Name | Description | Type | Package | Framework |
AbstractOffscreenThread | To be used in combination with the AbstractRepaintThread, as a thread to create graphics offscreen. | Class | ini.trakem2.display | Fiji |
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AbstractOffscreenThread .RepaintProperties | | Interface | ini.trakem2.display.AbstractOffscreenThread | Fiji |
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AbstractRepaintThread | | Class | ini.trakem2.display | Fiji |
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AbstractTreeTransferHandler | Adapted from freely available code by DeuDeu from http://forum. | Class | ini.trakem2.tree | Fiji |
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AddARGBComposite | | Class | ini.trakem2.display.graphics | Fiji |
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AffineTransformMode | | Class | ini.trakem2.display | Fiji |
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AmiraImporter | Parses an amira labelfield and imports the labels as AreaList instances into the project tree. | Class | ini.trakem2.io | Fiji |
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AreaContainer | | Interface | ini.trakem2.display | Fiji |
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AreaList | A list of brush painted areas similar to a set of labelfields in Amira. | Class | ini.trakem2.display | Fiji |
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AreaTree | | Class | ini.trakem2.display | Fiji |
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AreaTree .AreaNode | | Class | ini.trakem2.display.AreaTree | Fiji |
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AreaUtils | | Class | ini.trakem2.utils | Fiji |
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AreaWrapper | | Class | ini.trakem2.display | Fiji |
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AreaWrapper .PaintParameters | | Class | ini.trakem2.display.AreaWrapper | Fiji |
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Ball | | Class | ini.trakem2.display | Fiji |
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BigBrother | Supervise all threads, and report uncaught exceptions. | Class | ini.trakem2.utils | Fiji |
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BinaryInterpolation2D | Given two binary images of the same dimensions, generate an interpolated image that sits somewhere | Class | ini.trakem2.imaging | Fiji |
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Blending | Utility functions for blending images together, to remove contrast seams. | Class | ini.trakem2.imaging | Fiji |
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Bucket | A Bucket is a subarea of the Layer area, which contains either other Buckets or a map of stack_index vs. | Class | ini.trakem2.display | Fiji |
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Bucketable | | Interface | ini.trakem2.display | Fiji |
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Bureaucrat | Sets a Worker thread to work, and waits until it finishes, blocking all user interface input until then, except for zoom and pan, for all given projects. | Class | ini.trakem2.utils | Fiji |
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Cache | Access is not synchronized, that is your duty. | Class | ini.trakem2.persistence | Fiji |
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CachingThread | | Class | ini.trakem2.utils | Fiji |
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Centrality | Following pseudo-code from: Ulrik Brandes. | Class | ini.trakem2.analysis | Fiji |
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Centrality .EtchingStep | An entry of the number of remaining branch vertices versus the set of branches (each as a List>) removed. | Class | ini.trakem2.analysis.Centrality | Fiji |
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Channel | | Class | ini.trakem2.display | Fiji |
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ContrastAdjustmentMode | | Class | ini.trakem2.display | Fiji |
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ContrastEnhancerWrapper | | Class | ini.trakem2.imaging | Fiji |
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ContrastPlot | Copied and modified from Wayne Rasband's ImageJ ContrastPlot inner class in ij. | Class | ini.trakem2.imaging | Fiji |
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ControlClickBehavior | A class to provide the behavior on control-clicking oncontent in the 3D viewer. | Class | ini.trakem2.display.d3d | Fiji |
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ControlWindow | Static class that shows one project per tab in a JFrame. | Class | ini.trakem2 | Fiji |
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Coordinate | | Class | ini.trakem2.display | Fiji |
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CoordinateTransformXML | | Class | ini.trakem2.io | Fiji |
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CorrectBackground | | Class | ini.trakem2.imaging.filters | Fiji |
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CountingTaskFactory | | Class | ini.trakem2.parallel | Fiji |
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DBLoader | | Class | ini.trakem2.persistence | Fiji |
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DBObject | Base class of all objects that can be saved in a database or XML file. | Class | ini.trakem2.persistence | Fiji |
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DefaultExecutorProvider | Default Executor Provider, which creates ExecutorServices from java. | Class | ini.trakem2.parallel | Fiji |
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DefaultGraphicsSource | Handles default mode, i. | Class | ini.trakem2.display.graphics | Fiji |
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DefaultMinAndMax | Sets the minimum to zero and the maximum to the maximum supported, or 255 for FloatProcessor and any other unknown ImageProcessor. | Class | ini.trakem2.imaging.filters | Fiji |
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DefaultMode | | Class | ini.trakem2.display | Fiji |
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DefaultTreeTransferHandler | Adapted from freely available code by DeuDeu from http://forum. | Class | ini.trakem2.tree | Fiji |
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DifferenceARGBComposite | | Class | ini.trakem2.display.graphics | Fiji |
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Dispatcher | | Class | ini.trakem2.utils | Fiji |
