1. Download cygwin from
    http://www.cygwin.com/
    or
    http://www.cygwin.com/setup.exe

2. Run setup.exe, choose to install from Internet. The setup will ask you to choose packages to be installed 
after you choose which site to download. You may need to choose where you want to install cygwin, here we 
suppose you install it in c:\temp, we call it <cygwin home>. In addition to choose the default packages, be 
sure to choose all sub-categories associated with libtiff under the two categories, Graphics and Libs. If there 
are other sub-categories about tiff, to choose them will be fine.
After the installation of cygwin, it will create a green-with-black icon for cygwin window. The system 
may need to be restarted.
Double click the cygwin window icon, it will open a unix-emulating window.

Inside the cygwin window, some popular unix commands can be used:

        ls    
        df
        pwd
        cp

Cygwin environment may create a virtual file system, called "/". The windows partition, C: is mounted 
under /cygdrive/c, and d: is /cygdrive/d. You can use "df" command to check what file systems (or partition) 
is there. Now, you can correspond d:\shuku\abc.txt to "/cygdrive/d/shuku/abc.txt". Unix's file names are 
case-sensitive.
In the cygwin window, you can use the command "man" to check the usage of a command, like:
        man cp
        man ls

The start directory of a cygwin window will be
"/home/<user name>", where user name is your Windows user name. You can check this by type
pwd
when you just start the cygwin window.

3. Copy the four comands(batch_rfrt, rootflowrt, tensor_robust, mosaic) into "/usr/local/bin" in the cygwin 
environment. "/usr/local/bin" is chosen here because cygwin's default command parth includes it, so that the 
user can access the commands without specifying the parth. 
It is a little confusing to correspond "/usr/local/bin" in Windows explorer, it is actually in <cygwin 
home>\cygwin\usr\local\bin under windows system, if <cygwin home> is c:\temp, then it is 
c:\\temp\cygwin\usr\local\bin. 
The confusion comes from the situation that the sub-folder in the cygwin environment, /cygdrive/c, is 
containing the parent folder /, bcause the root / in cygwin environment is actually under c:\temp\cygwin in 
Windows environment. You can just forget the confusion here. In cygwin window you can use command in
       cd c:
to go to c:.

4. To run the plant root image sequence, you can create a working directory, say c:\plantroot\root1, 
corresponding to /cygdrive/c/plantroot/root1. Then you create sub-folders under it, curve, pgm, 
intermediate, tiff. You put the root image seuqences into tiff sub-folder, with the file names like 
"Stack00##Frame 00##".
In the cygwin window, type the following commands:

cd c:
cd plantroot/root1
batch_rfrt . < input.txt

Then RootflowRT will be launched.