Package qupath.imagej.detect.cells

Class WatershedCellMembraneDetection

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.WatershedCellMembraneDetection
All Implemented Interfaces:
PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>
public class WatershedCellMembraneDetection extends AbstractTileableDetectionPlugin<BufferedImage>
Cell detection that takes into consideration membrane staining.

This command only works (somewhat) for hematoxylin and DAB staining. If membrane quantification is not required, WatershedCellDetection is more robust and versatile.

Author:
Pete Bankhead

  • Constructor Details

    • WatershedCellMembraneDetection

      public WatershedCellMembraneDetection()
      Default constructor.

  • Method Details

    • getDefaultParameterList

      public ParameterList getDefaultParameterList(ImageData<BufferedImage> imageData)
      Description copied from class: AbstractInteractivePlugin
      This should return a default ParameterList containing any information that is needed to repeat the task exactly.
      Specified by:
      getDefaultParameterList in interface PathInteractivePlugin<BufferedImage>
      Specified by:
      getDefaultParameterList in class AbstractInteractivePlugin<BufferedImage>
      Parameters:
      imageData -
      Returns:

    • getName

      public String getName()
      Description copied from interface: PathPlugin
      Get the name of the plugin for display.

      This should be descriptive and, above all, short - as it may be used for menu item names & dialog box titles.

      Returns:

    • getLastResultsDescription

      public String getLastResultsDescription()
      Description copied from interface: PathPlugin
      (Optional) short one-line description of the results, e.g. to say how many objects detected. GUIs may choose to display this on a label during interactive processing.
      Returns:

    • getDescription

      public String getDescription()
      Description copied from interface: PathPlugin
      Get a brief description of the plugin's purpose & operation.

      If no description is provided, this may return null.

      Returns:

    • getPreferredPixelSizeMicrons

      protected double getPreferredPixelSizeMicrons(ImageData<BufferedImage> imageData, ParameterList params)
      Description copied from class: AbstractTileableDetectionPlugin
      Get the preferred pixel size that would be used for the specified ImageData and ParameterList.

      This is useful in deciding whether to break large regions into smaller, parallelizable tiles.

      Specified by:
      getPreferredPixelSizeMicrons in class AbstractTileableDetectionPlugin<BufferedImage>
      Parameters:
      imageData -
      params -
      Returns:

    • createDetector

      protected ObjectDetector<BufferedImage> createDetector(ImageData<BufferedImage> imageData, ParameterList params)
      Description copied from class: AbstractTileableDetectionPlugin
      Create a new ObjectDetector, compatible with the specified ImageData and ParameterList.
      Specified by:
      createDetector in class AbstractTileableDetectionPlugin<BufferedImage>
      Parameters:
      imageData -
      params -
      Returns:

    • getTileOverlap

      protected int getTileOverlap(ImageData<BufferedImage> imageData, ParameterList params)
      Description copied from class: AbstractTileableDetectionPlugin
      Get an appropriate overlap, in pixels, if analysis of the specified ImageData will be tiled.

      If the overlap is 0, then tile boundaries are likely to be visible in the results.

      If the overlap is > 0, then the overlap should also be > the expected largest size of a detected object - otherwise objects may be lost of trimmed when overlaps are resolved. This is because (currently) the resolution of overlapping detections involves taking the largest one, rather than (for example) merging them.

      (Merging may be permitted in later versions, but only where measurements are not made by the plugin - since merged objects may require different measurements, e.g. for area or mean than can be easily computed in a general way from the individual objects being merged).

      Specified by:
      getTileOverlap in class AbstractTileableDetectionPlugin<BufferedImage>
      Parameters:
      imageData -
      params -
      Returns:
      The overlap size in pixels, or 0 if overlapped tiles are not supported.