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.gitignore
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/
.gitignore
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# Editors #
*.swp
*~
# Maven #
/bin/apache-maven-*/
/src-plugins/*/target/
# Fiji Build #
/bin/maven-helper.sh
/.tmp.*/
# Eclipse #
.checksums
.metadata
.project
.classpath
.settings/
# IntelliJ #
*.iml
# Updater #
/db.xml.gz
# Vagrant #
/.vagrant/
# Cached sample images #
/samples/
# ImageJ Launcher #
/jvm.cfg
# MacOSX #
.DS_Store
/Contents/Resources/ImageJ.icns
# Wiki monitor #
/.recent-changes.*
/jssecacerts
# Micro-Manager #
*-stamp
/CoreLog.txt
hs_err*.log
/MMConfig_demo.cfg
/MMStartup.bsh
# Jython #
*$py.class
# Package Maker #
/fiji-*.7z
/fiji-*.dmg
/fiji-*.tar.bz2
/fiji-*.zip
/fiji-macosx.dmg
# Launchers #
/Contents/MacOS/ImageJ-macosx
/Contents/MacOS/ImageJ-tiger
/Contents/MacOS/fiji-macosx
/Contents/MacOS/fiji-tiger
/ImageJ
/ImageJ-linux32
/ImageJ-linux64
/ImageJ-win32.exe
/ImageJ-win64.exe
/ImageJ.cfg
/ImageJ.exe
/fiji
/fiji-linux
/fiji-linux64
/fiji-win32.exe
/fiji-win64.exe
/fiji.exe
# Files generated from sources in src-plugins/ #
/jars/ij1-patcher-[0-9]*.jar
/jars/log4j-[0-9]*.jar
/jars/scala-compiler-[0-9]*.jar
/jars/scala-library-[0-9]*.jar
/jars/scala-reflect-[0-9]*.jar
/jars/slf4j-log4j12-[0-9]*.jar
/plugins/Fiji_Updater.jar
# Former submodules #
/modules/TrakEM2/
/modules/ij-plugins/
/modules/imglib/
/modules/mpicbg/
# Files generated from submodules #
/jars/VectorString-[0-9]*.jar
/jars/autocomplete-[0-9]*.jar
/jars/batik-[0-9]*.jar
/jars/ij-[0-9]*.jar
/jars/imagej-launcher-[0-9]*.jar
/jars/jai-codec-[0-9]*.jar
/jars/jai-core-[0-9]*.jar
/jars/jython-[0-9]*.jar
/jars/mpicbg-[0-9]*.jar
/jars/rsyntaxtextarea-[0-9]*.jar
/plugins/Image_5D-[0-9]*.jar
/plugins/TrakEM2_-[0-9]*.jar
/plugins/mpicbg_-[0-9]*.jar
# Dependencies copied by MiniMaven #
/jars/VIB-lib-[0-9]*.jar
/jars/base64-[0-9]*.jar
/jars/bcmail-jdk14-[0-9]*.jar
/jars/bcprov-jdk14-[0-9]*.jar
/jars/bsh-[0-9]*.jar
/jars/clojure-[0-9]*.jar
/jars/commons-math3-[0-9]*.jar
/jars/fake-[0-9]*.jar
/jars/fiji-compat-[0-9]*.jar
/jars/fiji-lib-[0-9]*.jar
/jars/fiji-scripting-[0-9]*.jar
/jars/imagescience-[0-9]*.jar
/jars/imageware-[0-9]*.jar
/jars/itext-[0-9]*.jar
/jars/itextpdf-[0-9]*.jar
/jars/jama-[0-9]*.jar
/jars/java-cup-[0-9]*.jar
/jars/javac-[0-9]*.jar
/jars/javassist-[0-9]*.jar
/jars/jcommon-[0-9]*.jar
