KidneyStainTranslation
This repo provides a framework to train CycleGAN- and U-GAT-IT-based translators for unsupervised stain-to-stain translation in histology.
Training
To train a CycleGAN translator (e.g. incorporating a prior segmentation model), use the following command:
python ./KidneyStainTranslation/train.py --stain aSMA --stainB PAS --dataroot <path-to-data> --resultsPath <path-to-store-results> --netD n_layers --netG unet_7 --ngf 32 --ndf 32 --batch_size 3 --niters_init 0 --lr 0.0001 --preprocess none --niters 300000 --load_size 640 --crop_size 640 --lambda_A 1 --lambda_B 1 --lambda_id 1 --niters_linDecay 100 --saveModelEachNIteration 10000 --validation_freq 1000 --n_layers_D 4 --gpu_ids 0 --update_TB_images_freq 5000 --use_segm_model --lambda_Seg 1Testing
Use the same arguments to test the trained translator:
python ./KidneyStainTranslation/test.py --stain aSMA --stainB PAS --dataroot <path-to-data> --resultsPath <path-to-store-results> --netD n_layers --netG unet_7 --ngf 32 --ndf 32 --batch_size 3 --niters_init 0 --lr 0.0001 --preprocess none --niters 300000 --load_size 640 --crop_size 640 --lambda_A 1 --lambda_B 1 --lambda_id 1 --niters_linDecay 100 --saveModelEachNIteration 10000 --validation_freq 1000 --n_layers_D 4 --gpu_ids 0 --update_TB_images_freq 5000 --use_segm_model --lambda_Seg 1Contact
Nassim Bouteldja
Institute of Pathology
RWTH Aachen University Hospital
Pauwelsstrasse 30
52074 Aachen, Germany
E-mail: nbouteldja@ukaachen.de
/**************************************************************************
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* Copyright (C) 2021 by RWTH Aachen University *
* http://www.rwth-aachen.de *
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* License: *
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* This software is dual-licensed under: *
* • Commercial license (please contact: lfb@lfb.rwth-aachen.de) *
* • AGPL (GNU Affero General Public License) open source license *
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