Short user guide for SIMCEP simulation tool
Contents
1. Short user guide for SIMCEP simulation tool 1 Introduction SIMCEP is a simulation tool providing the functionality presented in the manuscript Computational framework for simulating fluorescence microscopy images with cell populations The tool is implemented with MATLAB and all source codes are freely available under terms of GNU General Public License The motivation behind the tool is to allow a hands on experience on the simulation methodology presented in the manuscript Moreover it provides a modular tool for future research SIMCEP is available at http www cs tut fi sgn csb simcep as a zip archive The tool requires MATLAB environment in order to work The SIM CEP is developed with MATLAB version 7 1 and downwards compatibility is not guaranteed 2 Getting started After downloading and extracting the archive run file make_simcep on MATLAB command line It compiles necessary C function into mex file us ing your operating system specific compiler Thereafter SIMCEP is ready for use You can now run the simulation with command Limage binary features simcep The command will simulate an example image with default parameters The output variables are the simulated RGB image image binary version of the simulated image binary and a struct containing selected information from the simulated objects features After simulation has finished you can visualize the simulated image with imshow image 3 Structure of2. the tool The SIMCEP tool consists of several functions implements as separate files The main function for simulation is available in the file simcep m De scription of each function is available by typing help functionName in the MATLAB command line where functionName is the name of the function The parameters controlling the simulation functions are modified using the file simcep_options m More detailed descriptions of the parameters are also available in the file The main function sets the parameters using the file and therefore all new parameters can be added to the file SIMCEP is implemented using object oriented programming The main class of the tool is cellobj from which classes nuclei cytoplasm and sub cell are inherited from The use of classes allows a modular way to define properties for different simulation objects Contact Antti Lehmussola Institute of Signal Processing Tampere University of Technology PO Box 553 33101 Tampere FINLAND lehmusso cs tut fi
Download Pdf Manuals
Related Search