Open EK_FRAPbatch.m and edit the pixel size if necessary. Editing the
initial guess for the recovery time scale may also be needed,
depending on the bleached area and lipid diffusivity.

Run the program
EK_FRAPbatch.m

by typing

>> [tall, fall, tauvalues, Dvalues]=EK_FRAPbatch

at the command prompt in MatLab.

When prompted for the list of filenames to be analyzed, choose

FRAPlist.txt (or any other text file listing the names of the movie
files that will be analyzed).

You'll then be prompted to choose any file to be analyzed. Go to 

\myData\  (or any other directory where you keep the movies)

and choose any one of the. This allows the program to register the
pathname of the folder containing the image files. The image files in
that folder are opened following the list of files in FRAPlist.txt.
Obviously all the files to be analyzed must be in the same folder.

The other programs are subroutines called by the main program. 

This Matlab package requires the bio-formats tools for Matlab
bfmatlab.zip

available at 

www.openmicroscopy.org/site/support/bio-formats/users/matlab/

Information on Bio-Formats is available at

www.openmicroscopy.org/site/support/bio-formats


The program should work with any file in OME-TIFF format.
Importantly, the program extracts the time stamp for every frame,
which is essential when using an acquisition sequence with variable
delays between different frames.


If you use these programs, or their modified versions, please cite
our manuscript.

NOTE: the recovery time tau is proportional to the bleached area. This
area is detected automatically in pixels. Converting the bleached area
in pixels to um^2 requires the pixel size to be known. Change the
corresponding line in EK_FRAPbatch.m depending on your pixel size
calibration.  You may also need to modify the initial guess for tau,
the fitted recovery time, depending on the bleached area and D.

More information is provided in the header of every MatLab program, 
which can be accessed either by opening the .m files in MatLab Editor, 
or by typing 

>>help filename.m

where filename.m is the file on which you wish to obtain help. 


--------------------------
Erdem Karatekin
Department of Cellular and Molecular Physiology
Nanobiology Institute
Yale University
850 West Campus Drive, ISTC 220C
West Haven, CT 06516