Package qupath.opencv

Class CellCountsCV

java.lang.Object
qupath.lib.plugins.AbstractPlugin<BufferedImage>
qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>
qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>
qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
qupath.opencv.CellCountsCV
All Implemented Interfaces:
qupath.lib.plugins.PathInteractivePlugin<BufferedImage>, qupath.lib.plugins.PathPlugin<BufferedImage>

public class CellCountsCV extends qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>
Simple plugin to attempt a very fast cell counting based upon (smoothed) peak detection.

Currently, only H&E or hematoxylin and DAB are supported.

An improved plugin would be desirable to perform the task in a more general way, and without requesting the 'magnification' by default (which is less meaningful than resolution/pixel size).

  • Field Summary

    Fields inherited from class qupath.lib.plugins.AbstractInteractivePlugin

    params
  • 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)
     
    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)
    Returns zero - indicating no overlap...
    protected boolean
    parseArgument(qupath.lib.images.ImageData<BufferedImage> imageData, String arg)
     

    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
  • Constructor Details

    • CellCountsCV

      public CellCountsCV()
  • Method Details

    • 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()
    • getDescription

      public String getDescription()
    • getLastResultsDescription

      public String getLastResultsDescription()
    • 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)
      Returns zero - indicating no overlap... the aim is speed.
      Specified by:
      getTileOverlap in class qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>