Fiji "Plzen" is out!

[dscho]

Dear all,

It is a great pleasure to announce a new Fiji version nick-named Plzen.

In case you do not know yet what Fiji is: Fiji is Just ImageJ -- batteries
included.  One of its missions in life is to make installation of ImageJ
and a lot of plugins and using them as hassle-free as possible.

This release was named after the city in which we had a very successful
image processing school, where we tested a few of the shiny new components
which are the goodies of this release.  The two most prominent new
features are

- the new and shiny Fiji Updater.  The updater knows whether your files
  are up-to-date, obsolete or locally modified.  It will check at startup
  whether there are updates available, and if so, offer you to run the
  updater.  You can also choose to be reminded later, or not ever again.

- the Script Editor.  Just call File>New>Script, select a language and
  start writing a script.  The editor has syntax highlighting and you can
  run the script without even saving it.

  For an introduction to the power of scripting, see e.g.
  http://pacific.mpi-cbg.de/wiki/index.php/Javascript_Scripting

Other changes include:

- lots of bug fixes (thanks to all!)
- many, many improvements in the Register Virtual Stack Slices plugin
  (thanks to Ignacio Arganda Carreras and Albert Cardona)
- a metric ton of improvements in TrakEM2 (thanks Stephan Saalfeld and
  Albert)
- substantial work has been performed on the Level Sets plugin (thanks to
  Erwin Frise and Albert)
- on Windows, a possible infinite loop upon startup was fixed
- the Sync Win plugin was added
- we ship a new Clojure version now, and support for this language was
  enhanced (thanks to Albert)
- our Stack Manipulation collection now has Bob Dougherty's Stack_Sorter
  (thanks to Bob, Jean-Yves Tinevez and Christophe Leterrier), Interleave
  and Deinterleave (thanks to Tony Collins and Jean-Yves), and Grouped
  ZProjector (thanks Jean-Yves)
- we have a circle fitter which can recognize a single circle, even if
  there are fluctuations in the signal
- a lot of encodings were fixed (you should no longer get funny little
  squares in place of non-ASCII characters)
- for better integration with the Swing library, we have a JImagePanel
  that can show a single ImagePlus (thanks to the FocalPoint developers!)
- we can read/write .xpm and .lss16 files now
- you can download a LiveCD image and an image you can put on a USB stick
  now
- lots and lots of improvements in the AnalyzeSkeleton plugin (thanks to
  Ignacio)
- we now bundle the Gray Morphology and several Colocalisation plugins,
  too
- Bio-Formats was updated to include the new AmiraMesh reader (thanks to
  Gregory Jefferis)
- changes in the bUnwarpJ plugin (amongst other enhancements) allow
  tighter integration with the Register Virtual Stack plugin (thanks
  Ignacio)
- the Level Sets plugin is now available inside TrakEM2, too
- if you have problems with a particular file format, you can send it to
  us using Help>Upload Sample Image
- on MacOSX/PowerPC64, Fiji does not try to launch a 64-bit Java (because
  Apple does not provide any 64-bit Java for PowerPC)
- scripts are sorted alphabetically before they are added to menus (for
  consistency between different computers)
- loading compressed NRRD images via network is much faster now (thanks
  Greg!)
- thanks to Bob Dougherty, we bundle the Local Thickness plugin, too
- compressed BioRad images are read correctly now (thanks Greg)
- fixed rendering in the SIFT Align plugin (thanks to Stephan Saalfeld and
  Gabriel Landini)
- upgraded the 3D Object Counter plugin (thanks to Fabrice Cordelières and
  Daniel James White)
- when launched on MacOSX by double-clicking the icon (or by running from
  the Dock), the current directory is set to Fiji's application directory
  (thanks Greg and Christophe)
- upgraded the LSM Toolbox/Reader to version 0.4f (thanks Mark Longair,
  Greg, Patrick Pirotte and Jerôme Mutterer)
- on MacOSX, the Lookup Tables from the luts/ directory are finally
  visible.
- Help>Update Menus handles not only .jar and .class plugins, but plugin
  scripts, too
- we have File>New>Fiji Tutorial, which makes it a breeze to write
  tutorials with screen shots for the Fiji Wiki
- on MacOSX, the default Java extensions were not available by mistake
- sample images can be stored in the samples/ subdirectory, allowing for
  completely off-line File>Open Sample>?
- the Stitching plugin now has a file and directory chooser (thanks to
  Stephan Preibisch)
- .lei and .dv files are opened with Bio-Formats now
- .rec and .st files are opened using our MRC reader, too
- updated the Java runtime environments on Windows and Linux to Java6u16
- we ship the Manual Tracking plugin now, too (thanks to Fabrice
  Cordelières)
- we ship the Calculator Plus plugin now, too (thanks to Daniel Hornung
  and Gabriel)
- the command line option "--run" can be used to tell Fiji to run a given
  plugin right away
- Fiji is built with Java5 every night to ensure that it continues to work
  on 32-bit MacOSX prior to 10.6.
- the Macro Interpreter outputs the help correctly again (thanks Gabriel)
- added two lookup tables, "thermal" and "glasbey" (thanks to Michael
  Doube and Gabriel)
- the Help>Report a Bug plugin is much more user-friendly now (thanks
  Mark)
- updated View5D, fixed interaction with Bio-Formats (thanks to Simon
  Kidd)
- when JAVA_HOME is set to a bogus location Fiji ignores it now (thanks
  Albert)
- avoid mistaking .jar files inside .rsrc/ directories for real .jar
  files, working around a MacOSX quirk (thanks to Maté Biro)
- ImageJ was updated to version 1.43h
- the Command Launcher (Ctrl-L in the Fiji window) was converted to Swing,
  and sports a fuzzy matching, and an option to show more information such
  as which .jar file that plugin is contained in, for a much-improved
  user-experience (thanks Mark)
- ImageJ now opens websites in the preferred browser on Linux
- cropping an image marks it as modified now
- Plugins>Install Plugin... can install .jar files now (provided you have
  permission to write to Fiji's plugins/ directory)
- On MacOSX, the .dmg opens with a background image instructing the user
  how to install Fiji by dragging it to the Applications folder
- allow scripting of Bio-Formats again
- allow the script interpreters to run in headless mode

The list is so long because we did not get the opportunity to meet and get
a new release done in July, as we all hoped.

A big thanks goes to all the contributors and users, especially those who
helped us find and fix bugs!

Ciao,
Johannes