/jars/jep-[0-9]*.jar
/jars/jfreechart-[0-9]*.jar
/jars/jgrapht-[0-9]*.jar
/jars/jgraphx-[0-9]*.jar
/jars/jna-[0-9]*.jar
/jars/jpedalSTD-[0-9]*.jar
/jars/jruby-complete-[0-9]*.jar
/jars/js-[0-9]*.jar
/jars/jsch-[0-9]*.jar
/jars/jzlib-[0-9]*.jar
/jars/legacy-imglib1-[0-9]*.jar
/jars/mij-[0-9]*.jar
/jars/mines-jtk-[0-9]*.jar
/jars/pal-optimization-[0-9]*.jar
/jars/pentaho-package-manager-[0-9]*.jar
/jars/postgresql-[0-9]*.jar
/jars/tools-[0-9]*.jar
/jars/udunits-[0-9]*.jar
/jars/wavelets-[0-9]*.jar
/jars/weave_jy2java-[0-9]*.jar
/jars/weka-dev-[0-9]*.jar
/plugins/3D_Blob_Segmentation-[0-9]*.jar
/plugins/3D_Objects_Counter-[0-9]*.jar
/plugins/3D_Viewer-[0-9]*.jar
/plugins/AnalyzeSkeleton_-[0-9]*.jar
/plugins/Analyze_Reader_Writer-[0-9]*.jar
/plugins/Anisotropic_Diffusion_2D-[0-9]*.jar
/plugins/Archipelago_Plugins-[0-9]*.jar
/plugins/Arrow_-[0-9]*.jar
/plugins/Auto_Threshold-[0-9]*.jar
/plugins/BalloonSegmentation_-[0-9]*.jar
/plugins/BeanShell_Interpreter-[0-9]*.jar
/plugins/Bug_Submitter-[0-9]*.jar
/plugins/CLI_-[0-9]*.jar
/plugins/CPU_Meter-[0-9]*.jar
/plugins/Calculator_Plus-[0-9]*.jar
/plugins/Clojure_Interpreter-[0-9]*.jar
/plugins/Colocalisation_Analysis-[0-9]*.jar
/plugins/Color_Histogram-[0-9]*.jar
/plugins/Color_Inspector_3D-[0-9]*.jar
/plugins/Colour_Deconvolution-[0-9]*.jar
/plugins/CorrectBleach_-[0-9]*.jar
/plugins/Descriptor_based_registration-[0-9]*.jar
/plugins/Dichromacy_-[0-9]*.jar
/plugins/Differentials_-[0-9]*.jar
/plugins/Directionality_-[0-9]*.jar
/plugins/Extended_Depth_Field-[0-9]*.jar
/plugins/FS_Align_TrakEM2-[0-9]*.jar
/plugins/FeatureJ_-[0-9]*.jar
/plugins/Feature_Detection-[0-9]*.jar
/plugins/Fiji_Archipelago-[0-9]*.jar
/plugins/Fiji_Developer-[0-9]*.jar
/plugins/Fiji_Package_Maker-[0-9]*.jar
/plugins/Fiji_Plugins-[0-9]*.jar
/plugins/FlowJ_-[0-9]*.jar
/plugins/Graph_Cut-[0-9]*.jar
/plugins/Gray_Morphology-[0-9]*.jar
/plugins/Helmholtz_Analysis-[0-9]*.jar
/plugins/IJ_Robot-[0-9]*.jar
/plugins/IO_-[0-9]*.jar
/plugins/Image_Expression_Parser-[0-9]*.jar
/plugins/Interactive_3D_Surface_Plot-[0-9]*.jar
/plugins/IsoData_Classifier-[0-9]*.jar
/plugins/JRuby_Interpreter-[0-9]*.jar
/plugins/Javascript_-[0-9]*.jar
/plugins/Jython_Interpreter-[0-9]*.jar
/plugins/Kuwahara_Filter-[0-9]*.jar
/plugins/Lasso_and_Blow_Tool-[0-9]*.jar
/plugins/Linear_Kuwahara-[0-9]*.jar
/plugins/LocalThickness_-[0-9]*.jar
/plugins/MTrack2_-[0-9]*.jar
