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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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LUT #1

Open manutdzou opened 7 years ago

manutdzou commented 7 years ago

thank you, the result shows good, but I am confused how to generate the '_LUT.tif' if there is some guided code

francescociompi commented 7 years ago

the _LUT.tif files contain the parameters theta explained in section 2.3 of the paper. In this case, the tif files were extracted using the algorithm in:

Babak Ehteshami Bejnordi et al., “Stain specific standardization of whole-slide histopathological images,” IEEE Transactions on Medical Imaging, vol. 35, no. 2, pp. 404–415, Sep 2016.

The code of the stain normalization algorithm is not available on this repository.

skn123 commented 6 years ago

Is there a place where you can find the code for computing the LUT or is this a closed implementation?

francescociompi commented 6 years ago

At the moment it is a close implementation, I will update this repo in case the stain normalization code is made publicly available.

gangli95 commented 5 years ago

Hi, I had the same question. Is the implementation open now?

francescociompi commented 5 years ago

Hi, thanks for bringing this up again. Yes, the implementation is open now, and can be found at this link: https://github.com/computationalpathologygroup/WSICS

gangli95 commented 5 years ago

wow, it's great! thanks very much.