Axial-to-lateral super-resolution for 3D fluorescence microscopy using unsupervised deep learning

Volumetric imaging by fluorescence microscopy is often limited by anisotropic spatial resolution from inferior axial resolution compared to the lateral resolution. To address this problem, here we present a deep-learning-enabled unsupervised super-resolution technique that enhances anisotropic images in volumetric fluorescence microscopy. In contrast to the existing deep learning approaches that require matched high-resolution target volume images, our method greatly reduces the effort to put into practice as the training of a network requires as little as a single 3D image stack, without a priori knowledge of the image formation process, registration of training data, or separate acquisition of target data. This is achieved based on the optimal transport driven cycle-consistent generative adversarial network that learns from an unpaired matching between high-resolution 2D images in lateral image plane and low-resolution 2D images in the other planes. Using fluorescence confocal microscopy and light-sheet microscopy, we demonstrate that the trained network not only enhances axial resolution beyond the diffraction limit, but also enhances suppressed visual details between the imaging planes and removes imaging artifacts.

Cycle-free CycleGAN using Invertible Generator for Unsupervised Low-Dose CT Denoising

Recently, CycleGAN was shown to provide high-performance, ultra-fast denoising for low-dose X-ray computed tomography (CT) without the need for a paired training dataset. Although this was possible thanks to cycle consistency, CycleGAN requires two generators and two discriminators to enforce cycle consistency, demanding significant GPU resources and technical skills for training. A recent proposal of tunable CycleGAN with Adaptive Instance Normalization (AdaIN) alleviates the problem in part by using a single generator. However, two discriminators and an additional AdaIN code generator are still required for training. To solve this problem, here we present a novel cycle-free Cycle-GAN architecture, which consists of a single generator and a discriminator but still guarantees cycle consistency. The main innovation comes from the observation that the use of an invertible generator automatically fulfills the cycle consistency condition and eliminates the additional discriminator in the CycleGAN formulation. To make the invertible generator more effective, our network is implemented in the wavelet residual domain. Extensive experiments using various levels of low-dose CT images confirm that our method can significantly improve denoising performance using only 10% of learnable parameters and faster training time compared to the conventional CycleGAN.

Vision Transformer using Low-level Chest X-ray Feature Corpus for COVID-19 Diagnosis and Severity Quantification

Developing a robust algorithm to diagnose and quantify the severity of COVID-19 using Chest X-ray (CXR) requires a large number of well-curated COVID-19 datasets, which is difficult to collect under the global COVID-19 pandemic. On the other hand, CXR data with other findings are abundant. This situation is ideally suited for the Vision Transformer (ViT) architecture, where a lot of unlabeled data can be used through structural modeling by the self-attention mechanism. However, the use of existing ViT is not optimal, since feature embedding through direct patch flattening or ResNet backbone in the standard ViT is not intended for CXR. To address this problem, here we propose a novel Vision Transformer that utilizes low-level CXR feature corpus obtained from a backbone network that extracts common CXR findings. Specifically, the backbone network is first trained with large public datasets to detect common abnormal findings such as consolidation, opacity, edema, etc. Then, the embedded features from the backbone network are used as corpora for a Transformer model for the diagnosis and the severity quantification of COVID-19. We evaluate our model on various external test datasets from totally different institutions to evaluate the generalization capability. The experimental results confirm that our model can achieve the state-of-the-art performance in both diagnosis and severity quantification tasks with superior generalization capability, which are sine qua non of widespread deployment.

Unifying domain adaptation and self-supervised learning for CXR segmentation via AdaIN-based knowledge distillation

As the segmentation labels are scarce, extensive researches have been conducted to train segmentation networks without labels or with only limited labels. In particular, domain adaptation, self-supervised learning, and teacher-student architecture have been intro- duced to distill knowledge from various tasks to improve the segmentation performance. However, these approaches appear different from each other, so it is not clear how these seemingly different approaches can be combined for better performance. Inspired by the recent StarGANv2 for multi-domain image translation, here we propose a novel seg- mentation framework via AdaIN-based knowledge distillation, where a single generator with AdaIN layers is trained along with the AdaIN code generator and style encoder so that the generator can perform both domain adaptation and segmentation. Specifically, our framework is designed to deal with difficult situations in chest X-ray (CXR) seg- mentation tasks where segmentation masks are only available for normal CXR data, but the trained model should be applied for both normal and abnormal CXR images. Since a single generator is used for abnormal to normal domain conversion and segmentation by simply changing the AdaIN codes, the generator can synergistically learn the com- mon features to improve segmentation performance. Experimental results using CXR data confirm that the trained network can achieve the state-of-the art segmentation per- formance for both normal and abnormal CXR images.

