3D viewer movie

[Benjamin Schmid-2]

Dear all,

sorry for my bad responsiveness.

The duplicate command error is not the problem. In fact, this error
will still occur. The actual problem was that some features of
the 3D viewer require Java3D >= 1.5. Mac OSX, however, has an older
version of Java3D pre-installed.

While it is possible to update the Java3D on Mac, it's not really
conveniant (you have not only to download Java 3D, but also Jogl).

I just uploaded a new version of the 3D viewer, which checks if Java3D
is available at all, and if, which version. If a version below 1.5 is
discovered, it offers the user to download automatically a newer
Java3D and installing it to the correct places. Afterwards, ImageJ has
to be restarted.

I tested it on the machines I have available here, but since the
installation process is OS dependant, there may remain problems which
I have not found so far, therefore I very much appreciate your
feedback.

Best wishes,
Bene

[Adelaine Leung]

Hi everyone,

I'm trying to write a simple macro that would save a stack as an avi  
movie.  I tried to run the macro exactly the same way as what was  
recorded using the macro recorder in ImageJ, but for some reason,  
this doesn't work.  At the end of the run, it'll ask me to select an  
AVI file.  I don't understand what's wrong.

run('AVI...', 'compression=Uncompressed jpeg=90 frame=7 save=temp');

Thanks in advance!

Adelaine


Adelaine Leung
Kravitz Lab
Department of Neurobiology
Harvard Medical School
220 Longwood Avenue
Boston, MA 02115, USA
Phone: [phone]
Fax: [phone]

[Wayne Rasband]

> Hi everyone,
>
> I'm trying to write a simple macro that would save a stack as an  
> avi movie.  I tried to run the macro exactly the same way as what  
> was recorded using the macro recorder in ImageJ, but for some  
> reason, this doesn't work.  At the end of the run, it'll ask me to  
> select an AVI file.  I don't understand what's wrong.
>
> run('AVI...', 'compression=Uncompressed jpeg=90 frame=7 save=temp');
>
> Thanks in advance!

This is what I get in the command recorder when I open the MRI Stack  
and save it in AVI format in my home directory:

   run("MRI Stack (528K)");
   run("AVI... ", "compression=Uncompressed jpeg=90 frame=5 save=/
Users/wayne/mri-stack.avi");

Note the space in "AVI... ". There are two AVI commands:  
File>Import>AVI and File>Save As>AVI. One has a space in the command  
name and the other doesn't. You can see this if you open the Command  
Finder (Plugins>Utilities>Find Commands), enter "AVI" in the search  
box and check "Show full information".

-wayne

[Knecht, David]

Dear Bene- I ran your new plugin and it told me that I was running 1.3  
Java3D and then downloaded and installed perfectly.  The plugin now  
works.  Thanks for you efforts.  I still don't understand where the  
old version came from and why it was not updated by OS updates, but at  
least it is fixed.  Thanks for your efforts.  Dave

On Apr 8, 2009, at 11:28 AM, Benjamin Schmid wrote:

> Dear all,
>
> sorry for my bad responsiveness.
>
> The duplicate command error is not the problem. In fact, this error
> will still occur. The actual problem was that some features of
> the 3D viewer require Java3D >= 1.5. Mac OSX, however, has an older
> version of Java3D pre-installed.
>
> While it is possible to update the Java3D on Mac, it's not really
> conveniant (you have not only to download Java 3D, but also Jogl).
>
> I just uploaded a new version of the 3D viewer, which checks if Java3D
> is available at all, and if, which version. If a version below 1.5 is
> discovered, it offers the user to download automatically a newer
> Java3D and installing it to the correct places. Afterwards, ImageJ has
> to be restarted.
>
> I tested it on the machines I have available here, but since the
> installation process is OS dependant, there may remain problems which
> I have not found so far, therefore I very much appreciate your
> feedback.
>
> Best wishes,
> Bene

Dr. David Knecht
Department of Molecular and Cell Biology
Co-head Flow Cytometry and Confocal Microscopy Facility
U-3125
91 N. Eagleville Rd.
University of Connecticut
Storrs, CT 06269
860-486-2200
860-486-4331 (fax)

[Benjamin Schmid-2]

Hi Dave,

> Dear Bene- I ran your new plugin and it told me that I was running 1.3  
> Java3D and then downloaded and installed perfectly.  The plugin now  
> works.  Thanks for you efforts.  I still don't understand where the old
> version came from and why it was not updated by OS updates, but at least
> it is fixed.  Thanks for your efforts.  Dave

Glad to hear it works. I think this is Apple politics. The Java3D with
which they ship their computers are ways outdated. The newer versions
not only provide more features, but also better support for graphics
cards and many bug fixes, so the update is worth the effort.

Cheers,
Bene