Package qupath.lib.analysis.features

Class ObjectMeasurements

java.lang.Object

qupath.lib.analysis.features.ObjectMeasurements

public class ObjectMeasurements
extends Object

Experimental class to generate object measurements.

May very well be moved, removed or refactored in a future release...

Nested Class Summary

Nested Classes

Modifier and Type	Class	Description
static enum	ObjectMeasurements.Compartments	Cell compartments.
static enum	ObjectMeasurements.Measurements	Requested intensity measurements.
static enum	ObjectMeasurements.ShapeFeatures	Standard measurements that may be computed from shapes.

Constructor Summary

Constructors

Constructor	Description
ObjectMeasurements()

Method Summary

Modifier and Type	Method	Description
static void	addIntensityMeasurements(ImageServer<BufferedImage> server, PathObject pathObject, double downsample, Collection<ObjectMeasurements.Measurements> measurements, Collection<ObjectMeasurements.Compartments> compartments)	Measure all channels of an image for one individual object or cell.
static void	addShapeMeasurements(Collection<? extends PathObject> pathObjects, PixelCalibration cal, ObjectMeasurements.ShapeFeatures... features)	Add shape measurements for multiple objects.
static void	addShapeMeasurements(PathObject pathObject, PixelCalibration cal, ObjectMeasurements.ShapeFeatures... features)	Add shape measurements for one object.

Methods inherited from class java.lang.Object

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

Constructor Details

ObjectMeasurements

public ObjectMeasurements()

Method Details

addShapeMeasurements

public static void addShapeMeasurements(PathObject pathObject,
 PixelCalibration cal,
 ObjectMeasurements.ShapeFeatures... features)

Add shape measurements for one object. If this is a cell, measurements will be made for both the nucleus and cell boundary where possible.

Parameters:

pathObject - the object for which measurements should be added

cal - pixel calibration, used to determine units and scaling

features - specific features to add; if empty, all available shape features will be added

addShapeMeasurements

public static void addShapeMeasurements(Collection<? extends PathObject> pathObjects,
 PixelCalibration cal,
 ObjectMeasurements.ShapeFeatures... features)

Add shape measurements for multiple objects. If any of these objects is a cell, measurements will be made for both the nucleus and cell boundary where possible.

Parameters:

pathObjects - the objects for which measurements should be added

cal - pixel calibration, used to determine units and scaling

features - specific features to add; if empty, all available shape features will be added

addIntensityMeasurements

public static void addIntensityMeasurements(ImageServer<BufferedImage> server,
 PathObject pathObject,
 double downsample,
 Collection<ObjectMeasurements.Measurements> measurements,
 Collection<ObjectMeasurements.Compartments> compartments)
                                     throws IOException

Measure all channels of an image for one individual object or cell. All compartments are measured where possible (nucleus, cytoplasm, membrane and full cell).

Note: This implementation is likely to change in the future, to enable neighboring cells to be measured more efficiently.

Parameters:

server - the server containing the pixels (and channels) to be measured

pathObject - the cell to measure (the MeasurementList will be updated)

downsample - resolution at which to request pixels

measurements - requested measurements to make

compartments - the cell compartments to measure; ignored if the object is not a cell

Throws:

IOException