This is a MATLAB script to take the output of a simulation from a csv file and create XML readable by the Microscope Simulator software.  

Instructions:

1) Clone the repository into a directory:
	$ mkdir newDir
	$ cd newDir
	$ git clone git://github.com/chrismullins/SpindleSimScript.git
	$ cd SpindleSimScript	

2) Edit the following value(s) to correspond to your machine:
	in initialize_cylinder.m, change the value "fn" to wherever you want SimDir, the directory containing all xml timesteps
	
3) In the MATLAB console (once you have navigated to the SpindleSimScript directory)
	>> spindleSimScript
	Then, choose the settings from the GUI based on your needs for visibility and fluorescence.
	Click "Generate Simulation".  A directory should be created (if it wasn't already there) named SimDir.  Feel free to change the name of this directory in spindleSimDriver.m
	When prompted for the simulation file, navigate to the SpindleSimScript/Examples directory and choose sample_output.csv
	
4)  Once MATLAB has finished generating all the xml, open a file in the Microscope Simulator by File->Open Simulation.


If you have any questions, bugs, or feature requests, please email Christopher Mullins at christopher.r.mullins@gmail.com

Many thanks to Rei Haggerty and Andrew Stephens of the Bloom biology lab at UNC Chapel Hill for the mathematical model of the spindle as well as data acquisition, and Cory Quammen, creator of the Microscope Simulator ( http://cismm.cs.unc.edu/downloads/ ), Dr. Russell Taylor, principal investigator of CISMM (cismm.org ) at UNC Chapel Hill.