Package qupath.lib.objects

Class CellTools

java.lang.Object
qupath.lib.objects.CellTools
public class CellTools extends Object
Helper class for working with PathObjects that represent cells.
Author:
Pete Bankhead

  • Constructor Details

    • CellTools

      public CellTools()

  • Method Details

    • constrainCellByScaledNucleus

      public static PathCellObject constrainCellByScaledNucleus(PathCellObject cell, double nucleusScaleFactor, boolean keepMeasurements)
      Constrain a cell boundary to fall within a maximum region, determined by scaling the nucleus ROI by a fixed scale factor about its centroid. This can be used to create more biologically plausible cell boundaries in cases where the initial boundary estimates may be too large.
      Parameters:
      cell - original cell object
      nucleusScaleFactor - scale factor by which the nucleus should be expanded to defined maximum cell size
      keepMeasurements - if true, retain the measurements of the original cell if creating a new cell; if false, discard existing measurements
      Returns:
      the updated cell object, or the original cell object either if its boundary falls within the specified limit or it lacks both boundary and nucleus ROIs

    • constrainCellOverlaps

      public static List<PathObject> constrainCellOverlaps(Collection<? extends PathObject> cells)
      Adjust cell boundary ROIs to be non-overlapping, by assigning overlaps to the cell with the closest nucleus. Results are returned as a new list of cells.
      Parameters:
      cells - input cells
      Returns:
      a new list of cells, potentially containing some of the original cells and other adjusted cells

    • detectionsToCells

      public static List<PathObject> detectionsToCells(Collection<? extends PathObject> detections, double distance, double nucleusScale)
      Create cell objects by expanding the (nucleus) ROIs from existing detections to approximate the full cell boundary.
      Parameters:
      detections - the detection objects from which to create the cells; these define the nuclei
      distance - the maximum distance (in pixels) to expand each nucleus
      nucleusScale - the maximum size of the cell relative to the nucleus (ignored if ≤ 1).
      Returns:
      cell objects derived from the supplied detections. This may have fewer entries if not all detections could be used successfully.

    • estimateCellBoundary

      public static Geometry estimateCellBoundary(Geometry geomNucleus, double distance, double nucleusScale)
      Estimate a cell boundary using Geometry objects. This avoids the need to create ROI or PathObject first.
      Parameters:
      geomNucleus - Geometry representing the cell nucleus
      distance - distance to expand the nucleus, in pixels
      nucleusScale - optional maximum expansion distance defined in terms of scaling the nucleus ROI about its centroid; ignored if ≤ 1
      Returns:
      a Geometry providing a cell boundary estimate

    • constrainCellByNucleusDistance

      public static PathCellObject constrainCellByNucleusDistance(PathCellObject cell, double distance, boolean keepMeasurements)
      Constrain a cell boundary to fall within a maximum region, determined by buffering the convex hull of the nucleus ROI by a fixed distance. This can be used to create more biologically plausible cell boundaries in cases where the initial boundary estimates may be too large.
      Parameters:
      cell - original cell object
      distance - distance (in pixels) by which the nucleus should be expanded to defined maximum cell size
      keepMeasurements - if true, retain the measurements of the original cell if creating a new cell; if false, discard existing measurements
      Returns:
      the updated cell object, or the original cell object either if its boundary falls within the specified limit or it lacks both boundary and nucleus ROIs