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Register a new userTowards Histopathological Stain Invariance by Unsupervised Domain Augmentation using Generative Adversarial Networks
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The application of supervised deep learning methods in digital pathology is limited due to their sensitivity to domain shift. Digital Pathology is an area prone to high variability due to many sources, including the common practice of evaluating several consecutive tissue sections stained with different staining protocols. Obtaining labels for each stain is very expensive and time consuming as it requires a high level of domain knowledge. In this article, we propose an unsupervised augmentation approach based on adversarial image-to-image translation, which facilitates the training of stain invariant supervised convolutional neural networks. By training the network on one commonly used staining modality and applying it to images that include corresponding, but differently stained, tissue structures, the presented method demonstrates significant improvements over other approaches. These benefits are illustrated in the problem of glomeruli segmentation in seven different staining modalities (PAS, Jones H&E, CD68, Sirius Red, CD34, H&E and CD3) and analysis of the learned representations demonstrate their stain invariance.
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Deep learning models that are trained on histopathological images obtained from a single lab and/or scanner give poor inference performance on images obtained from another scanner/lab with a different staining protocol. In recent years, there has been a good amount of research done for image stain normalization to address this issue. In this work, we present a novel approach for the stain normalization problem using fast neural style transfer coupled with adversarial loss. We also propose a novel stain transfer generator network based on High-Resolution Network (HRNet) which requires less training time and gives good generalization with few paired training images of reference stain and test stain. This approach has been tested on Whole Slide Images (WSIs) obtained from 8 different labs, where images from one lab were treated as a reference stain. A deep learning model was trained on this stain and the rest of the images were transferred to it using the corresponding stain transfer generator network. Experimentation suggests that this approach is able to successfully perform stain normalization with good visual quality and provides better inference performance compared to not applying stain normalization.
Digitized pathological diagnosis has been in increasing demand recently. It is well known that color information is critical to the automatic and visual analysis of pathological slides. However, the color variations due to various factors not only have negative impact on pathologists diagnosis, but also will reduce the robustness of the algorithms. The factors that cause the color differences are not only in the process of making the slices, but also in the process of digitization. Different strategies have been proposed to alleviate the color variations. Most of such techniques rely on collecting color statistics to perform color matching across images and highly dependent on a reference template slide. Since the pathological slides between hospitals are usually unpaired, these methods do not yield good matching results. In this work, we propose a novel network that we refer to as Transitive Adversarial Networks (TAN) to transfer the color information among slides from different hospitals or centers. It is not necessary for an expert to pick a representative reference slide in the proposed TAN method. We compare the proposed method with the state-of-the-art methods quantitatively and qualitatively. Compared with the state-of-the-art methods, our method yields an improvement of 0.87dB in terms of PSNR, demonstrating the effectiveness of the proposed TAN method in stain style transfer.
The shortage of annotated medical images is one of the biggest challenges in the field of medical image computing. Without a sufficient number of training samples, deep learning based models are very likely to suffer from over-fitting problem. The common solution is image manipulation such as image rotation, cropping, or resizing. Those methods can help relieve the over-fitting problem as more training samples are introduced. However, they do not really introduce new images with additional information and may lead to data leakage as the test set may contain similar samples which appear in the training set. To address this challenge, we propose to generate diverse images with generative adversarial network. In this paper, we develop a novel generative method named generative adversarial U-Net , which utilizes both generative adversarial network and U-Net. Different from existing approaches, our newly designed model is domain-free and generalizable to various medical images. Extensive experiments are conducted over eight diverse datasets including computed tomography (CT) scan, pathology, X-ray, etc. The visualization and quantitative results demonstrate the efficacy and good generalization of the proposed method on generating a wide array of high-quality medical images.
In digital pathology, different staining procedures and scanners cause substantial color variations in whole-slide images (WSIs), especially across different laboratories. These color shifts result in a poor generalization of deep learning-based methods from the training domain to external pathology data. To increase test performance, stain normalization techniques are used to reduce the variance between training and test domain. Alternatively, color augmentation can be applied during training leading to a more robust model without the extra step of color normalization at test time. We propose a novel color augmentation technique, HistAuGAN, that can simulate a wide variety of realistic histology stain colors, thus making neural networks stain-invariant when applied during training. Based on a generative adversarial network (GAN) for image-to-image translation, our model disentangles the content of the image, i.e., the morphological tissue structure, from the stain color attributes. It can be trained on multiple domains and, therefore, learns to cover different stain colors as well as other domain-specific variations introduced in the slide preparation and imaging process. We demonstrate that HistAuGAN outperforms conventional color augmentation techniques on a classification task on the publicly available dataset Camelyon17 and show that it is able to mitigate present batch effects.
Compressive sensing magnetic resonance imaging (CS-MRI) accelerates the acquisition of MR images by breaking the Nyquist sampling limit. In this work, a novel generative adversarial network (GAN) based framework for CS-MRI reconstruction is proposed. Leveraging a combination of patch-based discriminator and structural similarity index based loss, our model focuses on preserving high frequency content as well as fine textural details in the reconstructed image. Dense and residual connections have been incorporated in a U-net based generator architecture to allow easier transfer of information as well as variable network length. We show that our algorithm outperforms state-of-the-art methods in terms of quality of reconstruction and robustness to noise. Also, the reconstruction time, which is of the order of milliseconds, makes it highly suitable for real-time clinical use.
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