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Register a new userCustomized OCT images compression scheme with deep neural network
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We customize an end-to-end image compression framework for retina OCT images based on deep convolutional neural networks (CNNs). The customized compression scheme consists of three parts: data Preprocessing, compression CNNs, and reconstruction CNNs. Data preprocessing module reduces the speckle noise of the OCT images and the segments out the region of interest. We added customized skip connections between the compression CNNs and the reconstruction CNNs to reserve the detail information and trained the two nets together with the semantic segmented image patches from data preprocessing module. To train the two networks sensitive to both low frequency information and high frequency information, we adopted an objective function with two parts: A PatchGAN discriminator to judge the high frequency information and a differentiable MS-SSIM penalty to evaluate the low frequency information. The proposed framework was trained and evaluated on a publicly available OCT dataset. The evaluation showed above 99% similarity in terms of multi-scale structural similarity (MS-SSIM) when the compression ratio is as high as 40. Furthermore, the reconstructed images of compression ratio 80 from the proposed framework even have better quality than that of compression ratio 20 from JPEG by visual comparison. The testing result outperforms JPEG in term of both of MS-SSIM and visualization, which is more obvious as the increase of compression ratio. Our preliminary result indicates the huge potential of deep neural networks on customized medical image compression.
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The reliable and rapid identification of the COVID-19 has become crucial to prevent the rapid spread of the disease, ease lockdown restrictions and reduce pressure on public health infrastructures. Recently, several methods and techniques have been proposed to detect the SARS-CoV-2 virus using different images and data. However, this is the first study that will explore the possibility of using deep convolutional neural network (CNN) models to detect COVID-19 from electrocardiogram (ECG) trace images. In this work, COVID-19 and other cardiovascular diseases (CVDs) were detected using deep-learning techniques. A public dataset of ECG images consists of 1937 images from five distinct categories, such as Normal, COVID-19, myocardial infarction (MI), abnormal heartbeat (AHB), and recovered myocardial infarction (RMI) were used in this study. Six different deep CNN models (ResNet18, ResNet50, ResNet101, InceptionV3, DenseNet201, and MobileNetv2) were used to investigate three different classification schemes: two-class classification (Normal vs COVID-19); three-class classification (Normal, COVID-19, and Other CVDs), and finally, five-class classification (Normal, COVID-19, MI, AHB, and RMI). For two-class and three-class classification, Densenet201 outperforms other networks with an accuracy of 99.1%, and 97.36%, respectively; while for the five-class classification, InceptionV3 outperforms others with an accuracy of 97.83%. ScoreCAM visualization confirms that the networks are learning from the relevant area of the trace images. Since the proposed method uses ECG trace images which can be captured by smartphones and are readily available facilities in low-resources countries, this study will help in faster computer-aided diagnosis of COVID-19 and other cardiac abnormalities.
Optical coherence tomography (OCT) is a prevalent imaging technique for retina. However, it is affected by multiplicative speckle noise that can degrade the visibility of essential anatomical structures, including blood vessels and tissue layers. Although averaging repeated B-scan frames can significantly improve the signal-to-noise-ratio (SNR), this requires longer acquisition time, which can introduce motion artifacts and cause discomfort to patients. In this study, we propose a learning-based method that exploits information from the single-frame noisy B-scan and a pseudo-modality that is created with the aid of the self-fusion method. The pseudo-modality provides good SNR for layers that are barely perceptible in the noisy B-scan but can over-smooth fine features such as small vessels. By using a fusion network, desired features from each modality can be combined, and the weight of their contribution is adjustable. Evaluated by intensity-based and structural metrics, the result shows that our method can effectively suppress the speckle noise and enhance the contrast between retina layers while the overall structure and small blood vessels are preserved. Compared to the single modality network, our method improves the structural similarity with low noise B-scan from 0.559 +- 0.033 to 0.576 +- 0.031.
Embryo quality assessment based on morphological attributes is important for achieving higher pregnancy rates from in vitro fertilization (IVF). The accurate segmentation of the embryos inner cell mass (ICM) and trophectoderm epithelium (TE) is important, as these parameters can help to predict the embryo viability and live birth potential. However, segmentation of the ICM and TE is difficult due to variations in their shape and similarities in their textures, both with each other and with their surroundings. To tackle this problem, a deep neural network (DNN) based segmentation approach was implemented. The DNN can identify the ICM region with 99.1% accuracy, 94.9% precision, 93.8% recall, a 94.3% Dice Coefficient, and a 89.3% Jaccard Index. It can extract the TE region with 98.3% accuracy, 91.8% precision, 93.2% recall, a 92.5% Dice Coefficient, and a 85.3% Jaccard Index.
The novel Coronavirus Disease 2019 (COVID-19) is a global pandemic disease spreading rapidly around the world. A robust and automatic early recognition of COVID-19, via auxiliary computer-aided diagnostic tools, is essential for disease cure and control. The chest radiography images, such as Computed Tomography (CT) and X-ray, and deep Convolutional Neural Networks (CNNs), can be a significant and useful material for designing such tools. However, designing such an automated tool is challenging as a massive number of manually annotated datasets are not publicly available yet, which is the core requirement of supervised learning systems. In this article, we propose a robust CNN-based network, called CVR-Net (Coronavirus Recognition Network), for the automatic recognition of the coronavirus from CT or X-ray images. The proposed end-to-end CVR-Net is a multi-scale-multi-encoder ensemble model, where we have aggregated the outputs from two different encoders and their different scales to obtain the final prediction probability. We train and test the proposed CVR-Net on three different datasets, where the images have collected from different open-source repositories. We compare our proposed CVR-Net with state-of-the-art methods, which are trained and tested on the same datasets. We split three datasets into five different tasks, where each task has a different number of classes, to evaluate the multi-tasking CVR-Net. Our model achieves an overall F1-score & accuracy of 0.997 & 0.998; 0.963 & 0.964; 0.816 & 0.820; 0.961 & 0.961; and 0.780 & 0.780, respectively, for task-1 to task-5. As the CVR-Net provides promising results on the small datasets, it can be an auspicious computer-aided diagnostic tool for the diagnosis of coronavirus to assist the clinical practitioners and radiologists. Our source codes and model are publicly available at https://github.com/kamruleee51/CVR-Net.
The traditional image compressors, e.g., BPG and H.266, have achieved great image and video compression quality. Recently, Convolutional Neural Network has been used widely in image compression. We proposed an attention-based convolutional neural network for low bit-rate compression to post-process the output of traditional image compression decoder. Across the experimental results on validation sets, the post-processing module trained by MAE and MS-SSIM losses yields the highest PSNR of 32.10 on average at the bit-rate of 0.15.
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