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SimuCell specifications

Information


Unique identifier OMICS_16824
Name SimuCell
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline Lani Wu <>

Publication for SimuCell

SimuCell in publications

 (3)
PMCID: 5357336
PMID: 28315633
DOI: 10.1186/s12859-017-1591-2

[…] between these three lines. lehmussola et al. describe a cell shape model based on deformed regular polygons with cell texture generate with perlin noise []. the method is extended in the framework simucell []. in [] cells and nuclei are modeled using basic geometric shapes such as circles and ellipses and the borders are then varied. also some variations in illumination and noise […]

PMCID: 5075203
PMID: 27770786
DOI: 10.1186/s12859-016-1243-y

[…] from voronoi diagrams and does not reflect the variety of cell phenotypes found in real tissue. heterogeneous cell populations expressing different protein markers can be simulated using the simucell toolbox []. the first method for simulating bright-field microscopy was proposed for synthesising cervical smears []. however, tissue microenvironment was not taken into account […]

PMCID: 4919876
PMID: 27342072
DOI: 10.1186/s12859-016-1126-2

[…] from the voronoi diagrams and does not reflect the variety of cell phenotypes found in real tissue. heterogeneous cell populations expressing different protein markers can be simulated using the simucell toolbox []. on the other hand, zhao et al. [] presented a machine learning method to generate realistic cells with labelled nuclei, membranes and a protein expressed in a cell organelle. […]


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SimuCell institution(s)
Green Center for Systems Biology and Department of Pharmacology, University of Texas Southwestern Medical Center, Dallas, TX, USA; University of Virginia School of Medicine, Charlottesville, VA, USA
SimuCell funding source(s)
This research was supported by the National Institute of Health grants R01s (GM085442 and GM081549), the Welch Foundation (I-1619 and I-1644), and UTSW QP-SURF.

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