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Dispatcher .DispatcherThreadFactory | | Class | ini.trakem2.utils.Dispatcher | Fiji |
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Display | A Display is a class to show a Layer and enable mouse and keyboard manipulation of all its components. | Class | ini.trakem2.display | Fiji |
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Display3D | One Display3D instance for each LayerSet (maximum). | Class | ini.trakem2.display | Fiji |
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Display3D .VectorStringContent | | Class | ini.trakem2.display.Display3D | Fiji |
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Display3DGUI | | Class | ini.trakem2.display.d3d | Fiji |
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Displayable | The class that any element to be drawn on a Display must extend. | Class | ini.trakem2.display | Fiji |
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Displayable .DataPackage | | Class | ini.trakem2.display.Displayable | Fiji |
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Displayable .DoEdit | For any Displayable data, including: title, visible, locked, color, alpha, and a 'data' type which includes the actual data (points, areas, etc. | Class | ini.trakem2.display.Displayable | Fiji |
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Displayable .DoEdits | | Class | ini.trakem2.display.Displayable | Fiji |
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Displayable .DoTransforms | | Class | ini.trakem2.display.Displayable | Fiji |
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DisplayableChooser | A class to be used when a click to select Displayable objects on the Display detects that there are more than one under the mouse cursor. | Class | ini.trakem2.display | Fiji |
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DisplayablePanel | | Class | ini.trakem2.display | Fiji |
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DisplayCanvas | | Class | ini.trakem2.display | Fiji |
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DisplayNavigator | | Class | ini.trakem2.display | Fiji |
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Dissector | Each label is simply a cross marker with a number attached; labels are grouped; each member label of the group has the same number. | Class | ini.trakem2.display | Fiji |
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DLabel | This class is named funny to avoid confusion with java. | Class | ini.trakem2.display | Fiji |
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DNDInsertImage | | Class | ini.trakem2.utils | Fiji |
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DNDTree | A JTree which has a built-in drag and drop feature. | Class | ini.trakem2.tree | Fiji |
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DoStep | | Interface | ini.trakem2.display | Fiji |
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DownsamplerMipMaps | | Class | ini.trakem2.persistence | Fiji |
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DTDParser | Reads either a DOCTYPE chunk from an xml file or a . | Class | ini.trakem2.tree | Fiji |
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Editions | To extract and represent the sequence of editions that convert any N-dimensional vector string to any other of the same number of dimensions. | Class | ini.trakem2.vector | Fiji |
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Editions .Chunk | | Class | ini.trakem2.vector.Editions | Fiji |
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EnhanceContrast | Uses the @{link ContrastEnhancer. | Class | ini.trakem2.imaging.filters | Fiji |
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EqualizeHistogram | | Class | ini.trakem2.imaging.filters | Fiji |
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ExecutorProvider | Allow the source ExecutorServices in TrakEM2 to be configured. | Class | ini.trakem2.parallel | Fiji |
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FakeImagePlus | Need a non-null ImagePlus for the ImageCanvas, even if fake. | Class | ini.trakem2.display | Fiji |
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FakeImageWindow | A class to prevent ROIs from failing. | Class | ini.trakem2.display | Fiji |
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FastIntegralImage | Written following the code in ImgLib1's IntegralImage2 and ScaleAreaAveraging2d, authored by Stephan Preibisch and Albert Cardona. | Class | ini.trakem2.imaging | Fiji |
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FieldMapView | Classes extending this class acquire a read-only Map interface to access its declared fields via the reflection API provided by Class. | Class | ini.trakem2.utils | Fiji |
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FilePathRepair | A class to manage "file not found" problems. | Class | ini.trakem2.persistence | Fiji |
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Filter | | Interface | ini.trakem2.utils | Fiji |
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FilterEditor | | Class | ini.trakem2.imaging.filters | Fiji |
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FloatProcessorT2 | | Class | ini.trakem2.imaging | Fiji |
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FreeHandProfile | | Class | ini.trakem2.display | Fiji |
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FSLoader | A class to rely on memory only; except images which are rolled from a folder or their original location and flushed when memory is needed for more. | Class | ini.trakem2.persistence | Fiji |
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GaussianBlur | Smooth with a Gaussian. | Class | ini.trakem2.imaging.filters | Fiji |
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Graph | | Class | ini.trakem2.analysis | Fiji |
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GraphicsSource | | Interface | ini.trakem2.display.graphics | Fiji |
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GroupingMode | | Class | ini.trakem2.display | Fiji |
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GroupingMode .PatchRange | | Class | ini.trakem2.display.GroupingMode | Fiji |
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GroupingMode .ScreenPatchRange | | Class | ini.trakem2.display.GroupingMode | Fiji |
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History | A class to represent a generic undo/redo history. | Class | ini.trakem2.utils | Fiji |
