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.gitattributes//from w  w  w . j a  v  a  2s  .c  o  m
.gitignore
.gitmodules
.mailmap
Build.sh
Contents/Info.plist
Contents/Resources/Fiji.icns
LICENSES
Makefile
README.md
bin/.gitignore
bin/ImageJ.sh
bin/analyze-dependencies.bsh
bin/build-itk.sh
bin/build-last-imagej-versions.sh
bin/build-launcher.sh
bin/build-retrotranslator.sh
bin/calculate-checksums.bsh
bin/check-class-version.sh
bin/checkout-jdk.py
bin/cleanup.sh
bin/combined-gource-video.bsh
bin/commit-for-jar.bsh
bin/commit-plugin.py
bin/commit-submodule.py
bin/compat.py
bin/compat_jython.py
bin/configure-submodule.py
bin/copy-file.bsh
bin/create-jnlp.sh
bin/deserialize.bsh
bin/download-launchers.sh
bin/eclipse-project-generator.bsh
bin/enumerate-java-package.bsh
bin/find-jar-for-class.bsh
bin/find-package-directory-mismatches.py
bin/fix-java6-classes.sh
bin/force-glibc-compat.sh
bin/generate-download-arrow.py
bin/generate-fiji-images.py
bin/generate-finder-background.py
bin/generate-finder-dsstore.perl
bin/get-sample-images.py
bin/gitignore-in-submodules.sh
bin/googlecode_upload.py
bin/grant-all.py
bin/iconv.py
bin/identify-commit.py
bin/imagej-rootbeer.sh
bin/install-java3d.sh
bin/intellij-project-generator.bsh
bin/list-main-classes.bsh
bin/log-plugin-commits.bsh
bin/make-7z.py
bin/make-app.py
bin/make-dmg.py
bin/make-ij1-ico.bsh
bin/make-tar.py
bin/make-zip.py
bin/mark-exes-as-executable.sh
bin/maven.sh
bin/mpicbg-dependencees.bsh
bin/netbeans-project-generator.bsh
bin/open-in-gitweb.sh
bin/pdf-concat.py
bin/pdf-extract-images.py
bin/pdf-recompress.bsh
bin/pdf-reverse-pages.bsh
bin/pdf-rotate.py
bin/plugin-documentation-list.py
bin/plugin-list-parser.py
bin/pomize-project.bsh
bin/prepare-wiki-screenshot.py
bin/projects-generator.bsh
bin/ready-for-upload.bsh
bin/recalculate-dependencies.py
bin/renaming-merge.sh
bin/screenshot.py
bin/signJars.sh
bin/start-windows-jenkins-slave.sh
bin/summarize-git-log.sh
bin/synchronize-db.xml.gz.py
bin/tar2fiji.dmg.sh
bin/testcharsets.sh
bin/tijmp-build.sh
bin/topic-branches.sh
bin/up-to-date-check.py
bin/update-fiji.py
bin/update-launcher.sh
bin/updater-fix.js
bin/updater-jar-urls.bsh
bin/upload-bf4.sh
bin/upload-bf5.sh
bin/upload-mirrors.sh
bin/upload-to-googlecode.sh
bin/upload-update-site.sh
bin/verify-fiji.sc.sh
bin/which-jar-has-plugin.py
bin/wiki-monitor.py
bin/write-headless-jar.bsh
debian/.gitignore
debian/README.Debian
debian/README.plugins
debian/TODO
debian/build-command
debian/build-dependencies
debian/build-in-i386-chroot.py
debian/changelog
debian/common.py
debian/compat
debian/complete-build
debian/control
debian/control.template
debian/copyright
debian/create-i386-chroot.py
debian/dirs
debian/docs
debian/etc-default-fiji
debian/fiji-autocomplete.copyright
debian/fiji-barthel-plugins.copyright
debian/fiji-base.copyright
debian/fiji-bunwarpj.copyright
debian/fiji-color-histogram.copyright
debian/fiji-db-registration.copyright
debian/fiji-default.ex
debian/fiji-doc.docs
debian/fiji-doc.install
debian/fiji-edu-mines-jtk.copyright
debian/fiji-ij-imageio.copyright
debian/fiji-image5d.copyright
debian/fiji-imagej.copyright
debian/fiji-imglib.copyright
debian/fiji-io.copyright
debian/fiji-jpedal.copyright
debian/fiji-jruby.copyright
debian/fiji-jython.copyright
debian/fiji-loci-tools.copyright
debian/fiji-lsm-reader.copyright
debian/fiji-lsm-toolbox.copyright
debian/fiji-mip.copyright
debian/fiji-mpicbg.copyright
debian/fiji-mtrack2.copyright
debian/fiji-plugins.copyright
debian/fiji-rsyntaxtextarea.copyright
debian/fiji-scripting.copyright
debian/fiji-tcljava.copyright
debian/fiji-tracer.README.Debian
debian/fiji-tracer.copyright
debian/fiji-trakem2.copyright
debian/fiji-vib.copyright
debian/fiji-view5d.copyright
debian/fiji-weka.copyright
debian/fiji.1
debian/fiji.copyright
debian/fiji.desktop
debian/fiji.doc-base.EX
debian/fiji.manpages
debian/fiji.menu
debian/find-non-fiji-jars.py
debian/generate-debian-fiji-plugins-copyright.sh
debian/java-home
debian/mapping.json
debian/package-extras/default-description
debian/package-extras/fiji-autocomplete/description
debian/package-extras/fiji-barthel-plugins/description
debian/package-extras/fiji-base/description
debian/package-extras/fiji-bunwarpj/description
debian/package-extras/fiji-color-histogram/description
debian/package-extras/fiji-default.ex/description
debian/package-extras/fiji-doc.docs/description
debian/package-extras/fiji-doc.install/description
debian/package-extras/fiji-edu-mines-jtk/description
debian/package-extras/fiji-examples/description
debian/package-extras/fiji-ij-imageio/description
debian/package-extras/fiji-imagej/description
debian/package-extras/fiji-imglib/description
debian/package-extras/fiji-io/description
debian/package-extras/fiji-jai/description
debian/package-extras/fiji-jpedal/description
debian/package-extras/fiji-jruby/description
debian/package-extras/fiji-loci-tools/description
debian/package-extras/fiji-lsm-reader/description
debian/package-extras/fiji-lsm-toolbox/description
debian/package-extras/fiji-luts/description
debian/package-extras/fiji-mip/description
debian/package-extras/fiji-mpicbg/description
debian/package-extras/fiji-mtrack2/description
debian/package-extras/fiji-plugins/description
debian/package-extras/fiji-rsyntaxtextarea/description
debian/package-extras/fiji-scripting/description
debian/package-extras/fiji-tcljava/description
debian/package-extras/fiji-trakem2/description
debian/package-extras/fiji-vib/description
debian/package-extras/fiji-view5d/description
debian/package-extras/fiji-zs/description
debian/package-extras/fiji/description
debian/postinst.ex
debian/postrm.ex
debian/preinst.ex
debian/prerm.ex
debian/rewrite-pom-files.py
debian/rules
debian/simple-launcher
debian/update-debian.py
debian/upload-to-pacific.py
debian/watch.ex
debian/weekly-build.sh
images/fiji-logo-1.0-128x128.png
images/fiji-logo-1.0-256x256.png
images/fiji-logo-1.0.svg
images/fiji-logo-16x16.xpm
images/fiji-logo-32x32-b.xpm
images/fiji-logo-32x32.xpm
images/fiji.ico
images/function.png
images/icon-flat.png
images/icon.png
images/ij1.ico
images/var.png
includes/jni.h
includes/jni_md.h
jars/.gitignore
luts/16_colors.lut
luts/5_ramps.lut
luts/6_shades.lut
luts/Cyan Hot.lut
luts/Green Fire Blue.lut
luts/HiLo.lut
luts/ICA.lut
luts/ICA2.lut
luts/ICA3.lut
luts/Magenta Hot.lut
luts/Orange Hot.lut
luts/README.txt
luts/Rainbow RGB.lut
luts/Red Hot.lut
luts/Thermal.lut
luts/Yellow Hot.lut
luts/blue_orange_icb.lut
luts/brgbcmyw.lut
luts/cool.lut
luts/edges.lut
luts/gem.lut
luts/glasbey.lut
luts/glow.lut
luts/phase.lut
luts/physics.lut
luts/royal.lut
luts/sepia.lut
luts/smart.lut
luts/thal.lut
luts/thallium.lut
luts/unionjack.lut
macros/ImportResultsTable.txt
macros/StartupMacros.fiji.ijm
macros/listManagement.txt
macros/toolsets/Clear Custom Tools.txt
macros/toolsets/Drawing Tools.txt
macros/toolsets/Lookup Tables.txt
modules/pom.xml
native/FFMPEG_IO/.gitignore
native/FFMPEG_IO/ffmpeg/pom.xml
native/FFMPEG_IO/ffmpeg/src/main/java/fiji/ffmpeg/CompileFFMPEG.java
native/FFMPEG_IO/ffmpeg/src/main/java/fiji/ffmpeg/GenerateFFMPEGClasses.java
native/FFMPEG_IO/ffmpeg/src/other/c/avlog.c
native/FFMPEG_IO/plugin/pom.xml
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/Exporter.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/FFMPEG.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/FFMPEGSingle.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/IJProgress.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/IO.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/Importer.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/JNALibraryLoader.java
native/FFMPEG_IO/plugin/src/main/java/fiji/ffmpeg/Progress.java
native/FFMPEG_IO/plugin/src/main/resources/plugins.config
native/FFMPEG_IO/plugin/src/test/java/fiji/ffmpeg/FFMPEG_IO_Test.java
native/FFMPEG_IO/pom.xml
native/JNI_Example/.gitignore
native/JNI_Example/pom.xml
native/JNI_Example/src/main/c/JNI_Example.c
native/JNI_Example/src/main/java/JNI_Example.java
native/JNI_Example/src/main/resources/plugins.config
plugins/Analyze/Dynamic_ROI_Profiler.clj
plugins/Analyze/Measure_RGB.txt
plugins/Examples/Add_Popup_Split_Channels.bsh
plugins/Examples/Anaglyph_for_Red_Cyan_glasses.rb
plugins/Examples/Blobs_Demo_in_Ruby.rb
plugins/Examples/Command_Launchers/Command_Launcher_BeanShell.bsh
plugins/Examples/Command_Launchers/Command_Launcher_Clojure.clj
plugins/Examples/Command_Launchers/Command_Launcher_Javascript.js
plugins/Examples/Command_Launchers/Command_Launcher_Python.py
plugins/Examples/Command_Launchers/Command_Launcher_Ruby.rb
plugins/Examples/CoverMaker/Cover_Maker.py
plugins/Examples/CoverMaker/Prepare_Cover_Maker_Database.py
plugins/Examples/Delayed_Snapshot.py
plugins/Examples/Delayed_Snapshot_Window.bsh
plugins/Examples/Edit_LUT_As_Text.py
plugins/Examples/Extended_Profile_Plot.bsh
plugins/Examples/Fiji_Cube.ijm
plugins/Examples/Fiji_Logo_3D.js
plugins/Examples/Find_Dimension_of_Raw_Image.py
plugins/Examples/Image_To_Tool_Icon.bsh
plugins/Examples/Multithreaded_Image_Processing.clj
plugins/Examples/Multithreaded_Image_Processing_in_Javascript.js
plugins/Examples/Plasma_Cloud.rb
plugins/Examples/Same_Slice_in_Multiple_Images.rb
plugins/Examples/Scala_Test.scala
plugins/Examples/The_Hue_Game.bsh
plugins/Examples/TrakEM2_Add_Balls.java
plugins/Examples/TrakEM2_Example_Scripts/Homogenize_Ball_Radius.py
plugins/Examples/TrakEM2_Example_Scripts/Measure_AreaLists.py
plugins/Examples/TrakEM2_Example_Scripts/T2_Select_All.py
plugins/Examples/TrakEM2_Example_Scripts/T2_set_all_transforms_to_identity.py
plugins/Examples/TrakEM2_Example_Scripts/extract_stack_under_arealist.py
plugins/Examples/blend_two_images.clj
plugins/Examples/celsius_to_fahrenheit.clj
plugins/Examples/chess_.py
plugins/Examples/compose_rgb-stacks.bsh
plugins/Examples/downsample_.js
plugins/Examples/list_all_threads.py
plugins/Examples/random_noise_example.clj
plugins/JRuby/imagej.rb
plugins/Macros/About Plugin Macros
plugins/Macros/About_Plugin_Macros.txt
plugins/Macros/Bulls_Eye.txt
plugins/Macros/Polygon_.txt
plugins/Macros/RGB_Histogram.txt
plugins/Macros/batch_convert_any_to_tif.txt
plugins/Scripts/File/Make_Screencast.bsh
plugins/Scripts/File/Open_Samples/Adelsons_Squares.ijm
plugins/Scripts/File/Open_Samples/Spirals_.ijm
plugins/Scripts/Image/Adjust/Scale_to_DPI.js
plugins/Scripts/Image/Color/Set_Color_By_Wavelength.ijm
plugins/Scripts/Image/Hyperstacks/Temporal-Color_Code.ijm
plugins/Scripts/Plugins/Registration/Correct_3D_drift.py
plugins/Scripts/Plugins/Utilities/Create_Desktop_Icon.bsh
plugins/Scripts/Plugins/Utilities/Find_Jar_For_Class.bsh
plugins/Scripts/Plugins/Utilities/Fix_Updater.js
plugins/Scripts/Plugins/Utilities/Record_Desktop.py
plugins/Scripts/Plugins/Utilities/Record_Window.py
