Package qupath.ext.braian

Class ChannelDetections

java.lang.Object

qupath.ext.braian.AbstractDetections

qupath.ext.braian.ChannelDetections

public class ChannelDetections
extends AbstractDetections

This class allows to manage detections computed with WatershedCellDetection on a given image channel. It does so by leveraging AbstractDetections interface

Field Summary

Fields

Modifier and Type	Field	Description
static final String	FULL_IMAGE_DETECTIONS_NAME

Constructor Summary

Constructors

Constructor	Description
ChannelDetections(String channelName, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)	Creates an instance based on pre-computed cell detections.
ChannelDetections(ImageChannelTools channel, Collection<qupath.lib.objects.PathAnnotationObject> annotations, WatershedCellDetectionConfig config, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)	Computes the detections using WatershedCellDetection algorithm inside the given annotations
ChannelDetections(ImageChannelTools channel, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)	Creates an instance based on pre-computed cell detections.
ChannelDetections(ImageChannelTools channel, qupath.lib.objects.PathAnnotationObject annotation, WatershedCellDetectionConfig config, qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)	Computes the detections using WatershedCellDetection algorithm inside the given annotations

Method Summary

Modifier and Type	Method	Description
static qupath.lib.objects.classes.PathClass	createClassification(String channelName)
String	getContainersName()
static qupath.lib.objects.PathAnnotationObject	getFullImageDetectionAnnotation(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)	Returns the annotation used when working with detections on the whole image

Methods inherited from class qupath.ext.braian.AbstractDetections

applyClassifiers, createContainer, equals, fireUpdate, getChildrenDetections, getContainers, getContainersPathClass, getDetectionsInside, getDetectionsInside, getDetectionsPathClasses, getDiscardedDetectionsPathClass, getHierarchy, getId, getOverlappingObjectIfPresent, isChannelDetection, isCompatibleClassifier, isCompatibleWith, isContainer, isEmpty, toStream

Methods inherited from class java.lang.Object

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

Field Details

FULL_IMAGE_DETECTIONS_NAME

public static final String FULL_IMAGE_DETECTIONS_NAME

See Also:

• Constant Field Values

Constructor Details

ChannelDetections

public ChannelDetections(String channelName,
 qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
                  throws NoCellContainersFoundException

Creates an instance based on pre-computed cell detections. It selects all detections that are computed in a container identified by channelName.

Parameters:

channelName - the name of the channel to which the detections are linked to

hierarchy - where to find the detections

Throws:

NoCellContainersFoundException - if no pre-computed detection was found in the given hierarchy

See Also:

• getContainersName()
• AbstractDetections

ChannelDetections

public ChannelDetections(ImageChannelTools channel,
 qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
                  throws NoCellContainersFoundException

Creates an instance based on pre-computed cell detections. It selects all detections that are computed in a container identified by channel.

Parameters:

channel - the channel to which the detections are linked to

hierarchy - where to find the detections

Throws:

NoCellContainersFoundException - if no pre-computed detection was found in the given hierarchy

See Also:

• getContainersName()
• AbstractDetections

ChannelDetections

public ChannelDetections(ImageChannelTools channel,
 Collection<qupath.lib.objects.PathAnnotationObject> annotations,
 WatershedCellDetectionConfig config,
 qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
                  throws NoCellContainersFoundException

Computes the detections using WatershedCellDetection algorithm inside the given annotations

Parameters:

channel - the channel to which the detections are linked to

annotations - the annotations inside of which to compute the detections. If null or empty, it will compute them on the whole image

config - parameters to give to the WatershedCellDetection

hierarchy - where to compute the detections

Throws:

NoCellContainersFoundException

See Also:

• getFullImageDetectionAnnotation(PathObjectHierarchy)

ChannelDetections

public ChannelDetections(ImageChannelTools channel,
 qupath.lib.objects.PathAnnotationObject annotation,
 WatershedCellDetectionConfig config,
 qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)
                  throws NoCellContainersFoundException

Computes the detections using WatershedCellDetection algorithm inside the given annotations

Parameters:

channel - the channel to which the detections are linked to

annotation - the annotation inside of which to compute the detections. If null, it will compute them on the whole image

config - parameters to give to the WatershedCellDetection

hierarchy - where to compute the detections

Throws:

NoCellContainersFoundException

See Also:

• getFullImageDetectionAnnotation(PathObjectHierarchy)

Method Details

getFullImageDetectionAnnotation

public static qupath.lib.objects.PathAnnotationObject getFullImageDetectionAnnotation(qupath.lib.objects.hierarchy.PathObjectHierarchy hierarchy)

Returns the annotation used when working with detections on the whole image

Parameters:

hierarchy - where to find/compute the detections

Returns:

the full image detection named as FULL_IMAGE_DETECTIONS_NAME

createClassification

public static qupath.lib.objects.classes.PathClass createClassification(String channelName)

getContainersName

public String getContainersName()

Specified by:

getContainersName in class AbstractDetections

Returns:

the name used by the containers of detections of the instance kind