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History .Step | | Interface | ini.trakem2.utils.History | Fiji |
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IFilter | | Interface | ini.trakem2.imaging.filters | Fiji |
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IJError | A class to easily show the stack trace of an error in different operating systems. | Class | ini.trakem2.utils | Fiji |
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ImageBytes | Represent an image with byte arrays: 2 channels: grey + alpha | Class | ini.trakem2.persistence | Fiji |
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ImageData | | Interface | ini.trakem2.display | Fiji |
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ImageFileFilter | Filters out non-accepted image formats. | Class | ini.trakem2.io | Fiji |
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ImageFileHeader | | Class | ini.trakem2.io | Fiji |
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ImageJCommandListener | Intercept ImageJ menu commands if the current active image is a FakeImagePlus (from a ini. | Class | ini.trakem2.display | Fiji |
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ImagePreprocessor | Any class implementing this interface is suitable as an image preprocessor for a TrakEM2 project. | Interface | ini.trakem2.imaging | Fiji |
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ImageSaver | Provides the necessary thread-safe image file saver utilities. | Class | ini.trakem2.io | Fiji |
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ImgLibVolume | This class encapsulates an mpicbg. | Class | ini.trakem2.utils | Fiji |
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InspectPatchTrianglesMode | A view-only mode that shows, using LayerSet. | Class | ini.trakem2.display.inspect | Fiji |
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IntegerField | | Class | ini.trakem2.utils | Fiji |
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IntegralHistogram2d | An integral histogram for 2d images. | Class | ini.trakem2.imaging | Fiji |
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IntegralImageMipMaps | | Class | ini.trakem2.persistence | Fiji |
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Invert | | Class | ini.trakem2.imaging.filters | Fiji |
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Layer | | Class | ini.trakem2.display | Fiji |
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Layer .DoMoveDisplayable | | Class | ini.trakem2.display.Layer | Fiji |
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LayerPanel | | Class | ini.trakem2.display | Fiji |
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LayerSet | A LayerSet is a container for a list of Layer. | Class | ini.trakem2.display | Fiji |
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LayerSet .DoChangeTrees | Records the state of the LayerSet. | Class | ini.trakem2.display.LayerSet | Fiji |
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LayerSet .DoMoveZDisplayable | | Class | ini.trakem2.display.LayerSet | Fiji |
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LayerStack | This class represents an entire LayerSet of Patch objects only, as it is presented read-only to ImageJ. | Class | ini.trakem2.imaging | Fiji |
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LayerThing | | Class | ini.trakem2.tree | Fiji |
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LayerTree | | Class | ini.trakem2.tree | Fiji |
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LazyVirtualStack | | Class | ini.trakem2.imaging | Fiji |
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Line3D | By definition, only ZDisplayable objects may implement Line3D. | Interface | ini.trakem2.display | Fiji |
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Loader | Handle all data-related issues with a virtualization engine, including load/unload and saving, saving as and overwriting. | Class | ini.trakem2.persistence | Fiji |
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Lock | For thread synchronization. | Class | ini.trakem2.utils | Fiji |
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LoggingInputStream | A class to monitor an input stream for speed and total byte download. | Class | ini.trakem2.io | Fiji |
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LUTBlue | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTCustom | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTCyan | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTGreen | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTMagenta | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTOrange | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTRed | | Class | ini.trakem2.imaging.filters | Fiji |
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LUTYellow | | Class | ini.trakem2.imaging.filters | Fiji |
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M | TrakEM2's mathematician. | Class | ini.trakem2.utils | Fiji |
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ManualAlignMode | | Class | ini.trakem2.display | Fiji |
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MCCube | | Class | ini.trakem2.utils | Fiji |
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MCTriangulator | | Class | ini.trakem2.utils | Fiji |
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Merger | | Class | ini.trakem2.utils | Fiji |
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MipMapImage | A MipMap is a container for an Image and its corresponding inverse x/y scale relative to an original Image | Class | ini.trakem2.display | Fiji |
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Mode | | Interface | ini.trakem2.display | Fiji |
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Montage | | Class | ini.trakem2.utils | Fiji |
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MultiplyARGBComposite | | Class | ini.trakem2.display.graphics | Fiji |
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NeuroML | | Class | ini.trakem2.io | Fiji |
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New_DB_Project | | Class | ini.trakem2 | Fiji |
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New_Project | | Class | ini.trakem2 | Fiji |
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Node | Can only have one parent, so there aren't cyclic graphs. | Class | ini.trakem2.display | Fiji |