plugins/Utilities/Close_All_Without_Saving.txt
pom.xml
resources/.gitignore
resources/ImageJ.png
resources/download-arrow.svg
resources/download_button2.svg
retro/ASM-LICENSE.txt
retro/LICENSE.txt
retro/backport-util-concurrent-3.1.jar
retro/readme.html
retro/retrotranslator-runtime-1.2.9.jar
retro/retrotranslator-transformer-1.2.9.jar
scripts/InstallJava3D.m
scripts/IsJava3DInstalled.m
scripts/Matlab3DViewerDemo_1.m
scripts/Matlab3DViewerDemo_2.m
scripts/Matlab3DViewerDemo_3.m
scripts/Matlab3DViewerIntroduction.m
scripts/Miji.m
scripts/Miji_Test.m
scripts/bfopen.m
scripts/copytoImg.m
scripts/copytoImgPlus.m
scripts/copytoMatlab.m
scripts/importTrackMateTracks.m
src-plugins/3D_Blob_Segmentation/.factorypath
src-plugins/3D_Blob_Segmentation/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/3D_Blob_Segmentation/pom.xml
src-plugins/3D_Blob_Segmentation/src/main/java/ij3d/segmentation/Blob_Segmentation_in_3D.java
src-plugins/3D_Blob_Segmentation/src/main/resources/plugins.config
src-plugins/3D_Objects_Counter/.factorypath
src-plugins/3D_Objects_Counter/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/3D_Objects_Counter/pom.xml
src-plugins/3D_Objects_Counter/src/main/java/Utilities/Counter3D.java
src-plugins/3D_Objects_Counter/src/main/java/Utilities/Object3D.java
src-plugins/3D_Objects_Counter/src/main/java/_3D_OC_Options.java
src-plugins/3D_Objects_Counter/src/main/java/_3D_objects_counter.java
src-plugins/3D_Objects_Counter/src/main/resources/plugins.config
src-plugins/3D_Viewer/.factorypath
src-plugins/3D_Viewer/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/3D_Viewer/CHANGES
src-plugins/3D_Viewer/createAPIDocs.sh
src-plugins/3D_Viewer/createJar.sh
src-plugins/3D_Viewer/customnode/TestDynamicLineMesh.py
src-plugins/3D_Viewer/pom.xml
src-plugins/3D_Viewer/src/main/java/ImageJ_3D_Viewer.java
src-plugins/3D_Viewer/src/main/java/customnode/Box.java
src-plugins/3D_Viewer/src/main/java/customnode/Cone.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomIndexedTriangleMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomLineMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomMeshNode.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomMultiMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomPointMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomQuadMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomTransparentTriangleMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/CustomTriangleMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/EdgeContraction.java
src-plugins/3D_Viewer/src/main/java/customnode/FullInfoMesh.java
src-plugins/3D_Viewer/src/main/java/customnode/MeshLoader.java
src-plugins/3D_Viewer/src/main/java/customnode/MeshMaker.java
src-plugins/3D_Viewer/src/main/java/customnode/Mesh_Maker.java
src-plugins/3D_Viewer/src/main/java/customnode/Primitive.java
src-plugins/3D_Viewer/src/main/java/customnode/STLLoader.java
src-plugins/3D_Viewer/src/main/java/customnode/Sphere.java
src-plugins/3D_Viewer/src/main/java/customnode/Tube.java
src-plugins/3D_Viewer/src/main/java/customnode/WavefrontExporter.java
src-plugins/3D_Viewer/src/main/java/customnode/WavefrontLoader.java
src-plugins/3D_Viewer/src/main/java/customnode/u3d/BitStreamRead.java
src-plugins/3D_Viewer/src/main/java/customnode/u3d/BitStreamWrite.java
src-plugins/3D_Viewer/src/main/java/customnode/u3d/Constants.java
src-plugins/3D_Viewer/src/main/java/customnode/u3d/ContextManager.java
src-plugins/3D_Viewer/src/main/java/customnode/u3d/DataBlock.java
src-plugins/3D_Viewer/src/main/java/customnode/u3d/U3DExporter.java
src-plugins/3D_Viewer/src/main/java/ij3d/AxisConstants.java
src-plugins/3D_Viewer/src/main/java/ij3d/ColorTable.java
src-plugins/3D_Viewer/src/main/java/ij3d/Content.java
src-plugins/3D_Viewer/src/main/java/ij3d/ContentConstants.java
src-plugins/3D_Viewer/src/main/java/ij3d/ContentCreator.java
src-plugins/3D_Viewer/src/main/java/ij3d/ContentInstant.java
src-plugins/3D_Viewer/src/main/java/ij3d/ContentNode.java
src-plugins/3D_Viewer/src/main/java/ij3d/DefaultAnimatableUniverse.java
src-plugins/3D_Viewer/src/main/java/ij3d/DefaultUniverse.java
src-plugins/3D_Viewer/src/main/java/ij3d/Executer.java
src-plugins/3D_Viewer/src/main/java/ij3d/IJAdapter.java
src-plugins/3D_Viewer/src/main/java/ij3d/Image3DMenubar.java
src-plugins/3D_Viewer/src/main/java/ij3d/Image3DUniverse.java
src-plugins/3D_Viewer/src/main/java/ij3d/ImageCanvas3D.java
src-plugins/3D_Viewer/src/main/java/ij3d/ImageJ3DViewer.java
src-plugins/3D_Viewer/src/main/java/ij3d/ImageWindow3D.java
src-plugins/3D_Viewer/src/main/java/ij3d/ImgLibVolume.java
src-plugins/3D_Viewer/src/main/java/ij3d/Install_J3D.java
src-plugins/3D_Viewer/src/main/java/ij3d/MeshMaker.java
src-plugins/3D_Viewer/src/main/java/ij3d/Mesh_Maker.java
src-plugins/3D_Viewer/src/main/java/ij3d/NoopAdapter.java
src-plugins/3D_Viewer/src/main/java/ij3d/Pipe.java
src-plugins/3D_Viewer/src/main/java/ij3d/RegistrationMenubar.java
src-plugins/3D_Viewer/src/main/java/ij3d/SaveSession.java
src-plugins/3D_Viewer/src/main/java/ij3d/ScenegraphDebugger.java
src-plugins/3D_Viewer/src/main/java/ij3d/Test_Single_Voxel.java
src-plugins/3D_Viewer/src/main/java/ij3d/TimelapseListener.java
src-plugins/3D_Viewer/src/main/java/ij3d/UIAdapter.java
src-plugins/3D_Viewer/src/main/java/ij3d/UniverseListener.java
src-plugins/3D_Viewer/src/main/java/ij3d/UniverseSettings.java
src-plugins/3D_Viewer/src/main/java/ij3d/UniverseSynchronizer.java
src-plugins/3D_Viewer/src/main/java/ij3d/Utils.java
src-plugins/3D_Viewer/src/main/java/ij3d/Vector3.java
src-plugins/3D_Viewer/src/main/java/ij3d/VectorString3D.java
src-plugins/3D_Viewer/src/main/java/ij3d/ViewAdjuster.java
src-plugins/3D_Viewer/src/main/java/ij3d/Volume.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/BehaviorCallback.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/ContentTransformer.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/InteractiveBehavior.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/InteractiveViewPlatformTransformer.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/Picker.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/ViewPlatformTransformer.java
src-plugins/3D_Viewer/src/main/java/ij3d/behaviors/WaitForNextFrameBehavior.java
src-plugins/3D_Viewer/src/main/java/ij3d/contextmenu/ContextMenu.java
src-plugins/3D_Viewer/src/main/java/ij3d/gui/ContentCreatorDialog.java
src-plugins/3D_Viewer/src/main/java/ij3d/gui/InteractiveMeshDecimation.java
src-plugins/3D_Viewer/src/main/java/ij3d/gui/InteractiveTransformDialog.java
src-plugins/3D_Viewer/src/main/java/ij3d/gui/LUTDialog.java
src-plugins/3D_Viewer/src/main/java/ij3d/gui/PrimitiveDialogs.java
src-plugins/3D_Viewer/src/main/java/ij3d/pointlist/PointListDialog.java
src-plugins/3D_Viewer/src/main/java/ij3d/pointlist/PointListPanel.java
src-plugins/3D_Viewer/src/main/java/ij3d/pointlist/PointListShape.java
src-plugins/3D_Viewer/src/main/java/ij3d/shapes/BoundingBox.java
src-plugins/3D_Viewer/src/main/java/ij3d/shapes/BoundingSphere.java
src-plugins/3D_Viewer/src/main/java/ij3d/shapes/CoordinateSystem.java
src-plugins/3D_Viewer/src/main/java/ij3d/shapes/Scalebar.java
src-plugins/3D_Viewer/src/main/java/ij3d/shortcuts/ShortCutDialog.java
src-plugins/3D_Viewer/src/main/java/ij3d/shortcuts/ShortCutTable.java
src-plugins/3D_Viewer/src/main/java/ij3d/shortcuts/ShortCuts.java
src-plugins/3D_Viewer/src/main/java/isosurface/AmiraSurface.java
src-plugins/3D_Viewer/src/main/java/isosurface/MeshEditor.java
src-plugins/3D_Viewer/src/main/java/isosurface/MeshExporter.java
src-plugins/3D_Viewer/src/main/java/isosurface/MeshGroup.java
src-plugins/3D_Viewer/src/main/java/isosurface/MeshProperties.java
src-plugins/3D_Viewer/src/main/java/isosurface/Show_Colour_Surfaces.java
src-plugins/3D_Viewer/src/main/java/isosurface/SmoothControl.java
src-plugins/3D_Viewer/src/main/java/isosurface/Triangulator.java
src-plugins/3D_Viewer/src/main/java/marchingcubes/MCCube.java
src-plugins/3D_Viewer/src/main/java/marchingcubes/MCTriangulator.java
src-plugins/3D_Viewer/src/main/java/octree/AppearanceCreator.java
src-plugins/3D_Viewer/src/main/java/octree/Cube.java
src-plugins/3D_Viewer/src/main/java/octree/CubeData.java
src-plugins/3D_Viewer/src/main/java/octree/FilePreparer.java
src-plugins/3D_Viewer/src/main/java/octree/GeometryCreator.java
src-plugins/3D_Viewer/src/main/java/octree/OctreeDialog.java
src-plugins/3D_Viewer/src/main/java/octree/ShapeGroup.java
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src-plugins/Feature_Detection/src/main/java/fiji/features/MultiTaskProgress.java
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src-plugins/Fiji_Archipelago/.factorypath
src-plugins/Fiji_Archipelago/pom.xml
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/Cluster.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/FijiArchipelago.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/Fiji_Archipelago.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/compute/ArchipelagoFuture.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/compute/ProcessManager.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/compute/QuickCallable.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/compute/QuickRunnable.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/compute/SerializableCallable.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/data/ClusterMessage.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/data/DataChunk.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/data/Duplex.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/data/FileChunk.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/data/HeartBeat.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/data/SimpleChunk.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/example/Cluster_SIFT.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/example/Equality_Example.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/example/Test_Cluster.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/exception/ShellExecutionException.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/ClusterStateListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/MessageListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/MessageType.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/NodeShellListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/NodeStateListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/ProcessListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/QueueListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/TransceiverExceptionListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/listen/TransceiverListener.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/MessageXC.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/client/ArchipelagoClient.