/plugins/MTrackJ_-[0-9]*.jar
/plugins/M_I_P-[0-9]*.jar
/plugins/Manual_Tracking-[0-9]*.jar
/plugins/MosaicJ_-[0-9]*.jar
/plugins/Multi_Kymograph-[0-9]*.jar
/plugins/PIV_analyser-[0-9]*.jar
/plugins/PointPicker_-[0-9]*.jar
/plugins/QuickPALM_-[0-9]*.jar
/plugins/RATS_-[0-9]*.jar
/plugins/RandomJ_-[0-9]*.jar
/plugins/Reconstruct_Reader-[0-9]*.jar
/plugins/Refresh_Javas-[0-9]*.jar
/plugins/SPIM_Opener-[0-9]*.jar
/plugins/SPIM_Registration-[0-9]*.jar
/plugins/Samples_-[0-9]*.jar
/plugins/Scala_Interpreter-[0-9]*.jar
/plugins/Series_Labeler-[0-9]*.jar
/plugins/SheppLogan_-[0-9]*.jar
/plugins/Sholl_Analysis-[0-9]*.jar
/plugins/Simple_Neurite_Tracer-[0-9]*.jar
/plugins/Siox_Segmentation-[0-9]*.jar
/plugins/Skeletonize3D_-[0-9]*.jar
/plugins/Snakuscule_-[0-9]*.jar
/plugins/SplineDeformationGenerator_-[0-9]*.jar
/plugins/StackReg_-[0-9]*.jar
/plugins/Stack_Manipulation-[0-9]*.jar
/plugins/Statistical_Region_Merging-[0-9]*.jar
/plugins/Stitching_-[0-9]*.jar
/plugins/Sync_Win-[0-9]*.jar
/plugins/Thread_Killer-[0-9]*.jar
/plugins/Threshold_Colour-[0-9]*.jar
/plugins/Time_Stamper-[0-9]*.jar
/plugins/ToAST_-[0-9]*.jar
/plugins/TopoJ_-[0-9]*.jar
/plugins/TrackMate_-[0-9]*.jar
/plugins/Trainable_Segmentation-[0-9]*.jar
/plugins/TrakEM2_Archipelago-[0-9]*.jar
/plugins/TransformJ_-[0-9]*.jar
/plugins/TurboReg_-[0-9]*.jar
/plugins/UnwarpJ_-[0-9]*.jar
/plugins/VIB_-[0-9]*.jar
/plugins/Vaa3d_Reader-[0-9]*.jar
/plugins/Vaa3d_Writer-[0-9]*.jar
/plugins/Video_Editing-[0-9]*.jar
/plugins/View5D_-[0-9]*.jar
/plugins/Volume_Calculator-[0-9]*.jar
/plugins/Volume_Viewer-[0-9]*.jar
/plugins/bUnwarpJ_-[0-9]*.jar
/plugins/blockmatching_-[0-9]*.jar
/plugins/level_sets-[0-9]*.jar
/plugins/panorama_-[0-9]*.jar
/plugins/register_virtual_stack_slices-[0-9]*.jar
/plugins/registration_3d-[0-9]*.jar
# For maven-download.sh
/jars/minimaven-[0-9]*.jar
# SciJava
/jars/eventbus-[0-9]*.jar
/jars/gentyref-[0-9]*.jar
/jars/scijava-common-[0-9]*.jar
/jars/scijava-plugins-commands-[0-9]*.jar
/jars/scijava-plugins-platforms-[0-9]*.jar
/jars/scijava-plugins-text-markdown-[0-9]*.jar
/jars/scijava-plugins-text-plain-[0-9]*.jar
/jars/scijava-ui-awt-[0-9]*.jar
/jars/scijava-ui-swing-[0-9]*.jar
/jars/scripting-beanshell-[0-9]*.jar
/jars/scripting-clojure-[0-9]*.jar
/jars/scripting-java-[0-9]*.jar
/jars/scripting-javascript-[0-9]*.jar
/jars/scripting-jruby-[0-9]*.jar
/jars/scripting-jython-[0-9]*.jar
