Package qupath.imagej.processing

Class SimpleThresholding

java.lang.Object

qupath.imagej.processing.SimpleThresholding

public class SimpleThresholding
extends Object

Collection of static methods to threshold images, either with single global thresholds or using the pixel values of a second image.

Output is a ByteProcessor where 255 represents 'positive' pixels, and zero represents the background.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
SimpleThresholding()

Method Summary

Modifier and Type	Method	Description
static ByteProcessor	greaterThan(ImageProcessor ip1, ImageProcessor ip2)	Created a binary image by thresholding pixels to find where ip1 > ip2
static ByteProcessor	greaterThanOrEqual(ImageProcessor ip1, ImageProcessor ip2)	Created a binary image by thresholding pixels to find where ip1 >= ip2
static ByteProcessor	imagesEqual(ImageProcessor ip1, ImageProcessor ip2)	Created a binary image by identifying pixels where ip1 == ip2
static ByteProcessor	thresholdAbove(ImageProcessor ip, float threshold)	Created a binary image by thresholding pixels to find where ip1 > threshold
static ByteProcessor	thresholdAboveEquals(ImageProcessor ip, float threshold)	Created a binary image by thresholding pixels to find where ip1 >= threshold
static ByteProcessor	thresholdBelow(ImageProcessor ip, float threshold)	Created a binary image by thresholding pixels to find where ip1 < threshold
static ByteProcessor	thresholdBelowEquals(ImageProcessor ip, float threshold)	Created a binary image by thresholding pixels to find where ip1 <= threshold
static ByteProcessor	thresholdBetween(ImageProcessor ip, float lowThreshold, float highThreshold)	Created a binary image by thresholding pixels to find where ip >= lowThreshold and ip <= highThreshold
static ROI	thresholdToROI(ImageProcessor ip, RegionRequest request)	Generate a QuPath ROI from an ImageProcessor.
static ROI	thresholdToROI(BufferedImage img, double minThreshold, double maxThreshold, int band, RegionRequest request)	Generate a QuPath ROI by thresholding an image channel image.
static ROI	thresholdToROI(Raster raster, double minThreshold, double maxThreshold, int band, TileRequest request)	Generate a QuPath ROI by thresholding an image channel image, deriving coordinates from a TileRequest.

Methods inherited from class java.lang.Object

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

Constructor Details

SimpleThresholding

public SimpleThresholding()

Method Details

greaterThanOrEqual

public static ByteProcessor greaterThanOrEqual(ImageProcessor ip1,
 ImageProcessor ip2)

Created a binary image by thresholding pixels to find where ip1 >= ip2

Parameters:

ip1 -

ip2 -

Returns:

greaterThan

public static ByteProcessor greaterThan(ImageProcessor ip1,
 ImageProcessor ip2)

Created a binary image by thresholding pixels to find where ip1 > ip2

Parameters:

ip1 -

ip2 -

Returns:

thresholdBelow

public static ByteProcessor thresholdBelow(ImageProcessor ip,
 float threshold)

Created a binary image by thresholding pixels to find where ip1 < threshold

Parameters:

ip -

threshold -

Returns:

thresholdBelowEquals

public static ByteProcessor thresholdBelowEquals(ImageProcessor ip,
 float threshold)

Created a binary image by thresholding pixels to find where ip1 <= threshold

Parameters:

ip -

threshold -

Returns:

imagesEqual

public static ByteProcessor imagesEqual(ImageProcessor ip1,
 ImageProcessor ip2)

Created a binary image by identifying pixels where ip1 == ip2

Parameters:

ip1 -

ip2 -

Returns:

thresholdAbove

public static ByteProcessor thresholdAbove(ImageProcessor ip,
 float threshold)

Created a binary image by thresholding pixels to find where ip1 > threshold

Parameters:

ip -

threshold -

Returns:

thresholdAboveEquals

public static ByteProcessor thresholdAboveEquals(ImageProcessor ip,
 float threshold)

Created a binary image by thresholding pixels to find where ip1 >= threshold

Parameters:

ip -

threshold -

Returns:

thresholdBetween

public static ByteProcessor thresholdBetween(ImageProcessor ip,
 float lowThreshold,
 float highThreshold)

Created a binary image by thresholding pixels to find where ip >= lowThreshold and ip <= highThreshold

Parameters:

ip -

lowThreshold -

highThreshold -

Returns:

thresholdToROI

public static ROI thresholdToROI(BufferedImage img,
 double minThreshold,
 double maxThreshold,
 int band,
 RegionRequest request)

Generate a QuPath ROI by thresholding an image channel image.

Parameters:

img - the input image (any type)

minThreshold - minimum threshold; pixels >= minThreshold will be included

maxThreshold - maximum threshold; pixels <= maxThreshold will be included

band - the image band to threshold (channel)

request - a RegionRequest corresponding to this image, used to calibrate the coordinates. If null, we assume no downsampling and an origin at (0,0).

Returns:

See Also:

• thresholdToROI(ImageProcessor, TileRequest)

thresholdToROI

public static ROI thresholdToROI(Raster raster,
 double minThreshold,
 double maxThreshold,
 int band,
 TileRequest request)

Generate a QuPath ROI by thresholding an image channel image, deriving coordinates from a TileRequest.

This can give a more accurate result than depending on a RegionRequest because it is possible to avoid some loss of precision.

Parameters:

raster -

minThreshold -

maxThreshold -

band -

request -

Returns:

See Also:

• thresholdToROI(ImageProcessor, RegionRequest)

thresholdToROI

public static ROI thresholdToROI(ImageProcessor ip,
 RegionRequest request)

Generate a QuPath ROI from an ImageProcessor.

It is assumed that the ImageProcessor has had its min and max threshold values set.

Parameters:

ip -

request -

Returns: