[ImageJ-devel] [fiji-devel] New release: Fiji Madison

[Dan White]

:-) !!!


D


On Mar 7, 2011, at 5:36 PM, Johannes Schindelin wrote:

> Dear all!
> 
> I proudly announce a new version of Fiji (Fiji Is Just ImageJ -- batteries
> included).
> 
> So: what is Fiji? It is just a distribution of ImageJ, i.e. putting a nice
> and convenient infrastructure around ImageJ such as: automatic updates,
> extensive documentation, a powerful yet small Script Editor, reusable
> components for users and developers, bug tracking, etc.
> 
> For details and downloads, see: http://pacific.mpi-cbg.de/.
> 
> Note: if you already have a Fiji installation, you can use the Fiji
> Updater to upgrade; no need to download and install from scratch. Just
> make sure that you update just the Updater first if you have not updated
> in a long time, and update Java in the advanced mode (unless you are using
> MacOSX).
> 
> In our beloved tradition, the current version is named after the location
> of a big hackathon: Madison. It was not strictly a Fiji hackathon, but
> the first ImageJ2 hackathon, made possible by Kevin Eliceiri and Curtis
> Rueden. Nevertheless, quite some work on Fiji and its plugins got done,
> so here goes "Fiji Madison".
> 
> There have been more than 150 thousand lines added and 40 thousand removed,
> with the help of (in alphabetical order):
> 
> Albert Cardona, Benjamin Schmid, Christian Tischer, Curtis Rueden, Daniel
> James White, Daniel Sage, David Hovis, Francisco Jiménez Hernández, Gregory
> Jefferis, Ignacio Arganda Carreras, Jacques Pecreaux, Jan Eglinger, Jan
> Funke, Jean-Yves Tinevez, Johannes Schindelin, Kota Miura, Mark Longair,
> Michael Doube, Philippe Thévenaz, pogo, Robert Bryson-Richardson, Stephan
> Preibisch, Stephan Saalfeld, Tobias Pietzsch, Tom Kazimiers, Wilhelm Burger,
> Yili Zhao, and many other helpers.
> 
> Changes since Fiji Heidelberg:
> 
> New plugins
> ===========
> 
> The Time Stamper plugin was much enhanced and eventually renamed into
> Series Labeler, thanks to Daniel James White and Tom Kazimiers.
> 
> The plugin "TopoJ" was added, thanks to David Hovis.
> 
> A simple Graph Cut segmentation plugin was added, thanks to Jan Funke.
> 
> Two "Macro Examples" were added to demonstrate optical illusions which should
> convince everybody that quantitative analysis of biological images is really
> much better than looking at a red-green picture and convincing oneself that
> there might be colocalized signals. Thanks to Daniel James White and
> Gabriel Landini.
> 
> Thanks to a generous license by Michael Unser of the Biomedical Imaging Group
> at the EPFL, the Differentials plugin, MosaicJ, Philippe Thevenaz' PointPicker,
> his Shepp-Logan Phantom plugin, the StackReg plugin and the Snakuscule plugin
> and Daniel Sage's plugin "Extended Depth Field" are distributed with Fiji now.
> 
> Thanks to the generous license by Erik Meijering to distribute the source code
> for a few of his plugins with Fiji, FeatureJ, RandomJ and TransformJ are
> available in Fiji now, too.
> 
> The Linear Kuwahara plugin was contributed by Christian Tischer.
> 
> Daniel Sage's MIJ library to use Fiji/ImageJ from within Matlab is included
> with Fiji now. Just add Fiji.app/scripts/ to the search path and call 'Miji'.
> 
> Kota Miura contributed the Temporal Color Coder which makes a t-projection
> color-coding the original time points.
> 
> Bio-Format's bfopen.m was added to use Fiji's Bio-Formats from Matlab. Thanks
> to Curtis Rueden.
> 
> The new 3D Blob Segmentation plugin allows interactive 3D segmentation in
> the 3D Viewer backed by Fiji's level sets framework. Thanks to Erwin Frise,
> Albert Cardona and Benjamin Schmid.
> 
> Mark Longair contributed plugins to calculate the curvature of n-dimensional
> images, and to detect vessels according to Frangi's method.
> 
> The Correct 3D drift script registers time frames using the Stitching 3D
> plugin. Thanks to Stephan Preibisch, Robert Bryson-Richardson and Albert
> Cardona.
