wsi-normalizer 1.0.1

A tool used for whole slide images normalization, support macenko, reinhard, vahadane (GPU accelerate)

WSI Normalizer: a color stain normalization tool/package for whole slide images

Inspired by & reconstructed from this repository link

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Description

Repository for normalizing whole slide images (WSI) patches.

Updates

[04/2025] We have upload the PyPI package for this repository. You can directly install it by using pip and use it without clone the repository.

Support for:

1. Reinhard Reinhard, Erik, et al. "Color transfer between images." IEEE Computer graphics and applications 21.5 (2001): 34-41.
2. Macenko 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.
3. Vahadane 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.

Package Usage

Install the package via PyPI:

pip install wsi-normalizer

Then you can use it in your code:

import cv2
from wsi_normalizer import imread, MacenkoNormalizer  # or ReinhardNormalizer, VahadaneNormalizer, TorchVahadaneNormalizer

macenko_normalizer = MacenkoNormalizer()
macenko_normalizer.fit(imread('TARGET_IMAGE.jpg'))
norm_img = macenko_normalizer.transform(imread('INPUT_IMAGE.jpg'))

cv2.imwrite('OUTPUT_IMAGE.jpg', cv2.cvtColor(norm_img, cv2.COLOR_RGB2BGR))