MacenkoExtractor

class MacenkoExtractor[source]

Macenko stain extractor.

Get the stain matrix as defined in:

Macenko, Marc, et al. “A method for normalizing histology slides for quantitative analysis.” 2009 IEEE International Symposium on Biomedical Imaging: From Nano to Macro. IEEE, 2009.

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

Examples

>>> from tiatoolbox.tools.stainextract import MacenkoExtractor()
>>> from tiatoolbox.utils.misc import imread
>>> extractor = MacenkoExtractor()
>>> img = imread('path/to/image')
>>> stain_matrix = extractor.get_stain_matrix(img)

Methods

get_stain_matrix

Stain matrix estimation.
static get_stain_matrix(img, luminosity_threshold=0.8, angular_percentile=99)[source]

Stain matrix estimation.

Parameters

  • img (numpy.ndarray) – input image used for stain matrix estimation

  • luminosity_threshold (float) – threshold used for tissue area selection

  • angular_percentile (int) –

Returns

estimated stain matrix.

Return type

numpy.ndarray