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/node/ClusterNode.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/node/ClusterNodeState.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/node/NodeManager.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/server/ArchipelagoServer.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/shell/NodeShell.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/shell/NodeShellParameters.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/shell/SSHNodeShell.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/shell/SocketNodeShell.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/shell/ssh/JSchUtility.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/network/shell/ssh/NodeShellUserInfo.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/ui/ArchipelagoUI.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/ui/ClusterNodeStatusUI.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/ui/ClusterUI.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/ui/ClusterXML.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/ui/NodeConfigurationUI.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/ui/RootNodeConfigDialog.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/EasyLogger.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/IJLogger.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/IJPopupLogger.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/InputStreamLogger.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/NullLogger.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/PrintStreamLogger.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/ProcessManagerCoreComparator.java
src-plugins/Fiji_Archipelago/src/main/java/edu/utexas/clm/archipelago/util/XCErrorAdapter.java
src-plugins/Fiji_Archipelago/src/main/resources/plugins.config
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src-plugins/Fiji_Developer/pom.xml
src-plugins/Fiji_Developer/src/main/java/fiji/GraphicalMediaWikiClient.java
src-plugins/Fiji_Developer/src/main/java/fiji/MediaWikiClient.java
src-plugins/Fiji_Developer/src/main/java/fiji/Prettify_Wiki_Screenshot.java
src-plugins/Fiji_Developer/src/main/java/fiji/Upload_Image_To_Wiki.java
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src-plugins/Fiji_Package_Maker/pom.xml
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src-plugins/Fiji_Package_Maker/src/main/java/fiji/packaging/Packager.java
src-plugins/Fiji_Package_Maker/src/main/java/fiji/packaging/TarBz2Packager.java
src-plugins/Fiji_Package_Maker/src/main/java/fiji/packaging/TarGzPackager.java
src-plugins/Fiji_Package_Maker/src/main/java/fiji/packaging/TarPackager.java
src-plugins/Fiji_Package_Maker/src/main/java/fiji/packaging/ZipPackager.java
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src-plugins/Fiji_Plugins/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/Fiji_Plugins/build.xml
src-plugins/Fiji_Plugins/pom.xml
src-plugins/Fiji_Plugins/src/main/java/Retinex_.java
src-plugins/Fiji_Plugins/src/main/java/fiji/color/Convert_Red_To_Magenta.java
src-plugins/Fiji_Plugins/src/main/java/fiji/color/Convert_Red_To_Magenta_Clipboard.java
src-plugins/Fiji_Plugins/src/main/java/fiji/denoise/ROF_Denoise.java
src-plugins/Fiji_Plugins/src/main/java/fiji/drawing/Linear_Gradient.java
src-plugins/Fiji_Plugins/src/main/java/fiji/drawing/Radial_Gradient.java
src-plugins/Fiji_Plugins/src/main/java/fiji/geom/AreaCalculations.java
src-plugins/Fiji_Plugins/src/main/java/fiji/geom/Shape_Index_Map.java
src-plugins/Fiji_Plugins/src/main/java/fiji/help/Context_Help.java
src-plugins/Fiji_Plugins/src/main/java/fiji/process3d/EDT.java
src-plugins/Fiji_Plugins/src/main/java/fiji/process3d/SEDT.java
src-plugins/Fiji_Plugins/src/main/java/fiji/selection/Binary_to_Point_Selection.java
src-plugins/Fiji_Plugins/src/main/java/fiji/selection/Rounded_Rectangle.java
src-plugins/Fiji_Plugins/src/main/java/fiji/selection/Select_Bounding_Box.java
src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/CompositeConverter2.java
src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Dynamic_Reslice.java
src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Hyperstack_rearranger.java
src-plugins/Fiji_Plugins/src/main/java/fiji/stacks/Radial_Reslice.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/Circle_Fitter.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/CurrentSlice.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/DistanceComparator.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/Fiji_Uploader.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/KDTree.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/NNearestNeighborSearch.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/NearestNeighborSearch.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/RadiusNeighborSearch.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/Recent_Commands.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/RedirectErrAndOut.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/TestKDTree.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/node/Leaf.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/node/Node.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/node/NonLeaf.java
src-plugins/Fiji_Plugins/src/main/java/fiji/util/node/SimpleNode.java
src-plugins/Fiji_Plugins/src/main/resources/plugins.config
src-plugins/Fiji_Plugins/test/Script_dynamic_reslice.py
src-plugins/Fiji_Updater/.factorypath
src-plugins/Fiji_Updater/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/Fiji_Updater/fiji/updater/TODO
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src-plugins/Fiji_Updater/src/main/java/fiji/updater/Adapter.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/Bootstrap.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/ImageJ1UI.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/Main.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/StderrUI.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/UI.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/Updater.java
src-plugins/Fiji_Updater/src/main/java/fiji/updater/UptodateCheck.java
src-plugins/Fiji_Updater/src/main/resources/plugins.config
src-plugins/FlowJ_/.factorypath
src-plugins/FlowJ_/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/FlowJ_/pom.xml
src-plugins/FlowJ_/src/main/java/FlowJ/Demodulation.java
src-plugins/FlowJ_/src/main/java/FlowJ/Flow3JColorNoiseMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/Flow3JDynamicColorMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJColorNoiseMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJDisplay.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJDynamicColor.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJDynamicColorMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJError.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJException.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJFleet.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJFlow.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJLucas.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJQuiverMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJSingh.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJSpotNoise.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJSpotNoiseMapper.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJUras.java
src-plugins/FlowJ_/src/main/java/FlowJ/FlowJUserInterface.java
src-plugins/FlowJ_/src/main/java/FlowJ/SSD.java
src-plugins/FlowJ_/src/main/java/FlowJ_.java
src-plugins/FlowJ_/src/main/java/SurfaceJ_.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJAlphaColor.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJBackprojection.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJBinaryShell.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJCell.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifier.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierGradientCT.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierInteger.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierIsosurface.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierIsosurfaceGrayscale.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierLNoIndex.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierLNotIndex0.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierLevoy.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierLevoyCueing.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierLinear.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierRGB.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifierValue.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJClassifiers.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJCutout.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJGradient.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJInterpolator.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJIsosurfaceRender.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJLight.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJMatrix.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJNearestNeighbor.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJOutlineShader.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJPhongShader.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJPlane.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJProjection.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJReconstructor.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRender.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRenderView.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRenderViewCine.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRenderViewInteractive.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRenderViewSingle.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRenderViewStereo.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJRenderer.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJShade.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJShader.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJShape.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJSplineInterpolator.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJSurfaceJ.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJSurfacePlotShell.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJThresholdedVolume.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJTrilinear.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJUserInterface.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJValue.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJValueHSB.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJViewerCanvas.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJViewspaceRender.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJViewspaceUtil.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJVoxelLoc.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJZBuffer.java