/jars/swing-checkbox-tree-[0-9]*.jar
# ImgLib #
/jars/imglib2-[0-9]*.jar
/jars/imglib2-algorithms-[0-9]*.jar
/jars/imglib2-algorithms-gpl-[0-9]*.jar
/jars/imglib2-algorithms-legacy-[0-9]*.jar
/jars/imglib2-ij-[0-9]*.jar
/jars/imglib2-meta-[0-9]*.jar
/jars/imglib2-ops-[0-9]*.jar
/jars/imglib2-realtransform-[0-9]*.jar
# Bio-Formats #
/jars/JWlz-[0-9]*.jar
/jars/bio-formats/
/jars/c3p0-[0-9]*.jar
/jars/commons-codec-[0-9]*.jar
/jars/commons-httpclient-[0-9]*.jar
/jars/commons-logging-[0-9]*.jar
/jars/ehcache-core-[0-9]*.jar
/jars/formats-api-[0-9]*.jar
/jars/formats-bsd-[0-9]*.jar
/jars/formats-common-[0-9]*.jar
/jars/formats-gpl-[0-9]*.jar
/jars/jcip-annotations-[0-9]*.jar
/jars/jcl-over-slf4j-[0-9]*.jar
/jars/jdom2-[0-9]*.jar
/jars/je-[0-9]*.jar
/jars/jgoodies-common-[0-9]*.jar
/jars/jgoodies-forms-[0-9]*.jar
/jars/joda-time-[0-9]*.jar
/jars/kryo-[0-9]*.jar
/jars/logback-classic-[0-9]*.jar
/jars/logback-core-[0-9]*.jar
/jars/lwf-stubs-[0-9]*.jar
/jars/mdbtools-java-[0-9]*.jar
/jars/metakit-[0-9]*.jar
/jars/native-lib-loader-[0-9]*.jar
/jars/netcdf-[0-9]*.jar
/jars/ome-poi-[0-9]*.jar
/jars/ome-xml-[0-9]*.jar
/jars/perf4j-[0-9]*.jar
/jars/protobuf-java-[0-9]*.jar
/jars/quartz-[0-9]*.jar
/jars/serializer-[0-9]*.jar
/jars/slf4j-api-[0-9]*.jar
/jars/specification-[0-9]*.jar
/jars/turbojpeg-[0-9]*.jar
/jars/xalan-[0-9]*.jar
/jars/xml-apis-[0-9]*.jar
/plugins/bio-formats_plugins-[0-9]*.jar
# SCIFIO #
/jars/args4j-[0-9]*.jar
/jars/jai_imageio-[0-9]*.jar
/jars/mapdb-[0-9]*.jar
/jars/scifio-[0-9]*.jar
/jars/scifio-bf-compat-[0-9]*.jar
/jars/scifio-lifesci-[0-9]*.jar
/jars/scifio-ome-xml-[0-9]*.jar
/jars/scifio-tools-[0-9]*.jar
# ImageJ2 #
/jars/commons-lang3-[0-9]*.jar
/jars/imagej-[0-9]*.jar
/jars/imagej-common-[0-9]*.jar
/jars/imagej-legacy-[0-9]*.jar
/jars/imagej-ops-[0-9]*.jar
/jars/imagej-plugins-commands-[0-9]*.jar
/jars/imagej-plugins-tools-[0-9]*.jar
/jars/imagej-plugins-uploader-ssh-[0-9]*.jar
/jars/imagej-plugins-uploader-webdav-[0-9]*.jar
/jars/imagej-ui-awt-[0-9]*.jar
/jars/imagej-ui-swing-[0-9]*.jar
/jars/imagej-updater-[0-9]*.jar
/jars/jdatepicker-1.3.2.jar
/jars/jhotdraw-[0-9]*.jar
/jars/markdownj-[0-9]*.jar
/jars/miglayout-[0-9]*.jar
/jars/object-inspector-[0-9]*.jar
# Java3D #
/jars/j3d-core-[0-9]*.jar
/jars/j3d-core-utils-[0-9]*.jar
/jars/vecmath-[0-9]*.jar
# Miscellaneous #
/jars/meta-fiji-external-plugins-[0-9]*.jar