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Register a new userData Augmentation for Histopathological Images Based on Gaussian-Laplacian Pyramid Blending
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Data imbalance is a major problem that affects several machine learning (ML) algorithms. Such a problem is troublesome because most of the ML algorithms attempt to optimize a loss function that does not take into account the data imbalance. Accordingly, the ML algorithm simply generates a trivial model that is biased toward predicting the most frequent class in the training data. In the case of histopathologic images (HIs), both low-level and high-level data augmentation (DA) techniques still present performance issues when applied in the presence of inter-patient variability; whence the model tends to learn color representations, which is related to the staining process. In this paper, we propose a novel approach capable of not only augmenting HI dataset but also distributing the inter-patient variability by means of image blending using the Gaussian-Laplacian pyramid. The proposed approach consists of finding the Gaussian pyramids of two images of different patients and finding the Laplacian pyramids thereof. Afterwards, the left-half side and the right-half side of different HIs are joined in each level of the Laplacian pyramid, and from the joint pyramids, the original image is reconstructed. This composition combines the stain variation of two patients, avoiding that color differences mislead the learning process. Experimental results on the BreakHis dataset have shown promising gains vis-a-vis the majority of DA techniques presented in the literature.
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Deep convolutional neural networks(CNNs) have been successful for a wide range of computer vision tasks, including image classification. A specific area of the application lies in digital pathology for pattern recognition in the tissue-based diagnosis of gastrointestinal(GI) diseases. This domain can utilize CNNs to translate histopathological images into precise diagnostics. This is challenging since these complex biopsies are heterogeneous and require multiple levels of assessment. This is mainly due to structural similarities in different parts of the GI tract and shared features among different gut diseases. Addressing this problem with a flat model that assumes all classes (parts of the gut and their diseases) are equally difficult to distinguish leads to an inadequate assessment of each class. Since the hierarchical model restricts classification error to each sub-class, it leads to a more informative model than a flat model. In this paper, we propose to apply the hierarchical classification of biopsy images from different parts of the GI tract and the receptive diseases within each. We embedded a class hierarchy into the plain VGGNet to take advantage of its layers hierarchical structure. The proposed model was evaluated using an independent set of image patches from 373 whole slide images. The results indicate that the hierarchical model can achieve better results than the flat model for multi-category diagnosis of GI disorders using histopathological images.
Mammography is using low-energy X-rays to screen the human breast and is utilized by radiologists to detect breast cancer. Typically radiologists require a mammogram with impeccable image quality for an accurate diagnosis. In this study, we propose a deep learning method based on Convolutional Neural Networks (CNNs) for mammogram denoising to improve the image quality. We first enhance the noise level and employ Anscombe Transformation (AT) to transform Poisson noise to white Gaussian noise. With this data augmentation, a deep residual network is trained to learn the noise map of the noisy images. We show, that the proposed method can remove not only simulated but also real noise. Furthermore, we also compare our results with state-of-the-art denoising methods, such as BM3D and DNCNN. In an early investigation, we achieved qualitatively better mammogram denoising results.
Recently deep learning methods, in particular, convolutional neural networks (CNNs), have led to a massive breakthrough in the range of computer vision. Also, the large-scale annotated dataset is the essential key to a successful training procedure. However, it is a huge challenge to get such datasets in the medical domain. Towards this, we present a data augmentation method for generating synthetic medical images using cycle-consistency Generative Adversarial Networks (GANs). We add semi-supervised attention modules to generate images with convincing details. We treat tumor images and normal images as two domains. The proposed GANs-based model can generate a tumor image from a normal image, and in turn, it can also generate a normal image from a tumor image. Furthermore, we show that generated medical images can be used for improving the performance of ResNet18 for medical image classification. Our model is applied to three limited datasets of tumor MRI images. We first generate MRI images on limited datasets, then we trained three popular classification models to get the best model for tumor classification. Finally, we train the classification model using real images with classic data augmentation methods and classification models using synthetic images. The classification results between those trained models showed that the proposed SAG-GAN data augmentation method can boost Accuracy and AUC compare with classic data augmentation methods. We believe the proposed data augmentation method can apply to other medical image domains, and improve the accuracy of computer-assisted diagnosis.
Medical image analysis using deep neural networks has been actively studied. Deep neural networks are trained by learning data. For accurate training of deep neural networks, the learning data should be sufficient, of good quality, and should have a generalized property. However, in medical images, it is difficult to acquire sufficient patient data because of the difficulty of patient recruitment, the burden of annotation of lesions by experts, and the invasion of patients privacy. In comparison, the medical images of healthy volunteers can be easily acquired. Using healthy brain images, the proposed method synthesizes multi-contrast magnetic resonance images of brain tumors. Because tumors have complex features, the proposed method simplifies them into concentric circles that are easily controllable. Then it converts the concentric circles into various realistic shapes of tumors through deep neural networks. Because numerous healthy brain images are easily available, our method can synthesize a huge number of the brain tumor images with various concentric circles. We performed qualitative and quantitative analysis to assess the usefulness of augmented data from the proposed method. Intuitive and interesting experimental results are available online at https://github.com/KSH0660/BrainTumor
Pathological is crucial to cancer diagnosis. Usually, Pathologists draw their conclusion based on observed cell and tissue structure on histology slides. Rapid development in machine learning, especially deep learning have established robust and accurate classifiers. They are being used to analyze histopathological slides and assist pathologists in diagnosis. Most machine learning systems rely heavily on annotated data sets to gain experiences and knowledge to correctly and accurately perform various tasks such as classification and segmentation. This work investigates different granularity of annotations in histopathological data set including image-wise, bounding box, ellipse-wise, and pixel-wise to verify the influence of annotation in pathological slide on deep learning models. We design corresponding experiments to test classification and segmentation performance of deep learning models based on annotations with different annotation granularity. In classification, state-of-the-art deep learning-based classifiers perform better when trained by pixel-wise annotation dataset. On average, precision, recall and F1-score improves by 7.87%, 8.83% and 7.85% respectively. Thus, it is suggested that finer granularity annotations are better utilized by deep learning algorithms in classification tasks. Similarly, semantic segmentation algorithms can achieve 8.33% better segmentation accuracy when trained by pixel-wise annotations. Our study shows not only that finer-grained annotation can improve the performance of deep learning models, but also help extracts more accurate phenotypic information from histopathological slides. Intelligence systems trained on granular annotations may help pathologists inspecting certain regions for better diagnosis. The compartmentalized prediction approach similar to this work may contribute to phenotype and genotype association studies.
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