SIMCEP specifications

Information


Unique identifier OMICS_26049
Name SIMCEP
Software type Framework/Library
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux
Programming languages MATLAB
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Source code URL http://www.cs.tut.fi/sgn/csb/simcep/simcep.zip
Maintained Yes

Versioning


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Documentation


Maintainer


  • person_outline Antti Lehmussola <>

Publication for SIMCEP

SIMCEP in publications

 (9)
PMCID: 5357336
PMID: 28315633
DOI: 10.1186/s12859-017-1591-2

[…] also, ruusuvuori et al. [] describe the evaluation of image processing methods for micrographs using a synthetic benchmark data set which can be downloaded from: http://www.cs.tut.fi/sgn/csb/simcep/benchmark. , in summary, there has been quite some work in the field of fluorescent micrograph simulation, ranging from image rendering over geometric and biological modeling of cell […]

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

[…] important proteins localised in certain cell compartments in anatomically intact tissue as opposed to freely moving cells in culture., other frameworks for generating synthetic if data include the simcep simulator, which can simulate large 2d cell populations with realistically looking cytoplasm, nuclei and cell organelle []. svoboda et al. [] generated a model to fully simulate 3d image data […]

PMCID: 5001623
PMID: 27561654
DOI: 10.1038/srep32412

[…] the proposed method is suited to most conventional cell nuclei types, but we do not recommend its use when the major/minor axis ratio exceeds 1.75., to simulate real cell nuclei we used a framework, simcep, designed to generate and to evaluate algorithms for fluorescent microscopy images. 50 images were generated by the framework, each containing 30 nuclei with a 50% maximal allowed overlap. […]

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

[…] of shapes, such as curved spheres, discs, bananas, satellite discs, and dumbbells. more realistic simulations have also been presented. for example, lehmussola et al. [] designed a simulator called simcep, which can simulate large homogeneous 2d cell populations with realistically looking cytoplasm, nuclei and cell organelle. svoboda et al. [] generated a model to simulate fully 3d image data […]

PMCID: 4459105
PMID: 26054051
DOI: 10.1038/srep10849

[…] expectation estimates (which we will refer to as map-d in figures), we first simulated a fluorescence microscopy data set with fluorescence-stained cell populations using a modified version of simcep, a computational framework for simulating fluorescence microscopy images of fluorescence-stained cell populations (see and methods). for comparison purposes, three other bayesian-based […]


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SIMCEP institution(s)
Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
SIMCEP funding source(s)
Supported in part by the Academy of Finland (application number 213462, Finnish Programme for Centres of Excellence in Research 2006-2011) and in part by Tampere Graduate School, Information Science and Engineering (TISE).

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