StainNormalizer¶

tiatoolbox . tools . stainnorm . StainNormalizer

class StainNormalizer[source]¶

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.

stain_matrix_target¶

stain matrix of target.

target_concentrations¶

stain concentration matrix of target.

maxC_target¶

99th percentile of each stain.

stain_matrix_target_RGB¶

target stain matrix in RGB.

Methods

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

fit(target)[source]¶

Fit to a target image.

Parameters: target (numpy.ndarray of type numpy.uint8) – target/reference image.

static get_concentrations(img, stain_matrix)[source]¶

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)[source]¶

Transform an image.

Parameters: img (numpy.ndarray of type numpy.uint8) – RGB input source image.
Returns: RGB stain normalized image.
Return type: numpy.ndarray

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