PyNET-CA: Enhanced PyNET with Channel Attention for End-to-End Mobile Image Signal Processing

Reconstructing RGB image from RAW data obtained with a mobile device is related to a number of image signal processing (ISP) tasks, such as demosaicing, denoising, etc. Deep neural networks have shown promising results over hand-crafted ISP algorithms on solving these tasks separately, or even replacing the whole reconstruction process with one model. Here, we propose PyNET-CA, an end-to-end mobile ISP deep learning algorithm for RAW to RGB reconstruction. The model enhances PyNET, a recently proposed state-of-the-art model for mobile ISP, and improve its performance with channel attention and subpixel reconstruction module. We demonstrate the performance of the proposed method with comparative experiments and results from the AIM 2020 learned smartphone ISP challenge. The source code of our implementation is available at https://github.com/egyptdj/skyb-aim2020-public

Diagonal Attention and Style-based GAN for Content-Style Disentanglement in Image Generation and Translation

One of the important research topics in image generative models is to disentangle the spatial contents and styles for their separate control. Although StyleGAN can generate content feature vectors from random noises, the resulting spatial content control is primarily intended for minor spatial variations, and the disentanglement of global content and styles is by no means complete. Inspired by a mathematical understanding of normalization and attention, here we present a novel hierarchical adaptive Diagonal spatial ATtention (DAT) layers to separately manipulate the spatial contents from styles in a hierarchical manner. Using DAT and AdaIN, our method enables coarse-to-fine level disentanglement of spatial contents and styles. In addition, our generator can be easily integrated into the GAN inversion framework so that the content and style of translated images from multi-domain image translation tasks can be flexibly controlled. By using various datasets, we confirm that the proposed method not only outperforms the existing models in disentanglement scores, but also provides more flexible control over spatial features in the generated images.

Unsupervised Missing Cone Deep Learning in Optical Diffraction Tomography

Optical diffraction tomography (ODT) produces three dimensional distribution of refractive index (RI) by measuring scattering fields at various angles. Although the distribution of RI index is highly informative, due to the missing cone problem stemming from the limited-angle acquisition of holograms, reconstructions have very poor resolution along axial direction compared to the horizontal imaging plane. To solve this issue, here we present a novel unsupervised deep learning framework, which learns the probability distribution of missing projection views through optimal transport driven cycleGAN. Experimental results show that missing cone artifact in ODT can be significantly resolved by the proposed method.

Severity Quantification and Lesion Localization of COVID-19 on CXR using Vision Transformer

Under the global pandemic of COVID-19, building an automated framework that quantifies the severity of COVID-19 and localizes the relevant lesion on chest X-ray images has become increasingly important. Although pixel-level lesion severity labels, e.g. lesion segmentation, can be the most excellent target to build a robust model, collecting enough data with such labels is difficult due to time and labor-intensive annotation tasks. Instead, array-based severity labeling that assigns integer scores on six subdivisions of lungs can be an alternative choice enabling the quick labeling. Several groups proposed deep learning algorithms that quantify the severity of COVID-19 using the array-based COVID-19 labels and localize the lesions with explainability maps. To further improve the accuracy and interpretability, here we propose a novel Vision Transformer tailored for both quantification of the severity and clinically applicable localization of the COVID-19 related lesions. Our model is trained in a weakly-supervised manner to generate the full probability maps from weak array-based labels. Furthermore, a novel progressive self-training method enables us to build a model with a small labeled dataset. The quantitative and qualitative analysis on the external testset demonstrates that our method shows comparable performance with radiologists for both tasks with stability in a real-world application.

Vision Transformer for COVID-19 CXR Diagnosis using Chest X-ray Feature Corpus

Under the global COVID-19 crisis, developing robust diagnosis algorithm for COVID-19 using CXR is hampered by the lack of the well-curated COVID-19 data set, although CXR data with other disease are abundant. This situation is suitable for vision transformer architecture that can exploit the abundant unlabeled data using pre-training. However, the direct use of existing vision transformer that uses the corpus generated by the ResNet is not optimal for correct feature embedding. To mitigate this problem, we propose a novel vision Transformer by using the low-level CXR feature corpus that are obtained to extract the abnormal CXR features. Specifically, the backbone network is trained using large public datasets to obtain the abnormal features in routine diagnosis such as consolidation, glass-grass opacity (GGO), etc. Then, the embedded features from the backbone network are used as corpus for vision transformer training. We examine our model on various external test datasets acquired from totally different institutions to assess the generalization ability. Our experiments demonstrate that our method achieved the state-of-art performance and has better generalization capability, which are crucial for a widespread deployment.

CycleQSM: Unsupervised QSM Deep Learning using Physics-Informed CycleGAN

Quantitative susceptibility mapping (QSM) is a useful magnetic resonance imaging (MRI) technique which provides spatial distribution of magnetic susceptibility values of tissues. QSMs can be obtained by deconvolving the dipole kernel from phase images, but the spectral nulls in the dipole kernel make the inversion ill-posed. In recent times, deep learning approaches have shown a comparable QSM reconstruction performance as the classic approaches, despite the fast reconstruction time. Most of the existing deep learning methods are, however, based on supervised learning, so matched pairs of input phase images and the ground-truth maps are needed. Moreover, it was reported that the supervised learning often leads to underestimated QSM values. To address this, here we propose a novel unsupervised QSM deep learning method using physics-informed cycleGAN, which is derived from optimal transport perspective. In contrast to the conventional cycleGAN, our novel cycleGAN has only one generator and one discriminator thanks to the known dipole kernel. Experimental results confirm that the proposed method provides more accurate QSM maps compared to the existing deep learning approaches, and provide competitive performance to the best classical approaches despite the ultra-fast reconstruction.