New Fiji release: Dresden-2009

[dscho]

Dear all,

I proudly announce a new Fiji version (nick-named dee-dee-oh-nine).  It
got its name from the latest two-week brainstorm hosted by the
Max-Planck-Institute of Molecular Cell Biology and Genetics in Dresden,
Germany.  A list of the user-visible changes in this release:

This is the after-hackathon release, and so far we have these changes
(please correct me if I am wrong or forgot something):

- lots of bug fixes (thanks to all!)
- the scripting interpreters remember the previous commands (thanks to
  Albert Cardona): just use Cursor Up/Down to find out.
- we have a NRRD reader/writer now (thanks to Greg Jefferis)
- added the Turbo Reg plugin (thanks Philippe Thevenaz)
- Fiji Wiki is linked to in the Help menu (thanks Gabriel Landini)
- Lens Correction is a part of TrakEM2 now (thanks Stephan Saalfeld and
  Verena Kaynig)
- added the Radial Reslice plugin (thanks Julian Cooper and Albert
  Cardona)
- added Name Landmarks and Register plugin (thanks Mark Longair)
- updated bUnwarpJ (thanks Ignacio Arganda Carreras)
- the bundled ImageJA now uses a method to discover a running instance
  that is safe in a multi-user environment
- updated Bio#Formats (thanks Melissa Linkert and Curtis Rueden)
- added the Help>Report a Bug plugin (thanks Mark Longair)
- added the MTrack2 plugin (thanks Nico Stuurman)
- added the ToAST plugin (thanks Misha Kudryashev)
- Java 1.6 is used on 64-bit MacOSX, when possible
- added the Statistical Region Merging plugin
- the PDF writer can now save all slices of image stacks, instead of only
  the current one
- updated the AnalyzeSkeleton plugin (thanks Ignacio Arganda Carreras)
- added the Time Stamper plugin (thanks Daniel James White)
- added the Auto Threshold plugin (thanks Gabriel Landini)
- if you drop a .java file into the plugins/ directory and call
  Plugins>Scripting>Refresh Javas, it will be added to the Plugins menu
  and be compiled transparently upon being called.
- added scripting examples showing how to interact with the mouse and add
  Java listeners written in the scripting language
- added the Arrow plugin
- added the Stack Manipulation plugin (thanks Jean-Yves Tinevez)
- added the FlowJ plugin (thanks Michael Abramoff and Jean-Yves Tinevez)
- added the Edit LUT as Text script, allowing you to manipulate the
  numerical values of the color lookup table
- added the Auto Local Threshold plugin (thanks Gabriel Landini)
- added the PIV analyser plugin, for optical flow analysis (thanks
  Jean-Yves Tinevez)
- updated TrakEM2 to version 0.7a (read: lots and lots and lots of bug
  fixes as well as enhancements, thanks Albert Cardona and Stephan
  Saalfeld)
- renamed our 'Fill holes' plugin to 'Fill ROI holes' (thanks Gabriel
  Landini)
- added Record Desktop and Record Window commands to record screen movies
  from either the whole desktop or a single (Java) window into a stack,
  optionally a VirtualStack to overcome memory problems (thanks Albert
  Cardona)
- lots of bug fixes and enhancements to the 3D Viewer plugin (thanks
  Benjamin Schmid and Mark Longair)
- lots of bug fixes and enhancements to the Simple Neurite Tracer plugin,
  as well as tighter integration with the 3D Viewer (thanks Mark Longair)
- lots of bug fixes to the Segmentation Editor plugin (thanks Mark Longair
  and Greg Jefferis)
- added the Show Color Surfaces plugin to show 8#bit color stacks as
  colored surfaces in the 3D Viewer (thanks Mark Longair)
- the 3D Viewer's 4D option can now load hyperstacks (thanks Benjamin
  Schmid)
- the 3D Viewer can do free#hand recordings again, as well as convenience
  key bindings (thanks Benjamin Schmid)
- the Lasso/Blow Tool can optionally track dark lines, and actually
  respects the space/color ratio now
- lots of changes only relevant for developers (thanks to all!)
- FlowJ was integrated (thanks Jean-Yves Tinevez),
- The PIV Analyser (an optic flow technique) plugin was donated by
  Jean-Yves Tinevez,
- Refresh Javas is actually called on startup, so that you really can just
  drop .java files into plugins/ and they will be compiled and run
  automagically,
- a Clojure example was fixed so it runs with our current Clojure version,
- two Javascript examples for accessing TrakEM2 were fixed (thanks to
  Albert Cardona),
- the Fiji running on MacOSX can act as a drag 'n drop target now,
- the Dynamic Reslice plugin was contributed by Jean-Yves Tinevez and
  Albert Cardona,
- AbstractInterpreters cursor up/down behavior was fixed (hopefully for
  good now...),
- the Multi Thresholder plugin was removed, as we have something better in
  the form of Auto Threshold and Auto Local Threshold (thanks Jean-Yves
  Tinevez and Gabriel Landini),
- Jean-Yves Tinevez performed a massive task in getting plugin
  descriptions as well as maintainer information onto our Wiki; if you
  have not put yourself as maintainer of your own plugins, please do so
  now,
- a rather massive bug was fixed with Help>Update Menus; modified plugins
  were not loaded anew, but the old versions were retained in memory,
- Erwin Frise made some modifications to the Level Set plugin: it
  remembers previously set parameters, and is substantially faster now,
- Albert Cardona updated TrakEM2 to version 0.7c,
- Plugins>Scripting>Macro Interpreter uses our AbstractInterpreter
  framework now (thanks to Albert Cardona), with command line history and
  all,
- Gabriel Landini pointed out that our Daltonize plugin is misnamed: it
  simulates color blindness, rather than trying to compensate for it.
- ImageJA no longer opens a port, requiring user consent on Windows.
- Mark Longair and Benjamin Schmid contributed the Shape Based Average
  plugin based on a paper by Torsten Rohlfing.
- Benjamin Schmid added some tools to edit videos.

Let me take the opportunity to thank all the contributors (and of course,
that also means the many, many people who reported bugs and verified the
fixes)!

Ciao,
Johannes

[dscho]

Dear all,

On Wed, 29 Apr 2009, Johannes Schindelin wrote:

> I proudly announce a new Fiji version (nick-named dee-dee-oh-nine).  It
> got its name from the latest two-week brainstorm hosted by the
> Max-Planck-Institute of Molecular Cell Biology and Genetics in Dresden,
> Germany.

Just to show you how helpful the Fiji team is, Jean-Yves Tinevez told me
that I managed to forget to post a link to the website...  So here it
goes:

        http://pacific.mpi-cbg.de/

Ciao,
Johannes