Window and Leveling

[Prasad Rajagopal]

Hi all,

        I am pretty much new to the mailing list but I have been using
ImageJ in my application for about an year. Recently we are required to
offer a new feature for our Medical Images - Window & Leveling concept.

        After going through couple of articles I managed to understand
clearly what it means. But I also knew that, ImageJ does have W&L added in
the Menu Bar and I did play around with that for a while.

        But our requirements are like this. We have specific users who
wants to have these Window&Level values preset for them.

          For example:

                 Lungs = value1
                 Brain = value2
                 Bones = value3
                 etc.,

          So i was thinking to have a drop-down list and have lungs,
brain, bones etc., listed in them. So when the user chooses one of them,
it will change the intensity of the Image to their needs.

          So, can anybody help me find what API function should I exaclty
use for setting the values. I could not find any such function in the
documentation.

          But I am pretty much convinced that there is one, because W&L of
the ImageJ has an "Apply" button in it, which exactly does what I need.

          Any ideas ?

Thanks
Prasad

[Ted Ballou]

Hi,

Is this a windoze bug? I'm running XP pro and have a pile of tif's to
convert to a multiframe tif stack. If I File/Open a group of
sequence-named files all together (using shift and control keys to
select them) and then do either Image/Stacks/ConvertImagesToStack OR
Plugins/Stacks/StacksBuilding/StackBuilder (this is WCIF package) the
resulting stack is perfect. However, if I drag the files to ImageJ from
a WindozeExplorer screen, a bunch of slices that belong in the beginning
of the stack are tacked onto the end.

While we're on the subject, is there a plugin to directly read in
sequence-names files as a stack?

Thanks everyone -

Ted Ballou

[Wayne Rasband]

Use the setMinAndMax(min, max) function to set the display window and
level, where min and max are calculated from the window width and level
using

     min = level - width/2;
     max = level + width/2;

Use a macro set such as the one at

     http://rsb.info.nih.gov/ij/macros/WindowAndLevel.txt

to create menu commands for setting preset values for lungs, bones,
etc. This macro set creates keyboard shortcuts that allow you to switch
to the lung preset values by pressing 1 and to the bone values by
pressing 2. It also includes macros for changing the preset values
using a dialog box and to change them to values defined interactively
using the W&L or B&C tools.

Add the macros in this set to StartupMacros.txt to have them installed
automatically when ImageJ starts up. Information about the ImageJ macro
language can be found at

      http://rsb.info.nih.gov/ij/developer/macro/macros.html

-wayne

On Jun 13, 2006, at 2:40 PM, Prasad Rajagopal wrote:

> Hi all,
>
>         I am pretty much new to the mailing list but I have been using
> ImageJ in my application for about an year. Recently we are required to
> offer a new feature for our Medical Images - Window & Leveling concept.
>
>         After going through couple of articles I managed to understand
> clearly what it means. But I also knew that, ImageJ does have W&L
> added in
> the Menu Bar and I did play around with that for a while.
>
>         But our requirements are like this. We have specific users who
> wants to have these Window&Level values preset for them.
>
>           For example:
>
>                  Lungs = value1
>                  Brain = value2
>                  Bones = value3
>                  etc.,
>
>           So i was thinking to have a drop-down list and have lungs,
> brain, bones etc., listed in them. So when the user chooses one
> of them, it will change the intensity of the Image to their needs.
>
>           So, can anybody help me find what API function should I
> exaclty use for setting the values. I could not find any such function
> in the  documentation.
>
>           But I am pretty much convinced that there is one, because
> W&L of
> the ImageJ has an "Apply" button in it, which exactly does what I need.
>
>           Any ideas ?
>
> Thanks
> Prasad
>

[Guillermo Romero]

I use a macro, convert_tiffs_to_stack.  If you place all your tiffs  
in a folder, this macro will read them sequentially and create/save  
the resulting stack in the directory of your choice.

On Jun 14, 2006, at 2:29 PM, Ted Ballou wrote:

> Hi,
>
> Is this a windoze bug? I'm running XP pro and have a pile of tif's  
> to convert to a multiframe tif stack. If I File/Open a group of  
> sequence-named files all together (using shift and control keys to  
> select them) and then do either Image/Stacks/ConvertImagesToStack  
> OR Plugins/Stacks/StacksBuilding/StackBuilder (this is WCIF  
> package) the resulting stack is perfect. However, if I drag the  
> files to ImageJ from a WindozeExplorer screen, a bunch of slices  
> that belong in the beginning of the stack are tacked onto the end.
>
> While we're on the subject, is there a plugin to directly read in  
> sequence-names files as a stack?
>
> Thanks everyone -
>
> Ted Ballou

[Prasad Rajagopal]

Hi,

     Thanks for the reply. It was very helpful. It worked. But there is a
slight problem. I wrote a macro named it as StartupMacros.txt and put that
file in the "macros" directory. And when I restarted ImageJ it automatically
installed.

     But since I am using ImageJ as an applet, when i embed the "ij.jar" for
the ImageJ it does not inlcude the StartupMacros.txt functionalities. When I
load webpage, ImageJ starts and opens the Image. But when I pressed "1",
"2", etc., nothing happened because the Macro was not there.

     Do you know how to make it work when calling ImageJ as Applet ?


Thanks
Prasad

[Wayne Rasband]

>      Thanks for the reply. It was very helpful. It worked.
>      But there is a slight problem. I wrote a macro named it
>      as StartupMacros.txt and put that file in the "macros"
>      directory. And when I restarted ImageJ it automatically
>      installed.
>
>      But since I am using ImageJ as an applet, when i embed
>      the "ij.jar" for the ImageJ it does not inlcude the
>      StartupMacros.txt functionalities. When I load webpage,
>      ImageJ starts and opens the Image. But when I pressed
>      "1", "2", etc., nothing happened because the Macro was
>      not there.
>
>      Do you know how to make it work when calling ImageJ as
>      Applet ?

ImageJ 1.37i installs the macros in StartupMacros.txt when it is
running as an applet. The applet at
<http://rsb.info.nih.gov/ij/applet/>, for example, installs the macros
at <http://rsb.info.nih.gov/ij/applet/StartupMacros.txt>.

-wayne