Package qupath.opencv

Class CellCountsCV

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>

qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>

qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>

qupath.opencv.CellCountsCV

All Implemented Interfaces:

PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>

public class CellCountsCV
extends AbstractTileableDetectionPlugin<BufferedImage>

Simple plugin to attempt a very fast cell counting based upon (smoothed) peak detection.

Currently, only H&E or hematoxylin and DAB are supported.

An improved plugin would be desirable to perform the task in a more general way, and without requesting the 'magnification' by default (which is less meaningful than resolution/pixel size).

Author:

Pete Bankhead

Field Summary

Fields inherited from class qupath.lib.plugins.AbstractInteractivePlugin

params

Constructor Summary

Constructors

Constructor	Description
CellCountsCV()

Method Summary

Modifier and Type	Method	Description
protected ObjectDetector<BufferedImage>	createDetector(ImageData<BufferedImage> imageData, ParameterList params)	Create a new ObjectDetector, compatible with the specified ImageData and ParameterList.
ParameterList	getDefaultParameterList(ImageData<BufferedImage> imageData)	This should return a default ParameterList containing any information that is needed to repeat the task exactly.
String	getDescription()	Get a brief description of the plugin's purpose & operation.
String	getLastResultsDescription()	(Optional) short one-line description of the results, e.g.
String	getName()	Get the name of the plugin for display.
protected double	getPreferredPixelSizeMicrons(ImageData<BufferedImage> imageData, ParameterList params)	Get the preferred pixel size that would be used for the specified ImageData and ParameterList.
protected int	getTileOverlap(ImageData<BufferedImage> imageData, ParameterList params)	Returns zero - indicating no overlap...
protected boolean	parseArgument(ImageData<BufferedImage> imageData, String arg)	Parse the input argument, returning 'true' if the argument is valid and it's possible to run the plugin.

Methods inherited from class qupath.lib.plugins.AbstractTileableDetectionPlugin

addRunnableTasks

Methods inherited from class qupath.lib.plugins.AbstractDetectionPlugin

getParentObjects, getSupportedParentObjectClasses

Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin

alwaysPromptForObjects, getLoggableParameters, getParameterList

Methods inherited from class qupath.lib.plugins.AbstractPlugin

addWorkflowStep, getTasks, postprocess, preprocess, rearrangeByStride, requestHierarchyUpdate, runPlugin

Methods inherited from class java.lang.Object

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

Methods inherited from interface qupath.lib.plugins.PathPlugin

runPlugin

Constructor Details

CellCountsCV

public CellCountsCV()

Method Details

parseArgument

protected boolean parseArgument(ImageData<BufferedImage> imageData,
 String arg)

Description copied from class: AbstractPlugin

Parse the input argument, returning 'true' if the argument is valid and it's possible to run the plugin.

This is called from within runPlugin. If it returns 'true', getTasks will be called and then runTasks will submit these to the plugin runner to run. If it returns 'false', runPlugin will immediately abort and return false as well. Since this could result in some internal variables changed (e.g. a ParameterList), implementing classes can't be assumed to be thread-safe; plugins should be created and called from a single thread, although they may use multiple threads (via a PluginRunner) to complete their tasks.

Overrides:

parseArgument in class AbstractInteractivePlugin<BufferedImage>

Parameters:

imageData -

arg -

Returns:

getDefaultParameterList

public ParameterList getDefaultParameterList(ImageData<BufferedImage> imageData)

Description copied from class: AbstractInteractivePlugin

This should return a default ParameterList containing any information that is needed to repeat the task exactly.

Specified by:

getDefaultParameterList in interface PathInteractivePlugin<BufferedImage>

Specified by:

getDefaultParameterList in class AbstractInteractivePlugin<BufferedImage>

Parameters:

imageData -

Returns:

getName

public String getName()

Description copied from interface: PathPlugin

Get the name of the plugin for display.

This should be descriptive and, above all, short - as it may be used for menu item names & dialog box titles.

Returns:

getDescription

public String getDescription()

Description copied from interface: PathPlugin

Get a brief description of the plugin's purpose & operation.

If no description is provided, this may return null.

Returns:

getLastResultsDescription

public String getLastResultsDescription()

Description copied from interface: PathPlugin

(Optional) short one-line description of the results, e.g. to say how many objects detected. GUIs may choose to display this on a label during interactive processing.

Returns:

getPreferredPixelSizeMicrons

protected double getPreferredPixelSizeMicrons(ImageData<BufferedImage> imageData,
 ParameterList params)

Description copied from class: AbstractTileableDetectionPlugin

Get the preferred pixel size that would be used for the specified ImageData and ParameterList.

This is useful in deciding whether to break large regions into smaller, parallelizable tiles.

Specified by:

getPreferredPixelSizeMicrons in class AbstractTileableDetectionPlugin<BufferedImage>

Parameters:

imageData -

params -

Returns:

createDetector

protected ObjectDetector<BufferedImage> createDetector(ImageData<BufferedImage> imageData,
 ParameterList params)

Description copied from class: AbstractTileableDetectionPlugin

Create a new ObjectDetector, compatible with the specified ImageData and ParameterList.

Specified by:

createDetector in class AbstractTileableDetectionPlugin<BufferedImage>

Parameters:

imageData -

params -

Returns:

getTileOverlap

protected int getTileOverlap(ImageData<BufferedImage> imageData,
 ParameterList params)

Returns zero - indicating no overlap... the aim is speed.

Specified by:

getTileOverlap in class AbstractTileableDetectionPlugin<BufferedImage>

Parameters:

imageData -

params -

Returns:

The overlap size in pixels, or 0 if overlapped tiles are not supported.