Package qupath.lib.analysis.algorithms

Class EstimateStainVectors

java.lang.Object

qupath.lib.analysis.algorithms.EstimateStainVectors

public class EstimateStainVectors
extends Object

Code for estimating stain vectors automatically from an image, or to launch an editor for visually/interactively modifying stain vectors.

Aspects of the automated method take inspiration from Macenko's 2009 paper 'A METHOD FOR NORMALIZING HISTOLOGY SLIDES FOR QUANTITATIVE ANALYSIS' although it also differs through its use of preprocessing and parameters, as well as its selection of an actual pixel value rather than projecting on the identified plane.

Author:

Pete Bankhead

Constructor Summary

Constructors

Constructor	Description
EstimateStainVectors()

Method Summary

Modifier and Type	Method	Description
static ColorDeconvolutionStains	estimateStains(int[] rgbPacked, float[] redOD, float[] greenOD, float[] blueOD, ColorDeconvolutionStains stainsOriginal, double minStain, double maxStain, double ignorePercentage, boolean checkColors)	Check colors only currently applies to H&E.
static ColorDeconvolutionStains	estimateStains(BufferedImage img, ColorDeconvolutionStains stainsOriginal, boolean checkColors)	Estimate two stains from a BufferedImage, with default parameter settings.
static ColorDeconvolutionStains	estimateStains(BufferedImage img, ColorDeconvolutionStains stainsOriginal, double minStain, double maxStain, double ignorePercentage, boolean checkColors)	Estimate two stains from a BufferedImage.
static int[]	getModeRGB(int[] rgb)	Get the mode from an array of (packed) RGB pixel values.
static BufferedImage	smoothImage(BufferedImage img)	Smooth out compression artefacts by running 3x3 filter twice (roughly approximates a small Gaussian filter).
static int[]	subsample(int[] arr, int maxEntries)	Subsample an array so that it contains no more than maxEntries.

Methods inherited from class java.lang.Object

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

Constructor Details

EstimateStainVectors

public EstimateStainVectors()

Method Details

estimateStains

public static ColorDeconvolutionStains estimateStains(BufferedImage img,
 ColorDeconvolutionStains stainsOriginal,
 boolean checkColors)

Estimate two stains from a BufferedImage, with default parameter settings.

Parameters:

img - original RGB image

stainsOriginal - original stains, including the background (white) values for red, green and blue and stain names

checkColors - if true, avoid colors far from H&E

Returns:

estimateStains

public static ColorDeconvolutionStains estimateStains(BufferedImage img,
 ColorDeconvolutionStains stainsOriginal,
 double minStain,
 double maxStain,
 double ignorePercentage,
 boolean checkColors)

Estimate two stains from a BufferedImage.

Parameters:

img - original RGB image

stainsOriginal - original stains, including the background (white) values for red, green and blue and stain names

minStain - minimum optical density to use

maxStain - maximum optical density to use

ignorePercentage - percentage of extrema pixels to ignore

checkColors - if true, avoid colors far from H&E

Returns:

estimateStains

public static ColorDeconvolutionStains estimateStains(int[] rgbPacked,
 float[] redOD,
 float[] greenOD,
 float[] blueOD,
 ColorDeconvolutionStains stainsOriginal,
 double minStain,
 double maxStain,
 double ignorePercentage,
 boolean checkColors)

Check colors only currently applies to H&E.

Parameters:

rgbPacked -

redOD -

greenOD -

blueOD -

stainsOriginal -

minStain -

maxStain -

ignorePercentage -

checkColors -

Returns:

subsample

public static int[] subsample(int[] arr,
 int maxEntries)

Subsample an array so that it contains no more than maxEntries. No guarantee is made that the resulting array will contain *exactly* maxEntries, but rather equal spacing between entries will be used.

If arr.length <= maxEntries, the array is returned unchanged.

Parameters:

arr -

maxEntries -

Returns:

smoothImage

public static BufferedImage smoothImage(BufferedImage img)

Smooth out compression artefacts by running 3x3 filter twice (roughly approximates a small Gaussian filter).

Parameters:

img -

Returns:

getModeRGB

public static int[] getModeRGB(int[] rgb)

Get the mode from an array of (packed) RGB pixel values.

Parameters:

rgb -

Returns:

an array with 3 entries giving the Red, Green & Blue values (in order) corresponding to the mode of each channel from the packed RGB pixel array.