Focal Point Image Viewer
------------------------

Focal Point is an Image Browser designed for use with the more complex
image types commonly found in an imaging facility.  In addition to being
able to view standard single frame images (png, jpeg, bmp etc) it also
accommodates images stacks (tiff), and proprietary microscope formats 
(lsm, oib, oif).

Within the browser you can preview images and change the size of the
displayed thumbnails.

Installation
------------

Focal Point is a Java application.  You will therefore need to have a 
suitable java runtime environment installed before you try to run it.

It has been tested with Java 1.5, but should work on any versions newer
than that as well.  If you don't have java installed you can download
it from www.java.com.

Windows: Unzip the install file and double click on the run_focal_point.bat
file to launch the program.  It may be convenient to make a shortcut to
this .bat file.  If you do this you can make the shortcut run minimised to
avoid seeing the black cmd window when the program launches.  The program
also includes an icon file which you can associate with your shortcut to
make things look prettier.

OSX: Focal Point comes as a Mac application bundle.  Simply drag this into
your applications folder and double click to launch.

Linux: Unzip the install file to somewhere appropriate.  To launch the 
program it is easiest if you create a small shell script or desktop
launcher.  To see the java arguments you should use to do this look at the
.bat file from the windows install.  Please note that FocalPoint (well
ImageJ actually) currently doesn't work with IcedTea v1.7 so you'll need
to install the Sun Java runtime to get this program to run.

Configuring ImageJ
------------------

Focal point offers the ability to open any selected image in ImageJ.  To do
this you will also need to install ImageJ on your machine.  If you install
it in the default location (C:/Program Files/ImageJ on windows, or the
applications folder on OSX) then you don't need to do anything else.   If 
imageJ is in a non-standard location then you need to add an arguement to
the java command which launches FocalPoint.  The information you need to add
is :

-Dimagej=c:/wherever/imagej.exe

where the location is the location of the imagej executable.

If you're running under linux you will need to point to the 'run' file to get
this to work.  You will also need to edit the file to allow it to be launched
from anywhere and to take arguements.

The default run file looks like:

./jre/bin/java -Xmx512m -jar ij.jar

You need to change this to a 2 line file which looks like:

cd /home/andrewss/ImageJ
./jre/bin/java -Xmx512m -jar ij.jar "$1"

...where the first line uses the name of the directory in which ImageJ is installed
and the second line adds "$1" to the end of the command so you can pass in a file
name you want to open.


Problems / Bugs
---------------

If you have any problems installing or using FocalPoint then please let us
know.  You can report any issues either directly into our bug tracking
system at:

http://www.bioinformatics.bbsrc.ac.uk/bugzilla/

..or by email to

simon.andrews@bbsrc.ac.uk