Fiji release: Fiji is Just ImageJ (batteries included)

[Albert Cardona]

October 16th, 2008


We are glad to announce the first release of Fiji, codenamed Dresden.

http://pacific.mpi-cbg.de

Fiji is Just ImageJ, batteries included.

Fiji is an ImageJ distribution that bundles a collection of plugins, jar
libraries and scripting languages in a consistent framework.

Fiji includes Java JDK and java3d, and is available for Windows, MacOSX
and Linux.

Fiji aims at convenience in plugin use and reuse, and includes an
updater to keep up to date with bug fixes and improvements.

Fiji targets image registration, stitching, segmentation, feature
extraction and 3D visualization, among others.
For examples see http://pacific.mpi-cbg.de

Fiji brings together several ImageJ-based projects including ImageJA,
VIB, bUnwarpJ, TrakEM2, and others, kindly developed and distributed
under open source licenses.

For developers, Fiji provides its own build system, Fake (Fiji+Make),
and is distributed under version control with git. The main Fiji
executable is native, cross-platform, and provides numerous features for
easy plugin compilation and interaction.

For Fiji development see http://pacific.mpi-cbg.de/wiki/Developing_Fiji

Fiji core developers and main contributors:
 Ignacio Arganda, Albert Cardona, Erwin Frise, Greg Jefferis, Verena
Kaynig, Mark Longair, Stephan Preibisch, Stephan Saalfeld, Johannes
Schindelin, Benjamin Schmid, Cornelius Sicker, Jean-Yves Tinevez, Pavel
Tomancak.

We would like to thank Wayne Rasband for ImageJ, for his continuous
development efforts and for his infinite patience. Thank you so much!


--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Bill Mohler]

Unfortunately, I'm getting rccorrent crashes when I launch the
download on my Mac
10.5.5
2.4 GHZ Intel Core Duo
4 GB

>October 16th, 2008
>
>
>We are glad to announce the first release of Fiji, codenamed Dresden.
>
>http://pacific.mpi-cbg.de
>
>Fiji is Just ImageJ, batteries included.
>
>Fiji is an ImageJ distribution that bundles a collection of plugins,
>jar libraries and scripting languages in a consistent framework.
>
>Fiji includes Java JDK and java3d, and is available for Windows,
>MacOSX and Linux.
>
>Fiji aims at convenience in plugin use and reuse, and includes an
>updater to keep up to date with bug fixes and improvements.
>
>Fiji targets image registration, stitching, segmentation, feature
>extraction and 3D visualization, among others.
>For examples see http://pacific.mpi-cbg.de
>
>Fiji brings together several ImageJ-based projects including
>ImageJA, VIB, bUnwarpJ, TrakEM2, and others, kindly developed and
>distributed under open source licenses.
>
>For developers, Fiji provides its own build system, Fake
>(Fiji+Make), and is distributed under version control with git. The
>main Fiji executable is native, cross-platform, and provides
>numerous features for easy plugin compilation and interaction.
>
>For Fiji development see http://pacific.mpi-cbg.de/wiki/Developing_Fiji
>
>Fiji core developers and main contributors:
>Ignacio Arganda, Albert Cardona, Erwin Frise, Greg Jefferis, Verena
>Kaynig, Mark Longair, Stephan Preibisch, Stephan Saalfeld, Johannes
>Schindelin, Benjamin Schmid, Cornelius Sicker, Jean-Yves Tinevez,
>Pavel Tomancak.
>
>We would like to thank Wayne Rasband for ImageJ, for his continuous
>development efforts and for his infinite patience. Thank you so much!
>
>
>--
>Albert Cardona
>http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Albert Cardona]

Bill Mohler wrote:
> Unfortunately, I'm getting rccorrent crashes when I launch the
> download on my Mac
> 10.5.5
> 2.4 GHZ Intel Core Duo
> 4 GB



Runs great here on a MacOSX 10.5.4 intel core 2 duo.

We'd appreciate very much if you have a look at content of the
Applications/Utilities/Console.app for any error messages?

Also, could you paste the contents of the Plugins - Utilities - ImageJ
Properties command?

Thanks very much.

Albert

--
Albert Cardona
http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[Bill Mohler]

10/16/08 3:30:29 PM [0x0-0x1f91f9].org.fiji[6197] Invalid memory
access of location 8129d040 rip=8058f37e
10/16/08 3:30:31 PM com.apple.launchd[136]
([0x0-0x1f91f9].org.fiji[6197]) Exited abnormally: Bus error
10/16/08 3:30:35 PM [0x0-0x1fb1fb].fiji-macosx[6201] Invalid memory
access of location 8129d040 rip=8058f37e
10/16/08 3:30:38 PM com.apple.launchd[136]
([0x0-0x1fb1fb].fiji-macosx[6201]) Exited abnormally: Bus error
10/16/08 3:30:52 PM [0x0-0x1fc1fc].org.fiji[6202] Invalid memory
access of location 8129d040 rip=8058f37e
10/16/08 3:30:54 PM com.apple.launchd[136]
([0x0-0x1fc1fc].org.fiji[6202]) Exited abnormally: Bus error
10/16/08 3:32:28 PM [0x0-0x1fd1fd].org.fiji[6218] Invalid memory
access of location 8129d040 rip=8058f37e
10/16/08 3:32:31 PM com.apple.launchd[136]
([0x0-0x1fd1fd].org.fiji[6218]) Exited abnormally: Bus error
10/16/08 3:32:50 PM [0x0-0x1ff1ff].org.fiji[6222] Invalid memory
access of location 8129d040 rip=8058f37e

I'm afraid I can't get to the properties because the program crashes
immediately after launching. I will try again after a reboot.

Bill

>Bill Mohler wrote:
>>Unfortunately, I'm getting rccorrent crashes when I launch the
>>download on my Mac
>>10.5.5
>>2.4 GHZ Intel Core Duo
>>4 GB
>
>
>
>Runs great here on a MacOSX 10.5.4 intel core 2 duo.
>
>We'd appreciate very much if you have a look at content of the
>Applications/Utilities/Console.app for any error messages?
>
>Also, could you paste the contents of the Plugins - Utilities -
>ImageJ Properties command?
>
>Thanks very much.
>
>Albert
>
>--
>Albert Cardona
>http://www.mcdb.ucla.edu/Research/Hartenstein/acardona

[dscho]

Hi,

On Thu, 16 Oct 2008, Bill Mohler wrote:

> 10/16/08 3:30:29 PM [0x0-0x1f91f9].org.fiji[6197] Invalid memory access
> of location 8129d040 rip=8058f37e
> [...]

Thanks for the bug report.

I found the issue: due to a few last-minute changes, the Fiji launcher was
not compiled correctly, and Retrotranslator was not included.

Retrotranslator is a library that allows you to run Fiji on Java prior to
version 1.5; a lot of plugins rely on features of that version.  
Unfortunately, there will be no Java 1.5 for MacOSX 10.3 and earlier.

Retrotranslator is enabled per default when you run Fiji on MacOSX 10.3
(you cannot run Fiji on MacOSX 10.2 and earlier, as it was disabled due to
lack of tests; this might change if it is explicitely requested by users).

Retrotranslator comes at a slight performance penalty.

Also, and unfortunately, Retrotranslator is not able to run Java3D, as
that comes with a native library -- Retrotranslator can only handle Java.  
As a consequence, the "3D Viewer" plugin will not work.

A Fiji version that should run fine on all MacOSX platforms from 10.3
onwards can be found here:

        http://pacific.mpi-cbg.de/downloads/snapshots/fiji-macosx.dmg

Thank you for your attention,
Dscho