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Conference Papers Year : 2022

Region-Guided CycleGANs for Stain Transfer in Whole Slide Images


In whole slide imaging, commonly used staining techniques based on hematoxylin and eosin (H&E) and immunohistochemistry (IHC) stains accentuate different aspects of the tissue landscape. In the case of detecting metastases, IHC provides a distinct readout that is readily interpretable by pathologists. IHC, however, is a more expensive approach and not available at all medical centers. Virtually generating IHC images from H&E using deep neural networks thus becomes an attractive alternative. Deep generative models such as CycleGANs learn a semantically-consistent mapping between two image domains, while emulating the textural properties of each domain. They are therefore a suitable choice for stain transfer applications. However, they remain fully unsupervised, and possess no mechanism for enforcing biological consistency in stain transfer. In this paper, we propose an extension to CycleGANs in the form of a region of interest discriminator. This allows the CycleGAN to learn from unpaired datasets where, in addition, there is a partial annotation of objects for which one wishes to enforce consistency. We present a use case on whole slide images, where an IHC stain provides an experimentally generated signal for metastatic cells. We demonstrate the superiority of our approach over prior art in stain transfer on histopathology tiles over two datasets. Our code and model are available at


Medical Imaging
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Dates and versions

hal-03939229 , version 1 (14-01-2023)



Joseph Boyd, Irène Villa, Marie-Christine Mathieu, Eric Deutsch, Nikos Paragios, et al.. Region-Guided CycleGANs for Stain Transfer in Whole Slide Images. MICCAI 2022 - 25th International Conference on Medical Image Computing and Computer Assisted Intervention, Sep 2022, Singapore, Singapore. pp.356-365, ⟨10.1007/978-3-031-16434-7_35⟩. ⟨hal-03939229⟩
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