Class SegmentOnMaximumIntensityAndExpandInZ

Object
AnchorBean<SegmentChannelIntoObjects>
InitializableBean<SegmentChannelIntoObjects, ImageInitialization>
ImageBean<SegmentChannelIntoObjects>
SegmentationBean<SegmentChannelIntoObjects>
SegmentChannelIntoObjects
SegmentChannelIntoObjectsUnary
SegmentOnMaximumIntensityAndExpandInZ
public class SegmentOnMaximumIntensityAndExpandInZ extends SegmentChannelIntoObjectsUnary
Perform a segmentation in a MIP instead of z-stacks, and fits the result back into a 3D segmentation.

The upstream segmentation should return 2D objects as it is executed on the maximum-intensity projection.

A 3D binary-segmentation is applied to the z-stack with segmentStack to produce a mask over the z-stack. The the 2D objects are then expanded in the z-dimension to fit this mask.

Author:
Owen Feehan

  • Constructor Summary

    Constructors
    Constructor
    Description
    SegmentOnMaximumIntensityAndExpandInZ()
     

  • Method Summary

    Modifier and Type
    Method
    Description
    BinarySegmentation
    getSegmentStack()
     
    ObjectCollection
    segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter)
     
    void
    setSegmentStack(BinarySegmentation segmentStack)
     

    Methods inherited from class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjectsUnary

    getSegment, segment, setSegment

    Methods inherited from class org.anchoranalysis.image.bean.segment.object.SegmentChannelIntoObjects

    checkUnsupported3D, checkUnsupportedObjectMask, checkUnsupportedSeeds

    Methods inherited from class org.anchoranalysis.bean.initializable.InitializableBean

    getInitialization, getLogger, getPropertyInitializer, initialize, initializeRecursive, initRecursiveWithInitializer, isInitialized, onInitialization

    Methods inherited from class org.anchoranalysis.bean.AnchorBean

    checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • SegmentOnMaximumIntensityAndExpandInZ

      public SegmentOnMaximumIntensityAndExpandInZ()

  • Method Details

    • segment

      public ObjectCollection segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter) throws SegmentationFailedException
      Specified by:
      segment in class SegmentChannelIntoObjectsUnary
      Throws:
      SegmentationFailedException

    • getSegmentStack

      public BinarySegmentation getSegmentStack()

    • setSegmentStack

      public void setSegmentStack(BinarySegmentation segmentStack)