Package qupath.imagej.superpixels

Class SLICSuperpixelsPlugin

java.lang.Object

qupath.lib.plugins.AbstractPlugin<BufferedImage>

qupath.lib.plugins.AbstractInteractivePlugin<BufferedImage>

qupath.lib.plugins.AbstractDetectionPlugin<BufferedImage>

qupath.lib.plugins.AbstractTileableDetectionPlugin<BufferedImage>

qupath.imagej.superpixels.SLICSuperpixelsPlugin

All Implemented Interfaces:

PathInteractivePlugin<BufferedImage>, PathPlugin<BufferedImage>

public class SLICSuperpixelsPlugin
extends AbstractTileableDetectionPlugin<BufferedImage>

An implementation of SLIC superpixels, as described at http://ivrl.epfl.ch/research/superpixels

This largely follows the description at:

Radhakrishna Achanta, Appu Shaji, Kevin Smith, Aurelien Lucchi, Pascal Fua, and Sabine Süsstrunk
SLIC Superpixels Compared to State-of-the-art Superpixel Methods
IEEE Transactions on Pattern Analysis and Machine Intelligence, vol. 34, num. 11, p. 2274 - 2282, May 2012.

It doesn't follow the code made available by the authors, and differs in some details.

For example, the 'spacing' parameter is also used to determine the resolution at which the superpixel computation is performed, and a Gaussian filter is used to help reduce textures in advance. It is also possible to use color deconvolved images, rather than transforming RGB to CIELAB.

Author:

Pete Bankhead

Field Summary

Fields inherited from class qupath.lib.plugins.AbstractInteractivePlugin

params

Constructor Summary

Constructors

Constructor	Description
SLICSuperpixelsPlugin()

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 Collection<? extends PathObject>	getParentObjects(ImageData<BufferedImage> imageData)	Get all selected objects that are instances of a supported class.
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)	Get an appropriate overlap, in pixels, if analysis of the specified ImageData will be tiled.

Methods inherited from class qupath.lib.plugins.AbstractTileableDetectionPlugin

addRunnableTasks

Methods inherited from class qupath.lib.plugins.AbstractDetectionPlugin

getSupportedParentObjectClasses

Methods inherited from class qupath.lib.plugins.AbstractInteractivePlugin

alwaysPromptForObjects, getLoggableParameters, getParameterList, parseArgument

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

SLICSuperpixelsPlugin

public SLICSuperpixelsPlugin()

Method Details

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:

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)

Description copied from class: AbstractTileableDetectionPlugin

Get an appropriate overlap, in pixels, if analysis of the specified ImageData will be tiled.

If the overlap is 0, then tile boundaries are likely to be visible in the results.

If the overlap is > 0, then the overlap should also be > the expected largest size of a detected object - otherwise objects may be lost of trimmed when overlaps are resolved. This is because (currently) the resolution of overlapping detections involves taking the largest one, rather than (for example) merging them.

(Merging may be permitted in later versions, but only where measurements are not made by the plugin - since merged objects may require different measurements, e.g. for area or mean than can be easily computed in a general way from the individual objects being merged).

Specified by:

getTileOverlap in class AbstractTileableDetectionPlugin<BufferedImage>

Parameters:

imageData -

params -

Returns:

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

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:

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:

getParentObjects

protected Collection<? extends PathObject> getParentObjects(ImageData<BufferedImage> imageData)

Description copied from class: AbstractDetectionPlugin

Get all selected objects that are instances of a supported class.

Overrides:

getParentObjects in class AbstractDetectionPlugin<BufferedImage>

Parameters:

imageData -

Returns: