├── .formatter └── java-imagej-coding-style.xml ├── .github ├── build.sh ├── setup.sh └── workflows │ ├── build-main.yml │ └── build-pr.yml ├── .gitignore ├── LICENSE.txt ├── README.md ├── coding-style.xml ├── icons └── rotate_planes.svg ├── pom.xml ├── src ├── main │ ├── java │ │ └── sc │ │ │ └── fiji │ │ │ └── labkit │ │ │ └── ui │ │ │ ├── ActionsAndBehaviours.java │ │ │ ├── BasicLabelingComponent.java │ │ │ ├── BatchSegmenter.java │ │ │ ├── DefaultExtensible.java │ │ │ ├── Extensible.java │ │ │ ├── InitialLabeling.java │ │ │ ├── LabelingComponent.java │ │ │ ├── LabkitFrame.java │ │ │ ├── Main.java │ │ │ ├── MenuBar.java │ │ │ ├── Preferences.java │ │ │ ├── SegmentationComponent.java │ │ │ ├── actions │ │ │ ├── AbstractFileIoAction.java │ │ │ ├── AddLabelingIoAction.java │ │ │ ├── BatchSegmentAction.java │ │ │ ├── BitmapImportExportAction.java │ │ │ ├── ClassifierIoAction.java │ │ │ ├── ClassifierSettingsAction.java │ │ │ ├── LabelEditAction.java │ │ │ ├── LabelingIoAction.java │ │ │ ├── ResetViewAction.java │ │ │ ├── SegmentationAsLabelAction.java │ │ │ ├── SegmentationExportAction.java │ │ │ ├── SetLabelsAction.java │ │ │ └── ShowHelpAction.java │ │ │ ├── bdv │ │ │ ├── BdvAutoContrast.java │ │ │ ├── BdvLayer.java │ │ │ ├── BdvLayerLink.java │ │ │ ├── BdvShowable.java │ │ │ ├── ImgPlusBdvShowable.java │ │ │ ├── SimpleBdvShowable.java │ │ │ ├── SourceBdvShowable.java │ │ │ └── SpimBdvShowable.java │ │ │ ├── brush │ │ │ ├── BdvMouseBehaviourUtils.java │ │ │ ├── BrushCursor.java │ │ │ ├── ChangeLabel.java │ │ │ ├── FloodFill.java │ │ │ ├── FloodFillController.java │ │ │ ├── LabelBrushController.java │ │ │ ├── PlanarModeController.java │ │ │ ├── SelectLabelController.java │ │ │ └── neighborhood │ │ │ │ ├── Ellipsoid.java │ │ │ │ ├── MappingCursor.java │ │ │ │ └── RealPoints.java │ │ │ ├── inputimage │ │ │ ├── DatasetInputImage.java │ │ │ ├── ImgPlusViewsOld.java │ │ │ ├── InputImage.java │ │ │ ├── SpimDataInputException.java │ │ │ ├── SpimDataInputImage.java │ │ │ └── SpimDataToImgPlus.java │ │ │ ├── labeling │ │ │ ├── Label.java │ │ │ ├── Labeling.java │ │ │ ├── LabelingSerializer.java │ │ │ ├── Labelings.java │ │ │ └── LabelsLayer.java │ │ │ ├── menu │ │ │ ├── MenuFactory.java │ │ │ └── MenuKey.java │ │ │ ├── models │ │ │ ├── CachedImageFactory.java │ │ │ ├── ColoredLabelsModel.java │ │ │ ├── DefaultCachedImageFactory.java │ │ │ ├── DefaultHolder.java │ │ │ ├── DefaultSegmentationModel.java │ │ │ ├── ExtensionPoints.java │ │ │ ├── Holder.java │ │ │ ├── ImageLabelingModel.java │ │ │ ├── LabelingModel.java │ │ │ ├── MappedHolder.java │ │ │ ├── SegmentationItem.java │ │ │ ├── SegmentationModel.java │ │ │ ├── SegmentationResultsModel.java │ │ │ ├── SegmenterListModel.java │ │ │ ├── TransformationModel.java │ │ │ └── WeakListeningHolder.java │ │ │ ├── panel │ │ │ ├── AddSegmenterPanel.java │ │ │ ├── ComponentList.java │ │ │ ├── GuiUtils.java │ │ │ ├── ImageInfoPanel.java │ │ │ ├── LabelPanel.java │ │ │ ├── LabelToolsPanel.java │ │ │ └── SegmenterPanel.java │ │ │ ├── plugin │ │ │ ├── AbstractProcessFilesInDirectoryPlugin.java │ │ │ ├── CalculateProbabilityMapWithLabkitIJ1Plugin.java │ │ │ ├── CalculateProbabilityMapWithLabkitPlugin.java │ │ │ ├── CziOpener.java │ │ │ ├── LabkitImportPlugin.java │ │ │ ├── LabkitPlugin.java │ │ │ ├── LabkitProbabilityMapForImagesInDirectoryPlugin.java │ │ │ ├── LabkitSegmentImagesInDirectoryPlugin.java │ │ │ ├── MeasureConnectedComponents.java │ │ │ ├── ResolutionPyramidSource.java │ │ │ ├── SegmentImageWithLabkitIJ1Plugin.java │ │ │ ├── SegmentImageWithLabkitPlugin.java │ │ │ └── ui │ │ │ │ └── ImageSelectionDialog.java │ │ │ ├── project │ │ │ ├── LabeledImage.java │ │ │ ├── LabeledImagesListPanel.java │ │ │ ├── LabkitProjectEditor.java │ │ │ ├── LabkitProjectFileFilter.java │ │ │ ├── LabkitProjectFileSerializer.java │ │ │ ├── LabkitProjectModel.java │ │ │ └── NewProjectDialog.java │ │ │ ├── segmentation │ │ │ ├── ForwardingSegmenter.java │ │ │ ├── PredictionLayer.java │ │ │ ├── SegmentationPlugin.java │ │ │ ├── SegmentationPluginService.java │ │ │ ├── SegmentationTool.java │ │ │ ├── SegmentationUtils.java │ │ │ ├── Segmenter.java │ │ │ ├── TrainClassifier.java │ │ │ └── weka │ │ │ │ ├── PixelClassificationPlugin.java │ │ │ │ ├── TrainableSegmentationSegmenter.java │ │ │ │ └── TrainableSegmentationSettingsDialog.java │ │ │ └── utils │ │ │ ├── ARGBVector.java │ │ │ ├── BdvUtils.java │ │ │ ├── ColorSupplier.java │ │ │ ├── ConcurrentIntFunctionCache.java │ │ │ ├── DimensionUtils.java │ │ │ ├── FileChooserCellEditor.java │ │ │ ├── HDF5Saver.java │ │ │ ├── LabkitUtils.java │ │ │ ├── Notifier.java │ │ │ ├── NumberAwareStringComparator.java │ │ │ ├── ParallelUtils.java │ │ │ ├── ParametricNotifier.java │ │ │ ├── progress │ │ │ ├── DummyProgressWriter.java │ │ │ ├── PrintStreamToLines.java │ │ │ ├── ProgressDialog.java │ │ │ ├── StatusServiceProgressWriter.java │ │ │ └── SwingProgressWriter.java │ │ │ └── sparse │ │ │ ├── IntervalIndexer2.java │ │ │ ├── MappingCursor.java │ │ │ ├── ReadRetryWriteLock.java │ │ │ ├── SparseIterableRegion.java │ │ │ └── SparseRandomAccessIntType.java │ └── resources │ │ └── images │ │ ├── add.png │ │ ├── crosshair.png │ │ ├── draw.png │ │ ├── erase.png │ │ ├── fill.png │ │ ├── flooderase.png │ │ ├── gear.png │ │ ├── help.png │ │ ├── invisible-hover.png │ │ ├── invisible.png │ │ ├── labelviewmode1.png │ │ ├── labelviewmode2.png │ │ ├── labkit-layout.png │ │ ├── leaf.png │ │ ├── move.png │ │ ├── pipette.png │ │ ├── planes.png │ │ ├── remove.png │ │ ├── rotate.png │ │ ├── run.png │ │ ├── visible-hover.png │ │ └── visible.png └── test │ ├── java │ ├── demo │ │ ├── ChangingImageSegmentationComponentDemo.java │ │ ├── CustomizedSegmentationComponentDemo.java │ │ ├── LabelingComponentDemo.java │ │ ├── LabelingComponentHdf5Demo.java │ │ ├── MultiChannelMovieDemo.java │ │ ├── ReplaceImageTest.java │ │ ├── SegmentationComponentDemo.java │ │ ├── StartImageJAndLabkitDemo.java │ │ └── custom_segmenter │ │ │ ├── CustomSegmenter.java │ │ │ ├── CustomSegmenterDemo.java │ │ │ ├── CustomSegmenterPlugin.java │ │ │ └── MeanCalculator.java │ └── sc │ │ └── fiji │ │ └── labkit │ │ └── ui │ │ ├── GarbageCollectionTest.java │ │ ├── InitialLabelingTest.java │ │ ├── SegmentationUseCaseTest.java │ │ ├── brush │ │ ├── FloodFillTest.java │ │ └── neighborhood │ │ │ ├── EllipsoidTest.java │ │ │ └── RealPointsTest.java │ │ ├── imglib2 │ │ └── AffineTransform3DTest.java │ │ ├── inputimage │ │ ├── DatasetInputImageTest.java │ │ ├── ImgPlusViewsOldTest.java │ │ └── SpimDataToImgPlusTest.java │ │ ├── labeling │ │ ├── LabelingSerializationTest.java │ │ ├── LabelingSlicerTest.java │ │ ├── LabelingTest.java │ │ ├── SparseIterableRegionTest.java │ │ └── StartImageJ.java │ │ ├── models │ │ ├── CustomCachedImageFactoryDemo.java │ │ ├── DefaultSegmentationModelTest.java │ │ └── ImageLabelingModelTest.java │ │ ├── multi_image │ │ ├── CreateLabkitProjectPlugin.java │ │ ├── LabkitProjectFrame.java │ │ ├── OpenLabkitProjectPlugin.java │ │ └── ProjectSegmentationModel.java │ │ ├── panel │ │ ├── LabelPanelDemo.java │ │ └── SegmenterPanelDemo.java │ │ ├── plugin │ │ ├── CalculateProbabilityMapWithLabkitIJ1PluginTest.java │ │ ├── CalculateProbabilityMapWithLabkitPluginTest.java │ │ ├── CziOpenerDemo.java │ │ ├── LabkitProbabilityMapForImagesInDirectoryPluginTest.java │ │ ├── LabkitSegmentImagesInDirectoryPluginTest.java │ │ ├── MeasureConnectedComponentsTest.java │ │ ├── SegmentImageWithLabkitIJ1PluginTest.java │ │ ├── SegmentImageWithLabkitPluginTest.java │ │ └── SegmentRGBImageTest.java │ │ ├── progress │ │ ├── PrintStreamToLinesTest.java │ │ └── SwingProgressWriterDemo.java │ │ ├── project │ │ ├── LabeledImagesListPanelDemo.java │ │ └── LabkitProjectFileSerializerTest.java │ │ ├── segmentation │ │ ├── SegmentationToolTest.java │ │ └── weka │ │ │ └── TrainableSegmentationSegmenterTest.java │ │ └── utils │ │ ├── ConcurrentIntFunctionCacheTest.java │ │ ├── NotifierTest.java │ │ ├── NumberAwareStringComparatorTest.java │ │ ├── ParallelUtilsDemo.java │ │ ├── TestResources.java │ │ └── sparse │ │ ├── FlightRecord.java │ │ ├── HDF5SaverDemo.java │ │ ├── HDF5SaverTest.java │ │ ├── ReadRetryWriteLockTest.java │ │ ├── SparseIterableRegionTest.java │ │ ├── SparseRandomAccessIntTypeBenchmark.java │ │ ├── SparseRandomAccessIntTypeBenchmark2.java │ │ ├── SparseRandomAccessIntTypeTest.java │ │ └── ThreadSafeLongIntHasMapTest.java │ └── resources │ ├── blobs.classifier │ ├── blobs.tif │ ├── blobs_probability_map.tif │ ├── blobs_segmentation.tif │ ├── export.h5 │ ├── export.xml │ ├── leaf.classifier │ ├── leaf.tif │ ├── leaf.tif.labeling │ ├── leaf_probability_map.tif │ ├── leaf_segmentation.tif │ ├── multi-angle-dataset.xml │ ├── size-mismatch-dataset.xml │ └── test.tif └── start.sh /.formatter/java-imagej-coding-style.xml: -------------------------------------------------------------------------------- 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