src-plugins/FlowJ_/src/main/java/VolumeJ/VJrgbValue.java
src-plugins/FlowJ_/src/main/java/VolumeJ_.java
src-plugins/FlowJ_/src/main/java/Volume_Reconstructor_.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJJacobi.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJShortMatrix.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJfft.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJfht.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJfit.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJfunctions.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJgifa.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJknn.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJmatrix.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJmi.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJpca.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJpowell.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJstats.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJtransform.java
src-plugins/FlowJ_/src/main/java/bijnum/BIJutil.java
src-plugins/FlowJ_/src/main/java/bijnum/Blas.java
src-plugins/FlowJ_/src/main/java/bijnum/Jacobi.java
src-plugins/FlowJ_/src/main/java/bijnum/SVDC.java
src-plugins/FlowJ_/src/main/java/bijnum/SVDCException.java
src-plugins/FlowJ_/src/main/java/volume/Beaudetx.java
src-plugins/FlowJ_/src/main/java/volume/CentralDiff.java
src-plugins/FlowJ_/src/main/java/volume/Convolver.java
src-plugins/FlowJ_/src/main/java/volume/Diffusion.java
src-plugins/FlowJ_/src/main/java/volume/Diffusion3D.java
src-plugins/FlowJ_/src/main/java/volume/DoG.java
src-plugins/FlowJ_/src/main/java/volume/DoG2D.java
src-plugins/FlowJ_/src/main/java/volume/DoG3D.java
src-plugins/FlowJ_/src/main/java/volume/Equalize.java
src-plugins/FlowJ_/src/main/java/volume/GaborCos.java
src-plugins/FlowJ_/src/main/java/volume/GaborSin.java
src-plugins/FlowJ_/src/main/java/volume/Gaussian.java
src-plugins/FlowJ_/src/main/java/volume/Gaussian2D.java
src-plugins/FlowJ_/src/main/java/volume/Gaussian3D.java
src-plugins/FlowJ_/src/main/java/volume/GaussianDerivative.java
src-plugins/FlowJ_/src/main/java/volume/Hessian.java
src-plugins/FlowJ_/src/main/java/volume/HyperVolume.java
src-plugins/FlowJ_/src/main/java/volume/Kernel.java
src-plugins/FlowJ_/src/main/java/volume/Kernel1D.java
src-plugins/FlowJ_/src/main/java/volume/Kernel2D.java
src-plugins/FlowJ_/src/main/java/volume/Kernel3D.java
src-plugins/FlowJ_/src/main/java/volume/Kernel4D.java
src-plugins/FlowJ_/src/main/java/volume/LoG.java
src-plugins/FlowJ_/src/main/java/volume/Sobel.java
src-plugins/FlowJ_/src/main/java/volume/Sobel3D.java
src-plugins/FlowJ_/src/main/java/volume/Sobel4D.java
src-plugins/FlowJ_/src/main/java/volume/Transformer.java
src-plugins/FlowJ_/src/main/java/volume/Volume.java
src-plugins/FlowJ_/src/main/java/volume/VolumeFloat.java
src-plugins/FlowJ_/src/main/java/volume/VolumeIO.java
src-plugins/FlowJ_/src/main/java/volume/VolumeInteger.java
src-plugins/FlowJ_/src/main/java/volume/VolumeRGB.java
src-plugins/FlowJ_/src/main/java/volume/VolumeShort.java
src-plugins/FlowJ_/src/main/resources/plugins.config
src-plugins/Graph_Cut/.factorypath
src-plugins/Graph_Cut/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/Graph_Cut/pom.xml
src-plugins/Graph_Cut/src/main/java/graphcut/Graph.java
src-plugins/Graph_Cut/src/main/java/graphcut/GraphCut.java
src-plugins/Graph_Cut/src/main/java/graphcut/Graph_Cut.java
src-plugins/Graph_Cut/src/main/java/graphcut/ImageOverlay.java
src-plugins/Graph_Cut/src/main/resources/plugins.config
src-plugins/Gray_Morphology/.factorypath
src-plugins/Gray_Morphology/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/Gray_Morphology/pom.xml
src-plugins/Gray_Morphology/src/main/java/GrayMorphology_.java
src-plugins/Gray_Morphology/src/main/java/mmorpho/Constants.java
src-plugins/Gray_Morphology/src/main/java/mmorpho/LocalHistogram.java
src-plugins/Gray_Morphology/src/main/java/mmorpho/MorphoProcessor.java
src-plugins/Gray_Morphology/src/main/java/mmorpho/StructureElement.java
src-plugins/Gray_Morphology/src/main/resources/License.txt
src-plugins/Gray_Morphology/src/main/resources/plugins.config
src-plugins/Helmholtz_Analysis/.factorypath
src-plugins/Helmholtz_Analysis/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/Helmholtz_Analysis/pom.xml
src-plugins/Helmholtz_Analysis/src/main/java/Helmholtz_Analysis.java
src-plugins/Helmholtz_Analysis/src/main/resources/plugins.config
src-plugins/IJ_Robot/.factorypath
src-plugins/IJ_Robot/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/IJ_Robot/pom.xml
src-plugins/IJ_Robot/src/main/java/IJ_Robot.java
src-plugins/IJ_Robot/src/main/resources/IJRobotDemo.txt
src-plugins/IJ_Robot/src/main/resources/plugins.config
src-plugins/IO_/.factorypath
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src-plugins/SPIM_Opener/src/main/java/spimopener/Combine_SPIM_Projects.java
src-plugins/SPIM_Opener/src/main/java/spimopener/Count_Files.java
src-plugins/SPIM_Opener/src/main/java/spimopener/DoubleSlider.java
src-plugins/SPIM_Opener/src/main/java/spimopener/GaussianStackFocuser.java
src-plugins/SPIM_Opener/src/main/java/spimopener/MaximumProjector.java
src-plugins/SPIM_Opener/src/main/java/spimopener/MinimumProjector.java
src-plugins/SPIM_Opener/src/main/java/spimopener/OpenerGenericDialog.java
src-plugins/SPIM_Opener/src/main/java/spimopener/Projector.java
src-plugins/SPIM_Opener/src/main/java/spimopener/Rename.java
src-plugins/SPIM_Opener/src/main/java/spimopener/SPIMExperiment.java
src-plugins/SPIM_Opener/src/main/java/spimopener/SPIMRegularStack.java
src-plugins/SPIM_Opener/src/main/java/spimopener/SPIMStack.java
src-plugins/SPIM_Opener/src/main/java/spimopener/SPIMVirtualStack.java
src-plugins/SPIM_Opener/src/main/java/spimopener/SPIM_Opener.java
src-plugins/SPIM_Opener/src/main/java/spimopener/XMLReader.java
src-plugins/SPIM_Opener/src/main/resources/plugins.config
src-plugins/SPIM_Registration/.factorypath
src-plugins/SPIM_Registration/.settings/org.eclipse.jdt.apt.core.prefs
src-plugins/SPIM_Registration/pom.xml
src-plugins/SPIM_Registration/src/main/java/MultiChannel_SPIM_Registration.java
src-plugins/SPIM_Registration/src/main/java/SPIMRegistrationAbstract.java
src-plugins/SPIM_Registration/src/main/java/SPIM_Registration.java
src-plugins/SPIM_Registration/src/main/java/SPIM_Registration_File.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/Apply_External_Transformation.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/Bead_Registration.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/Multi_View_Deconvolution.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/Multi_View_Fusion.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/Regtest.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/timelapsedisplay/FileOpenMenuEntry.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/timelapsedisplay/GraphFrame.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/timelapsedisplay/MouseListenerTimelapse.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/timelapsedisplay/RegistrationStatistics.java
src-plugins/SPIM_Registration/src/main/java/fiji/plugin/timelapsedisplay/TimeLapseDisplay.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/icp/ICP.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/icp/PointMatchIdentification.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/icp/SimplePointMatchIdentification.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/AbstractPointDescriptor.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/LinkedPoint.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/LocalCoordinateSystemPointDescriptor.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/ModelPointDescriptor.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/SimplePointDescriptor.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/exception/NoSuitablePointsException.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/matcher/Matcher.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/matcher/ModelPriorMatcher.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/matcher/ModelPriorSubsetMatcher.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/matcher/Quaternion.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/matcher/SimpleMatcher.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/matcher/SubsetMatcher.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/FixedModel.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/RigidModelOld3D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantAffineModel3D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantFixedModel.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantModel.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantRigidModel2D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantRigidModel3D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/model/TranslationInvariantSimilarityModel3D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/similarity/LinearDistance.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/similarity/ManhattanDistance.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/similarity/SimilarityMeasure.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/similarity/SquareDistance.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/test/PointNode.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/test/TestPointDescriptor.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/pointdescriptor/test/VirtualPointNode.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/ClusterReconstruction.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/Reconstruction.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/AverageContent.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/AverageContentFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/Blending.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/BlendingFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/BlendingSimple.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/BlendingSimpleFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/CombinedPixelWeightener.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/CombinedPixelWeightenerFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/EntropyFast.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/EntropyFastFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/FusionControl.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/GaussContent.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/GaussContentFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/IsolatedPixelWeightener.