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.

  • Field Summary

    Fields
    Modifier and Type
    Field
    Description
    protected boolean
     
  • Constructor Summary

    Constructors
    Constructor
    Description
     
  • Method Summary

    Modifier and Type
    Method
    Description
    protected qupath.lib.plugins.ObjectDetector<BufferedImage>
    createDetector(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params)
     
    static boolean
    Get whether debug mode is on or off.
    qupath.lib.plugins.parameters.ParameterList
    getDefaultParameterList(qupath.lib.images.ImageData<BufferedImage> imageData)
     
     
     
     
    protected double
    getPreferredPixelSizeMicrons(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params)
     
    protected int
    getTileOverlap(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params)
     
    protected boolean
    parseArgument(qupath.lib.images.ImageData<BufferedImage> imageData, String arg)
     
    static void
    setDebugMode(boolean debug)
    Set whether to use debug mode.

    Methods inherited from class qupath.lib.plugins.AbstractTileableDetectionPlugin

    addRunnableTasks

    Methods inherited from class qupath.lib.plugins.AbstractDetectionPlugin

    getParentObjects, getSupportedParentObjectClasses

    Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin

    alwaysPromptForObjects, getLoggableParameters, getParameterList

    Methods inherited from class qupath.lib.plugins.AbstractPlugin

    addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate, runPlugin

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

    Methods inherited from interface qupath.lib.plugins.PathPlugin

    runPlugin
  • Field Details

    • parametersInitialized

      protected boolean parametersInitialized
  • Constructor Details

    • WatershedCellDetection

      public WatershedCellDetection()
  • Method Details

    • 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:
    • getDebugMode

      public static boolean getDebugMode()
      Get whether debug mode is on or off.
      Returns:
      See Also:
    • parseArgument

      protected boolean parseArgument(qupath.lib.images.ImageData<BufferedImage> imageData, String arg)
      Overrides:
      parseArgument in class qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
    • getDefaultParameterList

      public qupath.lib.plugins.parameters.ParameterList getDefaultParameterList(qupath.lib.images.ImageData<BufferedImage> imageData)
      Specified by:
      getDefaultParameterList in interface qupath.lib.plugins.PathInteractivePlugin<BufferedImage>
      Specified by:
      getDefaultParameterList in class qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
    • getName

      public String getName()
    • getLastResultsDescription

      public String getLastResultsDescription()
    • getDescription

      public String getDescription()
    • getPreferredPixelSizeMicrons

      protected double getPreferredPixelSizeMicrons(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params)
      Specified by:
      getPreferredPixelSizeMicrons in class qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
    • createDetector

      protected qupath.lib.plugins.ObjectDetector<BufferedImage> createDetector(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params)
      Specified by:
      createDetector in class qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
    • getTileOverlap

      protected int getTileOverlap(qupath.lib.images.ImageData<BufferedImage> imageData, qupath.lib.plugins.parameters.ParameterList params)
      Specified by:
      getTileOverlap in class qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>