> 
> The Retinex plugin was added by Francisco Jiménez Hernández and Gabriel
> Landini.
> 
> There is now a plugin calculating the 'Shape Index Map', a per-pixel value
> describing the shape of the height-field corresponding to the image.
> 
> It is now possible to turn a binary image of points into a point selection,
> by starting Edit>Selection>Points from Mask.
> 
> There is now a plugin that saves the current image in EPS (Encapsulated
> PostScript) format. Thanks to Wilhelm Burger.
> 
> Use "Plugins>Transform>Panorama equirectangular view" to look at 360° panorama
> photographs and pan around. Thanks to Stephan Saalfeld.
> 
> User-visible changes
> ====================
> 
> On Linux, the Fiji launcher will run even with older setups than the launcher
> was compiled on.
> 
> The Bio-Formats plugins were updated frequently to include bug fixes and
> improvements, e.h. support for the new LSM 710 format. Thanks to the LOCI
> & Glencoe team.
> 
> The Debian packages are being rebuilt on a weekly basis now. This was a lot
> of work competently completed by Mark Longair.
> 
> In the course of Debianization, a number of licenses have been clarified.
> 
> On Linux, RAM will not be overcommitted anymore (this used to lead to serious
> paging delays in multi-user environments).
> 
> Fiji will now correctly identify 64-bit Intel CPUs on MacOSX.
> 
> The Fiji launcher accepts --edit without paths now, opening the Script Editor
> with a new, empty file.
> 
> With newer MacOSX versions, the absence of the SECURITYSESSIONID does not
> imply headless operation.
> 
> When calling Fiji from a multi-platform Fiji.app/ directory, it will not
> try to use the Java Runtime environment for another architecture.
> 
> The Fiji launcher will interpret jvm.cfg before command line options so that
> the user has a chance to override faulty settings. Thanks to Jacques Pecreaux.
> 
> On MacOSX, when the user specified "Open in 32-bit mode", Fiji will no longer
> ignore the user's wish. Thanks to Erwin Frise and Arthur Edelstein.
> 
> Since many parts of Fiji's source code rely on Java 1.6 or better now, the
> retrotranslator is activated automatically on MacOSX when only Java 1.5 or
> earlier is available. Thanks to Mark Longair.
> 
> Fiji will be able to use native libraries put into Fiji.app/lib/<platform>/.
> 
> Calling "fiji-<platform> --updater" calls a command-line version of the Fiji
> Updater; this is useful in headless setups.
> 
> Any script or macro can now live in any menu, by putting it into
> Fiji.app/plugins/Scripts/. For example, if you want to have a macro in
> File>Import, you might save it to Fiji.app/plugins/Scripts/File/Import/.
> 
> As always, Fiji was synchronized frequently with ImageJ, and a few bug fixes
> were contributed to ImageJ through Fiji. Thanks to Wayne Rasband.
> 
> Fiji's bundled Java Runtime Environment is now at version 1.6u24 (to update,
> run "Update Java" from Fiji Updater's "Advanced mode").
> 
> Too many bug fixes and improvements to count in the TrakEM2 components. Thanks
> Albert Cardona and Stephan Saalfeld.
> 
> Add the Plugins>Examples>Extended Profile Plot script to get profile plots
> of closed polygons.
> 
> Add "Scale to DPI" function to Image>Adjust menu, thanks to Curtis Rueden.
> 
> Lots of bug fixes and improvements in the 3D Viewer. To name just a few:
> orthoslice changes are now recordable, the animation axis can be specified,
> the rotation step is adjustable, import/export for .stl files was added (for
> 3D printers), the bounding box now has ticks, the transfer function is
> adjustable, single objects are auto-selected, the current image is added
> by default, ImageJ is no longer allowed to intercept key presses, multiple
> 3D Viewers can be synchronized, there is now a "Take snapshot" menu item,
> fullscreen mode, colorize meshes from given images, load/save landmarks
> for all timepoints, make color of landmarks adjustable, etc. Thanks to
> Benjamin Schmid.
> 
> The Analyze Skeleton plugin underwent many bug fixes and improvements, thanks
> to Peter C. Marks, Huub Hovens, Michael Doube and Ignacio Arganda-Carreras.
