icsreadme.txt

cell migration resource imaging icsmatlab

ICS Analysis v1.0
February 26, 2006
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Copyright
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Copyright 2003-2006, Wiseman Research Group, McGill University.


System Requirements
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* MATLAB 7, with Image Processing and Optimization Toolboxes.  Earlier versions may work as well, but have not been tested.

* There are no hardware requirements, per se.  Processor speed will play a large role in the analysis time, and the amount of system RAM will dictate the maximum size of the image series which can be analyzed.  A 1.5 GHz machine with 512 MB RAM should be sufficient for most data sets.

* These .m files should be platform independent, but have only been tested on a Windows XP machine.


Installation Instructions
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Just unzip the .m files, and ensure they're in your MATLAB path. (From in MATLAB: File --> Set Path... --> Add with Subfolders...).


Tutorial
--------

A brief tutorial is included in /ICSMATLAB/tutorial/ICSTutorial.html.


File Formats
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Only 8-bit RAW and 16-bit Fluoview TIFF files can be imported in this release.  Support for additional formats may be added in a future release.


Disclaimer
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This software is provided as is, without any warranty whatsoever.


Contact Info
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Please send bug reports and suggestions to [e-mail].


File List
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%% Files for importing data %%

rd_img16.m % reads Fluoview tiff image series from Olympus microscopes
FluoInfo.m % gets acquisition parameters from a Fluoview file
reverse.m % needed by FluoInfo
serimcrop.m % interactively crops an image series
rd_imgser.m % reads 8-bit .raw files
wnCorr.m % interactively removes mean value of background counts from an image series

%% Files for ICS %%

corrfunc.m % calculates 2D spatial autocorrelation function (SACF)
gaussfit.m % fits 2D SACF with 2D Gaussian
gauss2d.m % used by gaussfit.m
gauss2dwxy.m % used by gaussfit.m
autocrop.m % used by gaussfit.m
initialguess.m % used by gaussfit.m
plotgaussfit.m % plots the 2D SACF superimposed with the fitted gaussian

%% Files for TICS %%

ticsNOAVG.m % calculates the temporal autocorrelation function (TACF)
difffit.m % fits TACF to 2D diffusion model
diffusion.m % used by difffit.m
flowfit.m % fits TACF to 2D flow model
flow.m % used by flowfit.m
diffflowfit.m % fits TACF to 2D diffusion/flow model
diffusionflow.m % used by diffflowfit.m
difffit3d.m % fits TACF to 3D diffusion model
diffusion3d.m % used by difffit3d.m

%% Files for STICS %%

tics.m % calculates full space time autocorrelation function (STACF)
immfilter.m % filters immobile population from image series
velocity.m % calculates velocity from STACF
gaussfit.m % used by velocity.m
gauss2d.m % used by gaussfit.m
initialguess.m % used by gaussfit.m

%% Files for simulation program %%

simul8tr.m % main simulation program
simul8trMovement.m % used by simul8tr.m
addBackgroundNoise.m % used by simul8tr.m
addCountingNoise.m % used by simul8tr.m
convolveGaussian.m % used by simul8tr.m
createImage.m % used by simul8tr.m
convolveAiry.m % used by simul8tr.m
airy2.m % used by convolveAiry.m
formatSeriesLikeMicroscope.m % used by simul8tr.m
QDBlink.m % used by simul8tr.m


Version History
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v1.0
February 26, 2006

* Spatial ICS
* Temporal ICS
* Spatio-temporal ICS