StainNormalizer

tiatoolbox . tools . stainnorm . StainNormalizer

class StainNormalizer

Stain normalization base class.

This class contains code inspired by StainTools [https://github.com/Peter554/StainTools] written by Peter Byfield.

extractor

Method specific stain extractor.

Type:

CustomExtractor, RuifrokExtractor

stain_matrix_target

Stain matrix of target.

Type:

numpy.ndarray

target_concentrations

Stain concentration matrix of target.

Type:

numpy.ndarray

maxC_target

99th percentile of each stain.

Type:

numpy.ndarray

stain_matrix_target_RGB

Target stain matrix in RGB.

Type:

numpy.ndarray

Initialize StainNormalizer.

Methods

fit	Fit to a target image.
get_concentrations	Estimate concentration matrix given an image and stain matrix.
transform	Transform an image.

fit(target)

Fit to a target image.

Parameters:

• target (numpy.ndarray of type numpy.uint8) – Target/reference image.

• self (StainNormalizer) –

Return type:

None

static get_concentrations(img, stain_matrix)

Estimate concentration matrix given an image and stain matrix.

Parameters:

• img (numpy.ndarray) – Input image.

• stain_matrix (numpy.ndarray) – Stain matrix for haematoxylin and eosin stains.

Returns:

Stain concentrations of input image.

Return type:

numpy.ndarray

transform(img)

Transform an image.

Parameters:

• img (numpy.ndarray of type numpy.uint8) – RGB input source image.

• self (StainNormalizer) –

Returns:

RGB stain normalized image.

Return type:

numpy.ndarray