> 
> Fiji's Arrow Tool is now recordable and -- as was intended originally,
> before ImageJ grew its own version of the tool -- gave rise to a generic
> tool infrastructure allowing new tools to be developed more easily (and
> using proper Java instead of macros).
> 
> The Auto Threshold plugin supports 16-bit images now, too. This mode respects
> the true 16-bit histogram rather than taking shortcuts. While at it, the
> Huang method has been accelerated tremendously.
> 
> Scripting with the scripting languages is quicker now because ImageJ, Java
> and ImgLib classes are imported by default when running scripts from the
> Script Editor.
> 
> The Bug Submitter plugin collects more information in the bug report
> automatically, to help developers understand the environment better. Thanks
> to Mark Longair.
> 
> Some bugs were fixed with Clojure scripting, thanks to Albert Cardona.
> 
> Some errors were fixed in the Colocalisation_Analysis plugins, thanks to
> Daniel James White.
> 
> Macro recording of the Directionality plugin was fixed, thanks to Jan
> Eglinger.
> 
> Fiji's handling of Help>Refresh Menus has seen a number of bug fixes, as
> well as Fiji's headless mode (which will stop being a clever hack with
> ImageJ2, but instead be a proper solution).
> 
> For teachers' and instructors' convenience, Fiji can cache sample images
> locally, avoiding huge network traffic during courses.
> 
> When using the Recent Commands (available via the '9' key), the Recorder
> properly records which action was chosen.
> 
> In addition to macros available as menu items, scripts are also opened
> in the Script Editor rather than executed when holding down the Shift key
> prior to opening the menu. While at it, the status of the main window tells
> the user what is currently happening.
> 
> The Fiji Updater now uses the system-wide proxy settings.
> 
> By caching the checksums of the files, the Updater was speeded up dramatically.
> 
> The Updater is disabled when Fiji was installed via the Debian packages.
> 
> The Fiji Updater supports multiple Update sites now. If you have a web server
> which you can access via SSH, you can publish your own plugin suites.
> 
> The Image Expression Parser was fixed for a regression in ImageJ 1.44n and
> later, as well as two bugs related to filename detection. Thanks to Albert
> Cardona and Jean-Yves Tinevez.
> 
> The extra file type handling when opening images was fixed with regard to
> the Bio-Formats plugin. Thanks to Curtis Rueden and Gregory Jefferis.
> 
> Thanks to Albert Cardona, the Jython Interpreter now prints the last evaluated
> expression return value.
> 
> The Lasso/Blow Tool is more robust now, using the new AbstractTool framework
> (thereby avoiding timing issues due to a macro handling all the mouse input).
> 
> The Multiple Image Processor now resets Escape before starting, and it handles
> .pgm files as claimed in the documentation.
> 
> The Compile & Run command no longer needs write access to Fiji.app/plugins/,
> and it offers to unlock images when appropriate.
> 
> A bug was fixed which prevented MBF plugins from being compiled and run on
> the fly when a .java file was present in a subdirectoy of Fiji.app/plugins/.
> 
> Register>Transform Virtual Stack Slices got a checkbox to toggle interpolation.
> Thanks to Stephan Saalfeld.
> 
> The Script_Editor can export scripts bundled in .jar files for other Fiji users
> to install and run.
> 
> A couple of templates have been added to the Script Editor.
> 
> In the script editor, the font and tab size can be adjusted. Thank you, Yili
> Zhao.
> 
> The Script Editor can auto-save before compiling now. Thanks to Philippe
> Thévenaz.
> 
> The output of multiple scripts in the Script Editor is now separate; you will
> see the output only when the corresponding script's tab is active. Likewise,
> the script interpreters running the scripts are now independent of each other.
> 
> When the Script Editor is asked to open images, it lets ImageJ open them
> rather than opening gibberish in a new tab. Thanks to Thomas Julou.
> 
> The Script Editor is now usable even if the user updated ImageJ to the
> daily version. Thanks to Wayne Rasband.
> 
> The Script Editor offers to File>Open Recent. Thanks to Albert Cardona.
> 
> The startup time of the Script Editor was reduced dramatically.
> 
> In the Script Editor, File>Open will no longer offer to open .class or .jar
> files.
> 
> For interoperability, the Script Editor now enforces UTF-8 encoding for both
> reading and writing files.
