201604128

[…] fluorescence imaging. p. selvin (university of illinois at urbana-champaign, urbana, il) provided the micromanipulator and injection system., 2d particle tracking was performed using the cmeanalysis software (obtained from unless stated otherwise. tracker software is a less sophisticated but faster tracking algorithm that lacks the advanced […]

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cmeAnalysis institution(s)
Department of Cell Biology, Harvard Medical School, Boston, MA, USA; Department of Cell Biology, The Scripps Research Institute, La Jolla, CA, USA
cmeAnalysis funding source(s)
Supported by National Institutes of Health grants R01 GM73165 and MH61345 and fellowships from the Swiss National Science Foundation and the American Heart Association.

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