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/IsolatedPixelWeightenerFactory.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/MappingFusionParalell.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/MappingFusionParalellMaxWeight.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/MappingFusionSequential.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/MappingFusionSequentialDifferentOutput.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/PreDeconvolutionFusion.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/PreDeconvolutionFusionInterface.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/PreDeconvolutionFusionSequential.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/SPIMImageFusion.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/entropy/Entropy.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/fusion/entropy/EntropyFloatArray3D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ConfigurationParserException.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ConfigurationParserGeneral.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ConfigurationParserObject.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ConfigurationParserSPIM.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/IOFunctions.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ImgLibSaver.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ParsePattern.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/ProgramConfiguration.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/SPIMConfiguration.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/TextFileAccess.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/io/XMLFunctions.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/mpicbg/Java3d.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/mpicbg/PointMatchGeneric.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/mpicbg/SketchTikZFileObject.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/mpicbg/TileConfigurationPhaseCorrelation.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/mpicbg/TileConfigurationSPIM.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/mpicbg/TileSPIM.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution/ExtractPSF.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution/LucyRichardsonFFT.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution/LucyRichardsonMultiViewDeconvolution.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/AdjustInput.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/BayesMVDeconvolution.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/Block.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/CUDAConvolution.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/CUDATools.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/Deconvolver.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/LRFFT.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/LRFFTThreads.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/postprocessing/deconvolution2/LRInput.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/preprocessing/AutomaticAngleSetup.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/ViewDataBeads.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/ViewStructure.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/Bead.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/BeadIdentification.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/BeadRegistration.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/BeadSegmentation.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/BeadStructure.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/SegmentationBenchmark.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/error/GlobalErrorStatistics.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/error/GlobalErrorStatisticsImpl.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/error/ViewErrorPairWise.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/error/ViewErrorStatistics.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/laplace/DoGMaximum.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/laplace/LaPlaceFunctions.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/bead/laplace/RejectStatistics.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/AbstractDetection.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/Detection.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/DetectionIdentification.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/DetectionRegistration.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/DetectionSegmentation.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/DetectionStructure.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/DetectionView.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/descriptor/CoordSystem3d.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/descriptor/CoordSystemSecure3d.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/descriptor/CorrespondenceExtraction.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/descriptor/ModelBased3d.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/detection/descriptor/SparseCorrespondenceExtraction.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/segmentation/NucleiConfiguration.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/segmentation/Nucleus.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/segmentation/NucleusIdentification.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/segmentation/NucleusStructure.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/threshold/ComponentProperties.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/registration/threshold/ConnectedComponent.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/segmentation/DOM.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/segmentation/IntegralImage3d.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/segmentation/InteractiveDoG.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/segmentation/InteractiveIntegral.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/segmentation/SimplePeak.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/simulation/SimulateBeadImage.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/FastMatrix.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/math3d/FastMatrixN.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/math3d/JacobiDouble.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/math3d/Line.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/math3d/Plane.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/math3d/Point3d.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vib/math3d/Triangle.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/BeadTransformGroup.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/Motion3D.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/PreviewRegistration.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/Viewer3dFunctions.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/VisualizationFunctions.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/VisualizationSketchTikZ.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/spim/vis3d/VisualizeBeads.java
src-plugins/SPIM_Registration/src/main/java/mpicbg/util/TransformUtils.java
src-plugins/SPIM_Registration/src/main/resources/LICENSE
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src-plugins/Scala_Interpreter/pom.xml
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src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/ManualDetectorFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/SpotDetector.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/SpotDetectorFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/semiauto/AbstractSemiAutoTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/semiauto/SemiAutoTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/subpixel/QuadraticSubpixelLocalization.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/subpixel/SubPixelLocalization.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/util/MedianFilter3x3.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/util/SquareNeighborhood3x3.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/detection/util/SquareNeighborhoodCursor3x3.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/AbstractFeatureGrapher.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/EdgeFeatureCalculator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/EdgeFeatureGrapher.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/FeatureAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/FeatureFilter.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/ModelFeatureUpdater.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/SpotFeatureCalculator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/SpotFeatureGrapher.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/TrackFeatureCalculator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/TrackFeatureGrapher.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/edges/EdgeAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/edges/EdgeTargetAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/edges/EdgeTimeLocationAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/edges/EdgeVelocityAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/edges/package-info.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/IndependentSpotFeatureAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotAnalyzerFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAnalyzerFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAndSNRAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotContrastAndSNRAnalyzerFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotIntensityAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotIntensityAnalyzerFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotMorphologyAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotMorphologyAnalyzerFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotRadiusEstimator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/spot/SpotRadiusEstimatorFactory.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/track/TrackAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/track/TrackBranchingAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/track/TrackDurationAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/track/TrackIndexAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/track/TrackLocationAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/features/track/TrackSpeedStatisticsAnalyzer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/Function1.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/Function2.