> 
> When saving a new file, the Script Editor will default to the Fiji.app/
> directory. This helps when trying to save macros on MacOSX, where the Save
> Dialog does not allow switching into .app directories.
> 
> You can ask the Script Editor to wrap the lines around instead of showing
> a horizontal scrollbar. Additionally, it can label whitespace and zap gremlins,
> thanks to Albert Cardona.
> 
> The Simple Neurite Tracer can perform Sholl analysis and export the graphs as
> .svg or .csv files now. Additionally, there were many fixes and improvements,
> including an export as .swc option, or being able to select the path nearest
> to the mouse pointer with the 'g' key. Further, selecting a path in the 3D
> Viewer selects it in the Neurite Tracer, too. For convenience, there is a
> button to run Fiji's "Analyze Skeleton (2D/3D)" plugin on the paths. The
> user interface was converted to the nicer Swing look.  Thanks to Mark Longair.
> 
> The SPIM Registration can now handle multi-channel files, too. It provides
> the cosine blending option and has many more improvements. Thanks to
> Stephan Preibisch.
> 
> The Stitching plugins were speeded up, and it uses calibration info by
> default now. Thanks to Stephan Preibisch.
> 
> The Thread Killer now unlock all images, and it is more careful about
> what it offers to kill.
> 
> The Trainable Segmentation plugin can handle image stacks now. Thanks to
> Verena Kaynig, Ignacio Arganda-Carreras and Albert Cardona.
> 
> The Particle Analyzer (3D) handles the case when there are less than 3 objects
> now.
> 
> The Align image plugin uses the target image's dimensions for the result.
> 
> The Segmentation Editor can be controllable by ImageJ macros. Thanks to
> Benjamin Schmid.
> 
> When zooming in the Three Panes, the right center point is used in all panes.
> Thanks to Mark Longair.
> 
> When scripting, you can accelerate crucial parts by inserting Java code
> snippets using the new Weaver.inline(...) method in any scripting language.
> Thanks to Albert Cardona.
> 
> Several fixes and improvements in the mpicbg submodule for feature extraction
> and transformation, e.g.:  Feature matching can be performed without geometric
> consensus filter.  Geometric consensus filter got a new parameter, minimal
> absolute number of inliers.  Added robust regression outlier filter to
> TileConfiguration.  Several fixes and improvements to the CLAHE local contrast
> enhancer, e.g.: Added a fast (real-time) version of the filter.  Fixed
> selection handling.  Fixed transfer of values beyond the current min/max range.
> Support CompositeImages in variable ways.  Added homogeneous least squares fit
> for perspective transformations using Jama SVD.  Interactive transforms can
> handle Composites, Stacks and HyperStacks.  Added a simple but comparably
> fast Optic Flow variant based on the sum of square differences in a Gaussian
> weighted neighborhood of a pixel.  Thanks to Stephan Saalfeld.
> 
> 
> Developer-visible changes
> =========================
> 
> There have been quite a few cleanups of the project structure; the sources
> for plugins and libraries which are not contained in submodules are supposed
> to live in src-plugins/<jarname>/<package>/<classname>.java, where <jarname>
> is the base name of the generated .jar file.
> 
> There is now a script to compile and cross-compile ITK.
> 
> JNA was extracted from Jython and JRuby so that a newer jna.jar can be used
> without being shadowed by Jython's or JRuby's idea of JNA.
> 
> There is a helper now to compile a few ImageJ versions.
> 
> We have helper scripts to build cross-compilers on Linux 64-bit to target
> win32, win64, MacOSX (32-bit and 64-bit Intel, 32-bit PowerPC).
> 
> There is a Fiji launcher for MacOSX PowerPC again, sadly not met with any
> feedback from the complaining person, let alone positive one.
> 
> We have a script now to generate Eclipse, Netbeans and IntelliJ projects
> from the master Fakefile.
> 
> FreeBSD is supported for developers, for now.
> 
> There is a fall-back shell script -- fiji-other.sh -- for otherwise
> unsupported platforms.
> 
> The get-sample-images script supports headless operations now.
> 
> To prevent long waiting times with "git status" when a number of submodules
> are checked out, gitignore-in-submodules now understands an 'ignoredirty'
> subcommand.
> 
> bin/identify-commit.py can be used on the precompiled Fiji launchers, too.
