Re: ImageJ on Linux

[Albert Cardona]

Christophe,


> - Where should I put the ImageJ directory ? I uncompressed it on the
> desktop, then put it in my home folder. Should I put it in a more
> universal place (that other users can access) lke usr/bin or anything
> ? Should I separate the plugin directory from the rest ? I still can't
> get used to the concept of file permissions and that "sudo everything"
> vibe...


There is no restriction. If you are going to be the only ImageJ user,
just put it under your home directory. Tradition dictates that you
create a ~/bin/ directory (that is, a directory to contain BINaries,
under your home '~' directory). But you are free to do as you please.


> - The ImageJ GUI is fugly. The menus are hideous, the menu fonts are
> not antialiased, there is no selection shadow when browsing trough the
> menus. I tried the latest ImageJ (1.38m) with both Java 1.5 and Java
> 1.6, but no luck to make it look decent (I mean, this kind of Java
> apps under Windows or Mac are not precisely "beautiful", but this is
> far better than what I got under Linux).

In my experience, Java 1.6.0 finally reads the GTK settings properly. So
the default ubuntu desktop with the "Human" theme will make ImageJ look
just fine. In addition, starting with java 1.6.0 ImageJ will use half as
much memory (the array is shared between the ImageProcessor and the
displayed java.awt.Image).
If you have no antialias, then check your desktop setup. I have no idea
what Mint is using.
In choice there is freedom, but also headaches. The default ubuntu,
though, manages the GUI details rather well.



> - I could'nt manage to get the IJprefs.txt from Tony Collins MBF
> ImageJ to distribute plugins correctly into the various menus (for
> example, AnisotropicDiffusion2D is supposed to go inside
> Process>Filters), they all show up under the Plugins menu. Should I
> put the file somewhere els than the ImageJ folder ?

In Linux, the IJ_prefs.txt should be in your home directory. Otherwise
ImageJ doesn't read it.
In any case, I'd suggest to use the standard way of editing menus which
is through the plugins.config file inside a jar file dropped in the
plugins folder. I can't understand why Tony isn't using it (perhaps his
package is older than the plugins.config functionality).



> - Is the "run" file the only way to start ImageJ ? It's a script
> without icon, and everytime I double click on it, it asks me if I want
> to edit or execute it. Not very user-friendly as a launcher.


Whereever you put the ImageJ folder with the ij.jar jar, create a little
text file with something similar to this:


cd /home/christopher/ImageJ/
java -Xmx512m -classpath ij.jar -jar ij.jar

Be sure to make the file executable. Suppose you named it 'run':

$ cd ~/ImageJ/
$ chmod +x run

Then, in your Gnome menu bar, right click and choose "Add to panel...".
Then select Custom Application Launcher, and push the "Browse" button.
Find the 'run' script and select it.
For an icon, I copied the icon from a MacOSX ImageJ installation and
saved it as PNG with a transparent background, which then I assigned by
clidking on the default icon and finding the new one.
Alternatively, the System/Preferences/Menus & Toolbars will let you add
a menu entry in the Gnome menus.



> I know a lot of people around here use ImageJ under linux, I hope
> there are some solutions to these problems.

True, and we should setup a .deb package to do all the above automatically.


As a final remark: the default java open/save dialogs are rather limited
and cumbersome. Either configure ImageJ to use the JFileChooser (under
the Edit/Options/Input-Output ImageJ menu), and/or simply use the file
browser to drag and drop images, stacks, ROI files and LUT files
directly to the ImageJ main window.


Albert