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/GraphUtils.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/OutputFunction.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/RecursiveCumSum.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/SortedDepthFirstIterator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/StringFormater.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/TimeDirectedDepthFirstIterator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/TimeDirectedNeighborIndex.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/TimeDirectedSortedDepthFirstIterator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/graph/package-info.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/ConfigurationPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/DisplaySettingsEvent.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/DisplaySettingsListener.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/GrapherPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/GuiUtils.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/LogPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/ManualTrackingGUIController.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/TrackMateGUIController.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/TrackMateGUIModel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/TrackMateWizard.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/ActionChooserDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/ConfigureViewsDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/DetectionDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/DetectorChoiceDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/DetectorConfigurationDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/GrapherDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/InitFilterDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/LoadDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/LogPanelDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/SaveDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/SomeDialogDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/SpotFilterDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/StartDialogDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/TrackFilterDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/TrackerChoiceDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/TrackerConfigurationDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/TrackingDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/ViewChoiceDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/descriptors/WizardPanelDescriptor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/ActionChooserPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/ActionListenablePanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/ConfigureViewsPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/FilterPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/InitFilterPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/ListChooserPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/StartDialogPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/CategoryJComboBox.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/ColorByFeatureGUIPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/FeaturePlotSelectionPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/FilterGuiPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/ImagePlusChooser.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/JNumericTextField.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/JPanelColorByFeatureGUI.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/JPanelFeaturePenalty.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/components/JPanelFeatureSelectionGui.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/detector/BasicDetectorConfigurationPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/detector/DogDetectorConfigurationPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/detector/DownSampleLogDetectorConfigurationPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/detector/LogDetectorConfigurationPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/tracker/JPanelTrackerSettingsMain.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/tracker/LAPTrackerSettingsPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/tracker/NearestNeighborTrackerSettingsPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/gui/panels/tracker/SimpleLAPTrackerSettingsPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/IOUtils.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlKeys.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlKeys_v12.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlKeys_v20.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlReader.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlReader_v12.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlReader_v20.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/io/TmXmlWriter.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/AbstractProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/ActionProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/DetectorProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/EdgeAnalyzerProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/SpotAnalyzerProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/TrackAnalyzerProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/TrackerProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/providers/ViewProvider.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/BadEdgeRemoval_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/ConcurrentSpotTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/DumbTracker_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/ExportStats_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/Graph_Test.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/HyperStackDisplayerTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/LAPTrackerTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/LogDetectorTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/ManualTrackingPlugIn_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/NNTrackerTest.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/SpotDisplayer3DModel_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/SpotDisplayer3DTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/SpotFeatureGrapher_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/SpotFilteringPerf_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/SpotGroupNodeTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/SpotNeighborhoodTest.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TmXmlReaderTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TmXmlReaderV12_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TmXmlReaderV20_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TrackBranchingAnalyzer_Test.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TrackLayout_Test.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TrackMateLoading_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TrackMate_TestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TrackSchemeTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tests/TrackVisualizerTestDrive.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/FastLAPTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/LAPTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/LAPUtils.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/ManualTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/SimpleFastLAPTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/SimpleLAPTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/SpotTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/TrackerKeys.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costfunction/CostFunctions.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costfunction/GapClosingCostFunction.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costfunction/LinkingCostFunction.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costfunction/MergingCostFunction.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costfunction/SplittingCostFunction.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costmatrix/LAPTrackerCostMatrixCreator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costmatrix/LinkingCostMatrixCreator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/costmatrix/TrackSegmentCostMatrixCreator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/dumb/DumbTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/hungarian/AssignmentAlgorithm.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/hungarian/AssignmentProblem.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/hungarian/HungarianAlgorithm.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/hungarian/MunkresKuhnAlgorithm.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/kdtree/FlagNode.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborFlagSearchOnKDTree.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/tracking/kdtree/NearestNeighborTracker.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/AlphanumComparator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/ChartExporter.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/CropImgView.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/DefaultFileFilter.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/ExportableChartPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/JLabelLogger.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/ModelTools.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/OnRequestUpdater.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/SpotNeighborhood.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/SpotNeighborhoodCursor.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/TMUtils.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/TrackSplitter.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/Version.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/XYEdgeRenderer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/XYEdgeSeries.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/util/XYEdgeSeriesCollection.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/AbstractTrackMateModelView.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/DummySpotColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/DummyTrackColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/FeatureColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/PerEdgeFeatureColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/PerTrackFeatureColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/SpotColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/TrackColorGenerator.