RELEASE-NOTES

Date: Mon, 14 June 2010
From: Johannes Schindelin <johannes.schindelin@gmx.de>

I proudly announce a new version of Fiji (Fiji Is Just ImageJ -- batteries
included).

In our cherished tradition, the current version is named after the location
of a big hackathon: Heidelberg. We were honored to have some Fiji developers
invited by the EMBL in Heidelberg from March 15 -- 26, 2010, thanks to the
generous support of Francesca Peri and Kota Miura.

There have been 524190 lines added and 245463 removed since the previous
release, with the help of (in alphabetical order): Albert Cardona, Andreas
Wiese, Benjamin Schmid, Ben Tupper, Chris Elliott, Curtis Rueden, Daniel
Hornung, Daniel James White, Davi Bock, Gabriel Landini, Gregory Jefferis,
Ignacio Arganda-Carreras, Jacques Pecreaux, Jan Eglinger, Jean-Yves Tinevez,
Johannes Schindelin, Larry Lindsey, Mark Longair, Nick Weiler, pixelhead,
pogo, Ricardo Henriques, Stephan Preibisch, Stephan Saalfeld, Tom Kazimiers
and Verena Kaynig, and many other helpers.

Changes since Fiji Plzeň:

- There is a new plugin called Trainable Segmentation:

	http://pacific.mpi-cbg.de/Trainable_Segmentation

  This plugin offers advanced machine learning techniques to train a model
  that segments your images into different classes.

  While it is developed actively, it is already quite powerful and easily
  usable by non-programmers.

- Fixed a critical bug in the Fiji Updater that affected MacOSX. Symptom:
  Fiji no longer starts after an update). If you have not updated between
  April 8, 2010 and June 3rd, 2010, this bug affects you and you have to
  follow the instructions at:

  http://pacific.mpi-cbg.de/Fix_non-functional_Fiji_after_Update_on_MacOSX

- Unfortunately, we had to drop support for MacOSX PPC. If you need Fiji
  on such a system, please contact fiji-devel@googlegroups.com, and we will
  try to provide a special edition.

- For Debian/Ubuntu users, there will be fine-grained packages of Fiji
  Heidelberg available soon.

Other changes:

- Fiji's core was frequently synchronized with ImageJ.

- many, many improvements in bUnwarpJ (thanks Ignacio Arganda-Carreras).

- Context Help: If you click on Help>Help on Menu Item, the next click on
  a menu item will open the corresponding page (if there is one) on the Fiji
  Wiki.

- Statistical Region Merging can work in 3D now (this uses lots of memory).

- The Stack Manipulation menu got another entry: Slice Keeper (thanks
  Jean-Yves Tinevez).

- many, many improvements to the Simple Neurite Tracer and 3D Viewer, which
  were split off from the VIB Protocol plugin (thanks Mark Longair and
  Benjamin Schmid).

- many updates for the Register Virtual Slices plugin (thanks Ignacio
  Arganda-Carreras).

- Auto Threshold was improved, and made accessible to other plugins (thanks
  Gabriel Landini).

- implemented CLAHE, a filter for adaptive local contrast enhancement
  (thanks to Stephan Saalfeld).

- removed dependency on Jama of mpicbg plugins (thanks to Stephan Saalfeld).

- separated libraries from plugins, e.g. mpicbg plugins from mpicbg library
  (thanks to Stephan Saalfeld).

- added several mpicbg library tools, many bug-fixes and improvements
  (thanks to Stephan Saalfeld).

- TrakEM2 was updated several times, with tons of new goodies (thanks Albert
  Cardona and Stephan Saalfeld). For example:

  * extended multi-layer-mosaic alignment to handle
    - adjustable weights for cross-section vs intra section features
    - handle multiple disconnected graphs
    - non-linearly deform section graphs
  * properly propagate non-linear manual deformations
  * speed up rendering of deformed images
  * calibrate exported snapshots
  * several bug-fixes

- A plugin was added that performs the SIOX algorithm (color segmentation
  by example, thanks Ignacio Arganda-Carreras).

