Finally! Fiji “dee-dee-oh-nine” is out!
The changes:
- 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.
Thanks to all the people who helped this release come about!