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/TrackMateModelView.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/ViewUtils.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/HyperStackDisplayer.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotEditTool.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotEditToolConfigPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/SpotOverlay.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/hyperstack/TrackOverlay.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/threedviewer/SpotDisplayer3D.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/threedviewer/SpotGroupNode.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/threedviewer/TrackDisplayNode.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/FeaturePlotSelectionPanel.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/InfoPane.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/JGraphXAdapter.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/SaveAction.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/SpotIconGrabber.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/SpotImageUpdater.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackScheme.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemeFrame.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemeGraphComponent.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemeGraphLayout.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemePopupMenu.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemeStylist.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemeSvgCanvas.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/TrackSchemeToolbar.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/mxScaledLabelShape.java
src-plugins/TrackMate_/src/main/java/fiji/plugin/trackmate/visualization/trackscheme/mxSideTextShape.java
src-plugins/TrackMate_/src/main/java/org/jfree/chart/annotations/XYTextSimpleAnnotation.java
src-plugins/TrackMate_/src/main/java/org/jfree/chart/renderer/InterpolatePaintScale.java
src-plugins/TrackMate_/src/main/java/org/jfree/data/statistics/LogHistogramDataset.java
src-plugins/TrackMate_/src/main/resources/fiji/plugin/trackmate/gui/images/EdgeIcon.png
src-plugins/TrackMate_/src/main/resources/fiji/plugin/trackmate/gui/images/EdgeIcon_small.png
src-plugins/TrackMate_/src/main/resources/fiji/plugin/trackmate/gui/images/EdgeIcon_supersmall.png
src-plugins/TrackMate_/src/main/resources/fiji/plugin/trackmate/gui/images/ISBIlogo.png
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src-plugins/Volume_Viewer/src/main/java/fiji/plugin/volumeviewer/TFalpha1.java
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src-plugins/fiji-lib/src/main/java/fiji/statistics/RoiStatistics.java
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src-plugins/fiji-lib/src/main/java/fiji/tool/AbstractTrackingTool.java
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src-plugins/fiji-lib/src/main/java/fiji/tool/ToolToggleListener.java
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src-plugins/fiji-lib/src/main/java/fiji/util/TicToc.java
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src-plugins/imagescience/pom.xml
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src-plugins/imagescience/src/main/java/imagescience/array/IntArray.java
src-plugins/imagescience/src/main/java/imagescience/array/LongArray.java
src-plugins/imagescience/src/main/java/imagescience/array/ShortArray.java
src-plugins/imagescience/src/main/java/imagescience/color/Palette.java
src-plugins/imagescience/src/main/java/imagescience/color/Wave2Color.java
src-plugins/imagescience/src/main/java/imagescience/feature/Differentiator.java
src-plugins/imagescience/src/main/java/imagescience/feature/Edges.java
src-plugins/imagescience/src/main/java/imagescience/feature/Hessian.java
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src-plugins/imagescience/src/main/java/imagescience/feature/Smoother.java
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src-plugins/imagescience/src/main/java/imagescience/fourier/FFT.java
src-plugins/imagescience/src/main/java/imagescience/image/Aspects.java
src-plugins/imagescience/src/main/java/imagescience/image/Axes.java
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src-plugins/imagescience/src/main/java/imagescience/image/ByteImage.java
src-plugins/imagescience/src/main/java/imagescience/image/ColorImage.java
src-plugins/imagescience/src/main/java/imagescience/image/Coordinates.java
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src-plugins/imagescience/src/main/java/imagescience/image/Image.java
src-plugins/imagescience/src/main/java/imagescience/image/ShortImage.java
src-plugins/imagescience/src/main/java/imagescience/random/BinomialGenerator.java
src-plugins/imagescience/src/main/java/imagescience/random/ExponentialGenerator.java
src-plugins/imagescience/src/main/java/imagescience/random/GammaGenerator.java
src-plugins/imagescience/src/main/java/imagescience/random/GaussianGenerator.java
src-plugins/imagescience/src/main/java/imagescience/random/PoissonGenerator.java
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src-plugins/imagescience/src/main/java/imagescience/segment/Extremizer.java
src-plugins/imagescience/src/main/java/imagescience/segment/Thresholder.java
src-plugins/imagescience/src/main/java/imagescience/segment/ZeroCrosser.java
src-plugins/imagescience/src/main/java/imagescience/shape/Bounds.java
src-plugins/imagescience/src/main/java/imagescience/shape/Circle.java
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src-plugins/imagescience/src/main/java/imagescience/shape/Point.java
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src-plugins/imagescience/src/main/java/imagescience/shape/Square.java
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src-plugins/imagescience/src/main/java/imagescience/utility/I5DResource.java
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src-plugins/imagescience/src/main/java/imagescience/utility/Messenger.java
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src-plugins/imageware/src/main/java/imageware/ByteAccess.java
src-plugins/imageware/src/main/java/imageware/ByteBuffer.java
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src-plugins/imageware/src/main/java/imageware/ByteSet.java
src-plugins/imageware/src/main/java/imageware/Convolver.java
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src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/cell/Cell.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/cell/CellContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/cell/CellContainerFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/constant/ConstantContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/constant/ConstantContainerFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/BitDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/BitDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/ByteDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/ByteDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/CharDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/CharDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/DoubleDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/DoubleDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/DynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/DynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/DynamicContainerFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/FloatDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/FloatDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/IntDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/IntDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/LongDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/LongDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/ShortDynamicContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/dynamic/ShortDynamicContainerAccessor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/imageplus/ByteImagePlus.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/imageplus/FloatImagePlus.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/imageplus/ImagePlusContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/imageplus/ImagePlusContainerFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/imageplus/IntImagePlus.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/imageplus/ShortImagePlus.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/planar/PlanarContainer.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/planar/PlanarContainerFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/shapelist/ShapeList.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/shapelist/ShapeListCached.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/container/shapelist/ShapeListContainerFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/Cursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/CursorImpl.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/Iterable.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/Localizable.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/Localizable3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizableByDim.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizableByDim3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizableByDimCursor3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizableCursor3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizablePlane.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/LocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/Array3DLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/Array3DLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/Array3DLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/ArrayCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/ArrayLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/ArrayLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/ArrayLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/array/ArrayLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/cell/CellCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/cell/CellLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/cell/CellLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/cell/CellLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/cell/CellLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/constant/ConstantCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/constant/ConstantLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/constant/ConstantLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/constant/ConstantLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/constant/ConstantLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/dynamic/DynamicCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/dynamic/DynamicLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/dynamic/DynamicLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/dynamic/DynamicLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/dynamic/DynamicLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/imageplus/ImagePlusCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/imageplus/ImagePlusCursor2D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/imageplus/ImagePlusLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/imageplus/ImagePlusLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/imageplus/ImagePlusLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/imageplus/ImagePlusLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/link/CursorLink.