- Some bugs in Stitching 2D/3D were fixed (thanks Stephan Preibisch and
  Ignacio Arganda-Carreras).

- A plugin "IsoData Classifier" was added that extends the default automatic
  threshold of ImageJ to multiple classes (more than two).

- Fiji's arrow tool offers interactive manipulation of the arrow (which is
  a ROI now), with different widths, head sizes, and head shapes (thanks
  to Jean-Yves Tinevez).

- A bug was fixed in the MTrack2 plugin (thanks to Chris Elliott).

- There is a GenericDialogPlus in fiji-lib.jar now that supports adding
  "file" and "directory" fields with a button to choose the value via a
  file dialog (thanks Stephan Preibisch and Ignacio Arganda-Carreras).

- Many improvements to the Analyze Skeleton/Skeletonize 3D plugins (thanks
  Ignacio Arganda-Carreras and Daniel Hornung).

- The Robust Automatic Threshold Selection plugin was added, providing a
  very powerful automatic local thresholding technique (thanks Ben Tupper).

- Jython was updated to version 2.5.

- The code of the VIB Protocol was improved (thanks to Mark Longair,
  Benjamin Schmid and Nick Weiler).

- Plugins>Macros>About Startup Macros works again (thanks Gabriel Landini).

- The Fiji launcher was modified to work around a Java 1.5 bug on Linux.

- The Java WebStart'able Fiji was fixed.

- The Script Editor offers code templates now (thanks Tom Kazimiers).

- The Find/Replace function in the Script Editor now defaults to the
  selected text (thanks Tom Kazimiers).

- The Tutorial Maker was renamed to Plugins>Utilities>Fiji>New Fiji Tutorial,
  and you can choose to upload to another Wiki than the Fiji Wiki (provided
  that it is powered by MediaWiki). It also uses the Script Editor for better
  usability now.

- The Image Expression Parser plugin was added, providing much more powerful
  operations on Images than the simple Image Calculator or Image Calculator
  Plus plugins (thanks to Jean-Yves Tinevez).

- There is an Image>Adjust>Auto Crop plugin (cropping the maximal border that
  matches the background color), and an Image>Adjust>Auto Crop (guess
  background color) plugin (estimating the most likely background color from
  the border).

- We have a Linear Gradient and Radial Gradient plugin now, to generate
  gradients in existing images.

- There was a bug fix in .mrc reading (thanks Jean-Marc Verbavatz and Quentin
  de Robillard).

- Fiji starts with Java settings optimized for heavy-duty usage now (thanks
  Albert Cardona).

- when using a .java plugin transparently (by putting it into
  Fiji's plugins/ directory), the error output will be shown now.

- The Script Editor offers tabs now.

- When a file changed outside the Script Editor, it offers to reload the
  file now.

- The Script Editor offers the ImageJ Macro Language in the Languages menu,
  with syntax-highlighting. Consequently, it is now the default editor for
  macros.

- The Script Editor got a function to run just the selected part of the script.

- Many more improvements in the Script Editor.

- Many improvements to the Colocalization plugins (e.g. the output of
  Colocalization Threshold can be saved to a file now, etc). Thanks to
  Daniel James White and Tom Kazimiers.

- The Directionality plugin was added to analyze images containing oriented
  structures (thanks Jean-Yves Tinevez).

- The Time Stamper plugin was updated (thanks Jean-Yves Tinevez, Daniel James
  White and Tom Kazimiers).

- Add a Recent Commands menu entry to list the most recent and the most
  frequent commands.

- The FileDialogs on Linux have more sensible keyboard handling now, and are
  Drag 'n Drop targets, as on other platforms, too.

- There is an Imglib Algorithm Launcher now, which makes it easy to use the
  full power of imglib for users, and which is easily extensible to future
  algorithms in imglib (thanks to Curtis Rueden).

- In Fiji, the menu entry is called Help>Refresh Menus instead of
  Help>Update Menus, to clarify what the function is about.

