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Project: TrakEM2 (GitHub Link)
  • TrakEM2-master
    • src
      • main
        • resources
          • plugins.config
          • img
            • link.svg
            • visibility.svg
            • lock.svg
          • ini
            • trakem2
              • utils
                • UncaughtExceptionReporter.java-disabled
        • java
          • lenscorrection
            • NonLinearTransform.java
            • DistortionCorrectionTask.java
            • Distortion_Correction.java
            • PolynomialModel2D.java
          • mpi
            • fruitfly
              • registration
                • CrossCorrelation2D.java
                • ImageFilter.java
              • math
                • datastructures
                  • FloatArray4D.java
                  • FloatArray2D.java
                  • FloatArray.java
                  • FloatArray3D.java
                • Quicksortable.java
                • General.java
              • general
                • ImageArrayConverter.java
                • MultiThreading.java
                • ArrayConverter.java
          • ini
            • trakem2
              • scripting
                • PatchScript.java
              • utils
                • Bureaucrat.java
                • Lock.java
                • ProjectToolbar.java
                • IntegerField.java
                • Render.java
                • RedPhone.java
                • Operation.java
                • Filter.java
                • BigBrother.java
                • DNDInsertImage.java
                • M.java
                • Search.java
                • Utils.java
                • MCTriangulator.java
                • StopWatch.java
                • Montage.java
                • CircularSequence.java
                • TypedHashMap.java
                • MCCube.java
                • OptionPanel.java
                • ImgLibVolume.java
                • Saver.java
                • CachingThread.java
                • FieldMapView.java
                • IJError.java
                • TaskOnEDT.java
                • StdOutWindow.java
                • Worker.java
                • Merger.java
                • Vector3.java
                • History.java
                • Dispatcher.java
                • AreaUtils.java
                • ReconstructArea.java
              • New_DB_Project.java
              • New_Project.java
              • plugin
                • TPlugIn.java
              • display
                • DisplayableChooser.java
                • d3d
                  • ControlClickBehavior.java
                  • Display3DGUI.java
                • Displayable.java
                • Paintable.java
                • Layer.java
                • Profile.java
                • Line3D.java
                • TransformationStep.java
                • AreaTree.java
                • Mode.java
                • inspect
                  • ShapeProxy.java
                  • InspectPatchTrianglesMode.java
                • LayerSet.java
                • Bucketable.java
                • Channel.java
                • Treeline.java
                • YesNoDialog.java
                • Display3D.java
                • VectorData.java
                • RollingPanel.java
                • Region.java
                • ContrastAdjustmentMode.java
                • LayerPanel.java
                • FreeHandProfile.java
                • paint
                  • USHORTPaintContext.java
                  • USHORTPaint.java
                • graphics
                  • DefaultGraphicsSource.java
                  • ColorYCbCrComposite.java
                  • DifferenceARGBComposite.java
                  • AddARGBComposite.java
                  • GraphicsSource.java
                  • MultiplyARGBComposite.java
                  • TestGraphicsSource.java
                  • SubtractARGBComposite.java
                • Pipe.java
                • SnapshotPanel.java
                • AreaWrapper.java
                • AbstractRepaintThread.java
                • FakeImagePlus.java
                • TreeConnectorsView.java
                • Node.java
                • Tree.java
                • Coordinate.java
                • ZDisplayable.java
                • Taggable.java
                • AffineTransformMode.java
                • AreaList.java
                • DoStep.java
                • AreaContainer.java
                • Bucket.java
                • DisplayablePanel.java
                • Dissector.java
                • NonLinearTransformMode.java
                • DLabel.java
                • Tag.java
                • Stack.java
                • ImageJCommandListener.java
                • ManualAlignMode.java
                • GroupingMode.java
                • ImageData.java
                • Patch.java
                • Polyline.java
                • FakeImageWindow.java
                • Overlay.java
                • Ball.java
                • VectorDataTransform.java
                • DefaultMode.java
                • Connector.java
                • MipMapImage.java
                • Selection.java
                • DisplayCanvas.java
                • AbstractOffscreenThread.java
                • DisplayNavigator.java
              • Project.java
              • Open_DB_Project.java
              • Open_Project.java
              • parallel