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Node .BranchAndEndNodeIterator | | Class | ini.trakem2.display.Node | Fiji |
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Node .BranchNodeIterator | | Class | ini.trakem2.display.Node | Fiji |
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Node .BreadthFirstSubtreeIterator | For a given starting node, iterates over the complete set of children nodes, recursively and breadth-first. | Class | ini.trakem2.display.Node | Fiji |
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Node .EndNodeIterator | | Class | ini.trakem2.display.Node | Fiji |
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Node .FilteredIterator | | Class | ini.trakem2.display.Node | Fiji |
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Node .NodeCollection | Read-only Collection with a very expensive size(). | Class | ini.trakem2.display.Node | Fiji |
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Node .NodeIterator | Stateful abstract Node iterator. | Class | ini.trakem2.display.Node | Fiji |
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Node .Operation | An operation to be applied to a specific Node. | Interface | ini.trakem2.display.Node | Fiji |
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Node .SlabIterator | For a given starting node, iterates all the way to the next end node or branch node, inclusive. | Class | ini.trakem2.display.Node | Fiji |
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Node .SubtreeIterator | | Class | ini.trakem2.display.Node | Fiji |
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NonLinearTransformMode | | Class | ini.trakem2.display | Fiji |
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Normalize | | Class | ini.trakem2.imaging.filters | Fiji |
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NormalizeLocalContrast | | Class | ini.trakem2.imaging.filters | Fiji |
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Open_DB_Project | | Class | ini.trakem2 | Fiji |
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Open_Project | | Class | ini.trakem2 | Fiji |
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Operation | | Interface | ini.trakem2.utils | Fiji |
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OptionPanel | | Class | ini.trakem2.utils | Fiji |
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OptionPanel .BooleanSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .ChoiceIntSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .ChoiceObjectSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .ChoiceStringSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .DoubleSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .FloatSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .IntSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .NumericalSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .Setter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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OptionPanel .StringSetter | | Class | ini.trakem2.utils.OptionPanel | Fiji |
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Overlay | | Class | ini.trakem2.display | Fiji |
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P | | Class | ini.trakem2.imaging | Fiji |
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Paintable | | Interface | ini.trakem2.display | Fiji |
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ParallelMapping | Like clojure's pmap, given a sequence of inputs obtained from an Iterable, this Iterable will apply a function to each input ahead of consumption | Class | ini.trakem2.parallel | Fiji |
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Patch | | Class | ini.trakem2.display | Fiji |
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Patch .PatchImage | | Class | ini.trakem2.display.Patch | Fiji |
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Patch .TransformProperties | | Class | ini.trakem2.display.Patch | Fiji |
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PatchScript | | Class | ini.trakem2.scripting | Fiji |
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PatchStack | Assumed is all Patch instances in the array are of the same size, live in consecutive layers of the same thickness. | Class | ini.trakem2.imaging | Fiji |
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PhaseCorrelationCalculator | | Class | ini.trakem2.imaging | Fiji |
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Pipe | | Class | ini.trakem2.display | Fiji |
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Polyline | A sequence of points that make multiple chained line segments. | Class | ini.trakem2.display | Fiji |
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Process | For all methods, if the number of processors given as argument is zero or larger than the maximum available plus 2, the number of processors will be adjusted to fall within the range [1, max+2]. | Class | ini.trakem2.parallel | Fiji |
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Profile | A class to be a user-outlined profile over an image, which is painted with a particular color and also holds an associated text label. | Class | ini.trakem2.display | Fiji |
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Project | The top-level class in control. | Class | ini.trakem2 | Fiji |
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ProjectThing | | Class | ini.trakem2.tree | Fiji |
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ProjectTiler | | Class | ini.trakem2.persistence | Fiji |
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ProjectToolbar | | Class | ini.trakem2.utils | Fiji |
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ProjectTree | A class to hold a tree of Thing nodesSee Also:Serialized Form | Class | ini.trakem2.tree | Fiji |
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RagMipMaps | Like RawMipMaps, but the alpha channel is compressed with GZIP. | Class | ini.trakem2.io | Fiji |
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RankFilter | | Class | ini.trakem2.imaging.filters | Fiji |
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RawMipMaps | | Class | ini.trakem2.io | Fiji |
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ReconstructArea | Reconstruct an Area from a list of XML Class | ini.trakem2.display | Fiji | |
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ZDisplayable | For Pipes and other objects that must be shown in all Layers of a LayerSet. | Class | ini.trakem2.display | Fiji |