- When Fiji detects that the user attempted to launch a plugin that was
  compiled for Java 1.6, but run on Java 1.5, it tries very hard to convert
  the classes to be usable on Java 1.5 nevertheless.

- There is another optical illusion in macros/grey-squares.ijm now:
  Adelson's checker illusion. It shows that we cannot trust our perception
  of absolute gray values. Thanks to Gabriel Landini for improvements of
  the script, and Daniel James White for the idea.

- The Exact Euclidean Distance Transform (3D) plugin was added, providing
  a real exact EDT, still with linear complexity. A signed version is
  available, too (attaching negative distances to outside pixels).

- The Script Editor supports bookmarks now.

- The 3D Viewer is now actually a 4D Viewer, handling hyperstacks correctly,
  and was improved in many other ways, too (thanks to Benjamin Schmid and
  Gabriel Landini).

- The 3D Viewer can export any kind of mesh now (thanks to Albert Cardona).

- The Anisotropic Diffusion 2D plugin was added.

- The LSM Toolbox was updated to version 4.0g (thanks to Patrick Pirotte and
  Jean-Yves Tinevez).

- The HandleExtraFileTypes class was synchronized with the upstream version,
  handling more file formats by default (thanks Albert Cardona for a fixup).

- There is no need for a StartupMacros.txt anymore, so you can create/modify
  it without making the Fiji Updater report it as "Locally modified". Thanks
  Ilan Tal for the suggestion.

- View5D was updated to version 1.2.17, thanks to Rainer Heintzmann and
  Jean-Yves Tinevez.

- The Find Connected Regions plugin was updated, thanks to Mark Longair.

- The Fiji launcher is no longer a C++ program, but a C program. This results
  in smaller executables, less requirements when building, and a larger range
  of supported Linux setups.

- The Fiji Updater up-to-date check is no longer run when you call Fiji with
  an argument (e.g. by Drag 'n Drop of an image onto the Fiji icon). Thanks to
  Jean-Marc Verbavatz for the suggestion.

- The Fiji Updater offers to update Java on Windows and Linux in the Advanced
  Mode, thanks to one of the rare less-exciting talks at the ELMI meeting.

- The Java WebStart generator was fixed, and is now run every night. The URL is:

	http://pacific.mpi-cbg.de/webstart/Fiji.jnlp

- The SPIM Registration plugin was added, offering multi-angle registration
  and reconstruction typically needed in Selective Plane Illumination
  Microscopy (thanks to Stephan Preibisch, Stephan Saalfeld and Pavel Tomancak).

- Clojure was updated to a newer version (thanks to Albert Cardona).

- clojure-contrib is no longer required, and was therefore removed (thanks to
  Albert Cardona).

- The QuickPALM plugin was added (thanks to Ricardo Henriques).

- Loads of bugfixes

Developer-visible changes:

- There are two nightly builds, one including all the submodules, and the
  other to make sure that Fiji builds using Java 5 (which we are stuck to,
  because there will not be any Java 6 for MacOSX 10.4, or for 32-bit
  MacOSX 10.5).

- The full javadocs are built after the nightly build, accessible at

	http://pacific.mpi-cbg.de/javadoc/

- Developers can upload new plugins or updates from the Fiji Updater GUI, if
  they have the write permissions on the server (includes bug fixes by
  Mark Longair).

- Many improvements in the build system (less unnecessary rebuilds, separate
  output directory, excluding files from a .jar target, etc). Thanks to
  Jacques Pecreaux, Mark Longair and Curtis Rueden.

- There is a generic way to define a tool in Java now, fiji.util.AbstractTool,
  rather than going the awkward way to define a macro that calls back into the
  Java code (thanks Jean-Yves Tinevez).

- The Script Editor can launch classes outside of plugins/ now.

- The Script Editor can make .jar files from .java plugins now.

- The Script Editor can build and launch Fiji plugins from
  $FIJI_ROOT/src-plugins/<name>/ now.

- The Script Editor recognizes errors from the Java compiler and offers to
  jump to the location of the next/previous error.

- The Script Editor recognizes exceptions thrown during the execution of a
  script and offers to jump to the next/previous location in the stacktrace.

