VahadaneExtractor

class VahadaneExtractor[source]

Vahadane stain extractor.

Get the stain matrix as defined in:

Vahadane, Abhishek, et al. “Structure-preserving color normalization and sparse stain separation for histological images.” IEEE transactions on medical imaging 35.8 (2016): 1962-1971.

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

Examples

>>> from tiatoolbox.tools.stainextract import VahadaneExtractor()
>>> from tiatoolbox.utils.misc import imread
>>> extractor = VahadaneExtractor()
>>> 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, regulariser=0.1)[source]

Stain matrix estimation.

Parameters

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

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

  • regulariser (float) – regulariser used in dictionary learning

Returns

estimated stain matrix.

Return type

numpy.ndarray