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/link/GenericCursorLink.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/link/NullLink.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/planar/PlanarCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/planar/PlanarCursor2D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/planar/PlanarLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/planar/PlanarLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/planar/PlanarLocalizableCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/planar/PlanarLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListCache.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListCacheFIFO.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListCachedLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListCachedLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListCachedLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListLocalizableByDimCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListLocalizableByDimOutOfBoundsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/shapelist/ShapeListLocalizablePlaneCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/AbstractSortedGrayLevelIterator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/AbstractSpecialCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/CoordsCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/DiscCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/DomainCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/HyperSphereIterator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/LocalNeighborhoodCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/LocalNeighborhoodCursor3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/LocalNeighborhoodCursor3DOptimized.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/LocalNeighborhoodCursorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/RegionOfInterestCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/SortedGrayLevelIteratorAllContainers.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/SortedGrayLevelIteratorArrayContainerOnly.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/SortedGrayLevelIteratorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/SphereCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/special/Utils.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/AbstractVector.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/Dimensionality.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/Vector.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/Vector1d.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/Vector2d.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/Vector3d.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/cursor/vector/Vector4d.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/exception/ImgLibException.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/function/Converter.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/function/Function.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/function/IntegerTypeConverter.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/function/RealTypeConverter.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/function/VoidConverter.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/Image.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/ImageFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/ImagePlusAdapter.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/BasePairTypeDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/BitTypeDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/ComplexTypeComplexValueDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/ComplexTypePhaseSpectrumDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/ComplexTypePowerSpectrumDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/ComplexTypeRealValueDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/Display.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/IntegerTypeDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/RealTypeDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/ImageJFunctions.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/ImageJVirtualDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/ImageJVirtualStack.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/InverseTransformDescription.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/RGBALegacyTypeDisplay.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/SliceTransformableExtraction.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/image/display/imagej/SliceTransformableExtractionFloat.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/Interpolator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/Interpolator1D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/Interpolator2D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/Interpolator3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/InterpolatorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/InterpolatorImpl.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/dct/DCTInterpolator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/dct/DCTInterpolatorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/lanczos/LanczosInterpolator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/lanczos/LanczosInterpolatorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolator1D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolator2D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolator2DRealType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolator3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolator3DRealType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/linear/LinearInterpolatorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/nearestneighbor/NearestNeighborInterpolator.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/nearestneighbor/NearestNeighborInterpolator1D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/nearestneighbor/NearestNeighborInterpolator2D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/nearestneighbor/NearestNeighborInterpolator3D.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/interpolation/nearestneighbor/NearestNeighborInterpolatorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/io/ImageOpener.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/io/LOCI.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/BoundingBox.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/DefaultLabelingCursorStrategy.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/DefaultLabelingCursorStrategyFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/Labeling.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/LabelingCursorStrategy.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/LabelingCursorStrategyFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/LabelingMapping.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/LabelingType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/LocalizableLabelingCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/labeling/LocalizableLabelingPerimeterCursor.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/multithreading/Chunk.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/multithreading/SimpleMultiThreading.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/multithreading/Stopable.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategy.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyMirror.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyMirrorExpWindowing.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyMirrorExpWindowingFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyMirrorFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyPeriodic.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyPeriodicFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyValue.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/outofbounds/OutOfBoundsStrategyValueFactory.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/BasePairType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/BooleanType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/Type.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/TypeConverter.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/TypeImpl.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/label/BasePairBitType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/label/BasePairCharType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/label/FakeType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/logic/BitType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/ComplexType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/ExponentialMathType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/IntegerType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/NumericType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/RGBALegacyType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/RealType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/complex/ComplexDoubleType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/complex/ComplexFloatType.java
src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/complex/ComplexTypeImpl.java
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src-plugins/legacy-imglib1/src/main/java/mpicbg/imglib/type/numeric/integer/GenericByteType.java
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staged-plugins/jython.Fakefile
staged-plugins/loci_tools.Fakefile
staged-plugins/loci_tools.config
staged-plugins/rsyntaxtextarea.Fakefile
staged-plugins/weka.Fakefile
tests/.gitignore
tests/3d.py
tests/Marching_Cubes_ImgLib.java
tests/class_versions.py
tests/crlf-in-javas.py
tests/extra_file_types.py
tests/lib.py
tests/menus.py
tests/plugin_jars.py
tests/record.py
tests/run.sh
tests/vib.py