- You can ask the Script Editor to open the JavaDoc for a given class using
  Tools>Open Help on Class...

- The WEKA library is now part of Fiji; the FijiClassLoader is now an instance
  of URLClassLoader just because of that (thanks for Verena Kaynig, Albert
  Cardona and Ignacio Arganda-Carreras for the prodding).

- There is an easy way to add a screenshot to be shown on the front page
  of the Fiji Wiki: Plugins>Utilities>Fiji>New Fiji Wiki Screenshot.

- The new versatile and most generic image processing library -- fully Open
  Source! -- was added (thanks Stephan Saalfeld and Stephan Preibisch).

- imglib was improved dramatically (thanks to Stephan Saalfeld, Stephan
  Preibisch, Larry Lindsey and Curtis Rueden).

- To use the imglib, just select the Imglib Plugin item of Script Editor's
  Templates menu.

- The Script Editor learnt quite a number of functions that are useful when
  developing plugins written in Java (e.g. opening the sources for a menu
  item, or opening the directory of the current file upon File>Open, or
  offering to search for the sources of a class).

- If you have an account on the Fiji Wiki, you can easily add News entries
  using the Plugins>Utilities>Fiji>New Fiji News menu item.

- There is a simple Object Inspector for Java objects now, accessible via
  fiji.debugging.Object_Inspector.openFrame(label, object).

- The MediaWikiClient is now scriptable.

- The Fiji Updater offers developers to see the plugin changes since the
  latest upload of said plugin.

- The sources for Jama are bundled now.

- Both plugins/*.jar and jars/*.jar are loaded via the FijiClassLoader now,
  which allows .jar files from jars/ to call functions in .jar files from
  plugins/ (notable exception: jars/ij.jar and jars/Fiji.jar).

- You can use the analyze-dependencies.bsh script to check dependencies
  of .jar files, reusing the functionality of the Fiji Updater's upload
  functionality.

- You can make your own "View on Fiji Development" movie, as seen on

	http://youtube.com/fijichannel

  using the combined-gource-video.bsh script (requires Gource:
  http://github.com/dscho/Gource).

- The VIB sources were moved from a submodule directly into fiji.git.

- The sources for plugins and libraries are now expected to live either in
  submodules, or in src-plugins/<name>/<package>/<class-name>.java, where
  <name> is the base name of the resulting .jar file.

- There is a command line interface to the Fiji Updater now (e.g. run
  'fiji --jar plugins/Fiji_Updater.jar --list jars/ij.jar' to find out
  the status of ij.jar).

- Fiji Build allows falling back to the updater if there is no precompiled/
  file for a not-checked-out submodule.

- The Fiji Build is more easily called via a public API now.

- Fiji now has a working implementation of a KD-Tree (thanks to Stephan
  Preibisch).

- All submodules' main branches are called 'master' now, thanks to Curtis
  Rueden.

- You can include plugins.config in src-plugins/<name>/ directly, instead of
  using staged-plugins/<name>.config.

- You may link VIB-lib.jar and APLv2-licensed code (such as commons-math)
  together now, due to a slight license change in VIB-lib.

- "git diff" shows Java method names in the hunk headers now.

- You can call "fiji --compile-and-run /path/to/class.java" now.

- You can rebuild the Windows 64-bit launcher on said platform now, using
  the mingw-w64 compiler (e.g. by running /src/mingw-w64/release-easy.sh in
  msysGit).

- There are functions in fiji.Main now to identify and recall AWT components
  by a "component path" a la "Some Dialog>Panel[2]>TextField{Name:}".

- Fiji can be asked to use the G1 garbace collector available since Java 1.6
  Update 20, via the --gc-g1 option (thanks to Albert Cardona).

- When developing a Fiji plugin in the Script Editor, one can see the diff
  and commit the changes from within the Script Editor now.

- You can open the source for a class with 'fiji --edit class:<class-name>'.

- There is a maven helper in bin/maven.sh now, you can call it from Fakefiles
  to download maven if necessary, and then run it.