Package qupath.imagej.detect.cells
Class WatershedCellDetection
java.lang.Object
qupath.lib.plugins.AbstractPlugin<BufferedImage>
qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>
qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
qupath.imagej.detect.cells.WatershedCellDetection
- All Implemented Interfaces:
qupath.lib.plugins.PathInteractivePlugin<BufferedImage>,qupath.lib.plugins.PathPlugin<BufferedImage>
- Direct Known Subclasses:
PositiveCellDetection
public class WatershedCellDetection
extends qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
Default command for cell detection within QuPath, assuming either a nuclear or cytoplasmic staining.
To automatically classify cells as positive or negative along with detection, see PositiveCellDetection.
To quantify membranous staining see WatershedCellMembraneDetection.
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Field Summary
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionprotected qupath.lib.plugins.ObjectDetector<BufferedImage> createDetector(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params) static booleanGet whether debug mode is on or off.qupath.lib.plugins.parameters.ParameterListgetDefaultParameterList(qupath.lib.images.ImageData<BufferedImage> imageData) getName()protected doublegetPreferredPixelSizeMicrons(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params) protected intgetTileOverlap(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params) protected booleanparseArgument(qupath.lib.images.ImageData<BufferedImage> imageData, String arg) static voidsetDebugMode(boolean debug) Set whether to use debug mode.Methods inherited from class qupath.lib.plugins.AbstractTileableDetectionPlugin
addRunnableTasksMethods inherited from class qupath.lib.plugins.AbstractDetectionPlugin
getParentObjects, getSupportedParentObjectClassesMethods inherited from class qupath.lib.plugins.AbstractInteractivePlugin
alwaysPromptForObjects, getLoggableParameters, getParameterListMethods inherited from class qupath.lib.plugins.AbstractPlugin
addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate, runPluginMethods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitMethods inherited from interface qupath.lib.plugins.PathPlugin
runPlugin
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Field Details
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parametersInitialized
protected boolean parametersInitialized
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Constructor Details
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WatershedCellDetection
public WatershedCellDetection()
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Method Details
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setDebugMode
public static void setDebugMode(boolean debug) Set whether to use debug mode. If this is on, images will be shown during processing to visualize how the algorithm is working at each stage.- Parameters:
debug-- See Also:
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getDebugMode
public static boolean getDebugMode()Get whether debug mode is on or off.- Returns:
- See Also:
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parseArgument
- Overrides:
parseArgumentin classqupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
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getDefaultParameterList
public qupath.lib.plugins.parameters.ParameterList getDefaultParameterList(qupath.lib.images.ImageData<BufferedImage> imageData) - Specified by:
getDefaultParameterListin interfacequpath.lib.plugins.PathInteractivePlugin<BufferedImage>- Specified by:
getDefaultParameterListin classqupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
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getName
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getLastResultsDescription
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getDescription
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getPreferredPixelSizeMicrons
protected double getPreferredPixelSizeMicrons(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params) - Specified by:
getPreferredPixelSizeMicronsin classqupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
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createDetector
protected qupath.lib.plugins.ObjectDetector<BufferedImage> createDetector(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params) - Specified by:
createDetectorin classqupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
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getTileOverlap
protected int getTileOverlap(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params) - Specified by:
getTileOverlapin classqupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
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