public class SegmentOnMaximumIntensityAndExpandInZ extends SegmentChannelIntoObjectsUnary
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.
Constructor and Description |
---|
SegmentOnMaximumIntensityAndExpandInZ() |
Modifier and Type | Method and Description |
---|---|
BinarySegmentation |
getSegmentStack() |
ObjectCollection |
segment(Channel channel,
Optional<ObjectMask> objectMask,
Optional<ObjectCollection> seeds,
SegmentChannelIntoObjects upstreamSegmenter)
Creates an
ObjectCollection given the segmentation-results provided by the delegate. |
void |
setSegmentStack(BinarySegmentation segmentStack) |
getSegment, segment, setSegment
checkUnsupported3D, checkUnsupportedObjectMask, checkUnsupportedSeeds
getInitialization, getLogger, getPropertyInitializer, initialize, initializeRecursive, initRecursiveWithInitializer, isInitialized, onInitialization
checkMisconfigured, describeBean, describeChildren, duplicateBean, fields, findFieldsOfClass, getBeanName, getLocalPath, localise, toString
public SegmentOnMaximumIntensityAndExpandInZ()
public ObjectCollection segment(Channel channel, Optional<ObjectMask> objectMask, Optional<ObjectCollection> seeds, SegmentChannelIntoObjects upstreamSegmenter) throws SegmentationFailedException
SegmentChannelIntoObjectsUnary
ObjectCollection
given the segmentation-results provided by the delegate.segment
in class SegmentChannelIntoObjectsUnary
channel
- the channel as passed to SegmentChannelIntoObjectsUnary.segment(Channel, Optional, Optional)
.objectMask
- the object-mask as passed to SegmentChannelIntoObjectsUnary.segment(Channel, Optional, Optional)
.seeds
- the seeds as passed to SegmentChannelIntoObjectsUnary.segment(Channel, Optional, Optional)
.upstreamSegmenter
- the delegate segmenter.ObjectCollection
that is returned by the segmentation.SegmentationFailedException
- if segmentation cannot complete successfully.public BinarySegmentation getSegmentStack()
public void setSegmentStack(BinarySegmentation segmentStack)
Copyright © 2010–2023 Owen Feehan, ETH Zurich, University of Zurich, Hoffmann-La Roche. All rights reserved.