                • ExecutorProvider.java
                • ParallelMapping.java
                • Process.java
                • CountingTaskFactory.java
                • TaskFactory.java
                • DefaultExecutorProvider.java
              • analysis
                • Compare.java
                • Vertex.java
                • Centrality.java
                • Graph.java
              • io
                • ImageSaver.java
                • AmiraImporter.java
                • RagMipMaps.java
                • LoggingInputStream.java
                • ImageFileFilter.java
                • XMLFileFilter.java
                • ImageFileHeader.java
                • CoordinateTransformXML.java
                • RawMipMaps.java
                • NeuroML.java
              • tree
                • Thing.java
                • LayerThing.java
                • AbstractTreeTransferHandler.java
                • LayerTree.java
                • DTDParser.java
                • ProjectThing.java
                • TemplateThing.java
                • ProjectTree.java
                • DNDTree.java
                • TitledThing.java
                • TemplateTree.java
                • TransferableNode.java
                • DefaultTreeTransferHandler.java
                • TrakEM2MLParser.java
                • RenameThingStep.java
              • ControlWindow.java
              • imaging
                • IntegralHistogram2d.java
                • ContrastEnhancerWrapper.java
                • FloatProcessorT2.java
                • ContrastPlot.java
                • LazyVirtualStack.java
                • ImagePreprocessor.java
                • LayerStack.java
                • Segmentation.java
                • PatchStack.java
                • filters
                  • Normalize.java
                  • DefaultMinAndMax.java
                  • LUTCyan.java
                  • ValueToNoise.java
                  • RobustNormalizeLocalContrast.java
                  • LUTCustom.java
                  • FilterEditor.java
                  • CLAHE.java
                  • EqualizeHistogram.java
                  • EnhanceContrast.java
                  • NormalizeLocalContrast.java
                  • CorrectBackground.java
                  • GaussianBlur.java
                  • LUTMagenta.java
                  • LUTYellow.java
                  • IFilter.java
                  • Invert.java
                  • RankFilter.java
                  • LUTGreen.java
                  • ResetMinAndMax.java
                  • LUTRed.java
                  • LUTBlue.java
                  • LUTOrange.java
                  • SubtractBackground.java
                • PhaseCorrelationCalculator.java
                • Blending.java
                • FastIntegralImage.java
                • StitchingTEM.java
                • BinaryInterpolation2D.java
                • P.java
              • persistence
                • FSLoader.java
                • StaleFiles.java
                • ProjectTiler.java
                • TMLHandler.java
                • FilePathRepair.java
                • DBObject.java
                • XMLOptions.java
                • DBLoader.java
                • DownsamplerMipMaps.java
                • ExportMultilevelTiles.java
                • IntegralImageMipMaps.java
                • Loader.java
                • ImageBytes.java
                • Cache.java
          • mpicbg
            • trakem2
              • util
                • RobustNormalizeLocalContrast.java
              • align
                • AlignLayersTask.java
                • RigidTile2D.java
                • TileConfiguration.java
                • GenericAffineTile2D.java
                • ElasticMontage.java
                • AbstractAffineTile2D.java
                • SimilarityTile2D.java
                • AbstractLayerAlignmentParam.java
                • AffineTile2D.java
                • TranslationTile2D.java
                • Util.java
                • AlignmentUtils.java
                • RegularizedAffineLayerAlignment.java
                • concurrent
                  • BlockMatchPairCallable.java
                • Align.java
                • ElasticLayerAlignment.java
                • AlignTask.java
              • transform
                • ExportARGB.java
                • ExportBestFlatImage.java
                • ExportUnsignedShort.java
                • ExportUnsignedByte.java
          • org
            • janelia
              • intensity
                • PointMatchFilter.java
                • LinearIntensityMap.java
                • Render.java
                • RansacRegressionFilter.java
                • RansacRegressionReduceFilter.java
                • MatchIntensities.java
          • bunwarpj
            • trakem2
              • transform
                • CubicBSplineTransform.java
    • TODO
    • .mailmap
    • pom.xml
    • .travis
      • signingkey.asc.enc
      • build.sh
    • grep
    • test
      • lenscorrection.js
      • test_lenscorrection_trakem2.js
      • alignmultilayermosaics.bsh
      • movingleastsquarestransform.js
      • test_distortioncorrection_trakem2.js
      • transformmeshmapping.js
      • clonepatch.bsh
      • patch.clj
      • TestMovingLeastSquaresTransform2.java
    • README
    • .travis.yml
    • README.md
    • DownsamplerTest.java
    • TODO.ElasticAlign
    • .gitignore
    • LICENSE.txt