> 
> In developer mode, the Updater's "Show changes" also lists changes for
> the Fiji launchers and the .jar file's manifest.
> 
> When samples/ is present, it is included in generated Fiji.app bundles.
> 
> A convenience script was added to use Maven.
> 
> There is a helper now to find all dependencees (even transitive ones) of
> a given .jar file.
> 
> The nightly build generates a stable WebStart (reflecting the current version
> according to the Fiji Updater) and the PluginList on the Wiki.
> 
> A simple script to reverse the page order of a .pdf file was added, as an
> example how to use iText.
> 
> The helper script bin/ready-for-upload.bsh can determine whether all
> prerequisite steps prior to uploading have been completed.
> 
> The commons-math library from the Apache project is now available.
> 
> Fiji Build can now build JNI-backed plugins; just add .c or .cxx files to
> a .jar rule, and a shared library of the same name as the .jar file will
> be generated from the native sources. Use fiji.JNI.loadLibrary("<name>") to
> load the shared library.
> 
> Upgrade jfreechart to 1.0.13 (from 1.0.9).
> 
> Update JNA to version 3.2.7.
> 
> Fiji contains a base class fiji.tool.AbstractTool which makes it easy to add
> tools to the toolbar that are not backed by polling macros, but by a proper
> event-driven Java class.
> 
> To generate tool icons from 16x16 pictures, use Plugins>Examples>Image To
> Tool Icon.
> 
> The Auto Threshold plugin has an API usable by developers of other plugins
> now.
> 
> The Fiji Build system handles rules involving Jython or Beanshell more
> efficiently now. It avoids to include unwanted files such as .DS_Store into
> .jar targets. The code uses generics now, and is more accessible to scripts
> and plugins. Fiji Build can use multiple CPU cores simultaneously now.
> A target can be force-rebuilt by appending "-rebuild" to the parameter.
> Building rules depending on Java3D is now possible even on MacOSX.
> Thanks to Mark Longair, Jacques Pecreaux and Curtis Rueden.
> 
> There is an easy way for developers to run external programs now:
> fiji.SimpleExecuter. This class offers a number of convenience functions
> to execute programs with specified parameters in a given working directory,
> and it offers several modes how the output should be handled: print to
> ImageJ's Log window, print to a stream, or save into Strings.
> 
> For Fiji Developer, adding documentation to the Fiji Wiki has been made
> even more convenient with enhancements to Plugins>Utilities>Fiji>New Fiji
> Tutorial and New Fiji Wiki Screenshot in the same menu.
> 
> The file and directory fields in the GenericDialogPlus class have been
> improved, and the methods addImageChoice() and getNextImage() have been
> added.
> 
> fiji-lib now offers a class to split command lines and macro option strings,
> and a TicToc helper for simple performance benchmarking.
> 
> If you want to add functionality similar to ImageJ's Command Finder to your
> own code, you can use fiji.util.gui.CommandFinderBase. If you have a JMenuBar
> you want to make accessible, you can use the JFrameCommandFinder class in
> the same package straight away. Thanks to Benjamin Schmid.
> 
> When looking at a specific file and number in a developer checkout of Fiji,
> the Script Editor offers to open that particular location via gitweb in
> the web browser (this helps collaboration via IRC, for example).
> 
> The submodules have been moved into the modules/ directory.
> 
> You can use the short-cut URL http://pacific.mpi-cbg.de/<filename> for
> source files in Fiji's Git-managed repositories.
> 
> Added IntegralImages as library components to the mpicbg submodule for
> rapid box-filter operations (mean, scale, difference of mean, ...).  Thanks
> to Stephan Saalfeld.
> 
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> 

Dr. Daniel James White BSc. (Hons.) PhD
Senior Microscopist / Image Processing and Analysis
Light Microscopy Facility
Max Planck Institute of Molecular Cell Biology and Genetics
Pfotenhauerstrasse 108
01307 DRESDEN
Germany

+49 (0)15114966933 (German Mobile)
+49  (0)351 210 2627 (Work phone at MPI-CBG)
+49  (0)351 210 1078 (Fax MPI-CBG LMF)

http://www.bioimagexd.net		BioImageXD
http://pacific.mpi-cbg.de		Fiji (is just ImageJ - batteries included)
http://www.chalkie.org.uk
dan at chalkie.org.uk
( white at mpi-cbg.de )