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francescociompi / stain-normalization-isbi-2017

Stain normalization parameters used in the paper "F. Ciompi et al., The importance of stain normalization in colorectal tissue classification with convolutional networks, ISBI 2017"
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The importance of stain normalization

This repository contains stain normalization parameters and code used in the paper:

F. Ciompi, O. Gessinnk, B. E. Bejnordi, G. Silva de Souza, A. Baidoshvili, G. Litjens, B. van Ginneken, I. Nagtegaal, J. van der Laak, The importance of stain normalization in colorectal tissue classification with convolutional networks, IEEE International Symposium in Biomedical Imaging, 2017.

Installation

Download the input images from this link: https://zenodo.org/record/53169/files/Kather_texture_2016_larger_images_10.zip and unzip it. Adapt the path in apply_stain_normalization.py to point to the folder that contains the input images.

Code example

python apply_stain_normalization.py

Code to compute Look-up tables

The code that was used to compute the look-up table files used in this project can be found at this link: https://github.com/computationalpathologygroup/WSICS