Image and Video Processing (eess.IV)

Abstract: Retinal diseases (RD) are the leading cause of severe vision loss or blindness. Deep learning-based automated tools play an indispensable role in assisting clinicians in diagnosing and monitoring RD in modern medicine. Recently, an increasing number of works in this field have taken advantage of Vision Transformer to achieve state-of-the-art performance with more parameters and higher model complexity compared to Convolutional Neural Networks (CNNs). Such sophisticated and task-specific model designs, however, are prone to be overfitting and hinder their generalizability. In this work, we argue that a channel-aware and well-calibrated CNN model may overcome these problems. To this end, we empirically studied CNN's macro and micro designs and its training strategies. Based on the investigation, we proposed a no-new-MobleNet (nn-MobileNet) developed for retinal diseases. In our experiments, our generic, simple and efficient model superseded most current state-of-the-art methods on four public datasets for multiple tasks, including diabetic retinopathy grading, fundus multi-disease detection, and diabetic macular edema classification. Our work may provide novel insights into deep learning architecture design and advance retinopathy research.

Abstract: Microsatellites and drones are often equipped with digital cameras whose sensing system is based on color filter arrays (CFAs), which define a pattern of color filter overlaid over the focal plane. Recent commercial cameras have started implementing RGBW patterns, which include some filters with a wideband spectral response together with the more classical RGB ones. This allows for additional light energy to be captured by the relevant pixels and increases the overall SNR of the acquisition. Demosaicking defines reconstructing a multi-spectral image from the raw image and recovering the full color components for all pixels. However, this operation is often tailored for the most widespread patterns, such as the Bayer pattern. Consequently, less common patterns that are still employed in commercial cameras are often neglected. In this work, we present a generalized framework to represent the image formation model of such cameras. This model is then exploited by our proposed demosaicking algorithm to reconstruct the datacube of interest with a Bayesian approach, using a total variation regularizer as prior. Some preliminary experimental results are also presented, which apply to the reconstruction of acquisitions of various RGBW cameras.

Abstract: Focal cortical dysplasia (FCD) is a leading cause of drug-resistant focal epilepsy, which can be cured by surgery. These lesions are extremely subtle and often missed even by expert neuroradiologists. "Ground truth" manual lesion masks are therefore expensive, limited and have large inter-rater variability. Existing FCD detection methods are limited by high numbers of false positive predictions, primarily due to vertex- or patch-based approaches that lack whole-brain context. Here, we propose to approach the problem as semantic segmentation using graph convolutional networks (GCN), which allows our model to learn spatial relationships between brain regions. To address the specific challenges of FCD identification, our proposed model includes an auxiliary loss to predict distance from the lesion to reduce false positives and a weak supervision classification loss to facilitate learning from uncertain lesion masks. On a multi-centre dataset of 1015 participants with surface-based features and manual lesion masks from structural MRI data, the proposed GCN achieved an AUC of 0.74, a significant improvement against a previously used vertex-wise multi-layer perceptron (MLP) classifier (AUC 0.64). With sensitivity thresholded at 67%, the GCN had a specificity of 71% in comparison to 49% when using the MLP. This improvement in specificity is vital for clinical integration of lesion-detection tools into the radiological workflow, through increasing clinical confidence in the use of AI radiological adjuncts and reducing the number of areas requiring expert review.

Abstract: This work provides a solution to the challenge of small amounts of training data in Non-Destructive Ultrasonic Testing for composite components. It was demonstrated that direct simulation alone is ineffective at producing training data that was representative of the experimental domain due to poor noise reconstruction. Therefore, four unique synthetic data generation methods were proposed which use semi-analytical simulated data as a foundation. Each method was evaluated on its classification performance of real experimental images when trained on a Convolutional Neural Network which underwent hyperparameter optimization using a genetic algorithm. The first method introduced task specific modifications to CycleGAN, to learn the mapping from physics-based simulations of defect indications to experimental indications in resulting ultrasound images. The second method was based on combining real experimental defect free images with simulated defect responses. The final two methods fully simulated the noise responses at an image and signal level respectively. The purely simulated data produced a mean classification F1 score of 0.394. However, when trained on the new synthetic datasets, a significant improvement in classification performance on experimental data was realized, with mean classification F1 scores of 0.843, 0.688, 0.629, and 0.738 for the respective approaches.

Abstract: Advancements in digital pathology and computing resources have made a significant impact in the field of computational pathology for breast cancer diagnosis and treatment. However, access to high-quality labeled histopathological images of breast cancer is a big challenge that limits the development of accurate and robust deep learning models. In this systematic review, we identified the publicly available datasets of breast H&E stained whole-slide images (WSI) that can be used to develop deep learning algorithms. We systematically searched nine scientific literature databases and nine research data repositories. We found twelve publicly available datasets, containing 5153 H&E WSIs of breast cancer. Moreover, we reported image metadata and characteristics for each dataset to assist researchers in selecting proper datasets for specific tasks in breast cancer computational pathology. In addition, we compiled a list of patch and private datasets that were used in the included articles as a supplementary resource for researchers. Notably, 22% of the included articles utilized multiple datasets, and only 12% of the articles used an external validation set, suggesting that the performance of other developed models may be susceptible to overestimation. The TCGA-BRCA was used in 47.4% of the selected studies. This dataset has a considerable selection bias that can impact the robustness and generalizability of the trained algorithms. There is also a lack of consistent metadata reporting of breast WSI datasets that can be an issue in developing accurate deep learning models, indicating the necessity of establishing explicit guidelines for documenting breast WSI dataset characteristics and metadata.

Abstract: Magnetic resonance (MR) and computer tomography (CT) imaging are valuable tools for diagnosing diseases and planning treatment. However, limitations such as radiation exposure and cost can restrict access to certain imaging modalities. To address this issue, medical image synthesis can generate one modality from another, but many existing models struggle with high-quality image synthesis when multiple slices are present in the dataset. This study proposes an attention-based dual contrast generative model, called ADC-cycleGAN, which can synthesize medical images from unpaired data with multiple slices. The model integrates a dual contrast loss term with the CycleGAN loss to ensure that the synthesized images are distinguishable from the source domain. Additionally, an attention mechanism is incorporated into the generators to extract informative features from both channel and spatial domains. To improve performance when dealing with multiple slices, the $K$-means algorithm is used to cluster the dataset into $K$ groups, and each group is used to train a separate ADC-cycleGAN. Experimental results demonstrate that the proposed ADC-cycleGAN model produces comparable samples to other state-of-the-art generative models, achieving the highest PSNR and SSIM values of 19.04385 and 0.68551, respectively. We publish the code at https://github.com/JiayuanWang-JW/ADC-cycleGAN.

Abstract: Accelerated magnetic resonance (MR) imaging attempts to reduce acquisition time by collecting data below the Nyquist rate. As an ill-posed inverse problem, many plausible solutions exist, yet the majority of deep learning approaches generate only a single solution. We instead focus on sampling from the posterior distribution, which provides more comprehensive information for downstream inference tasks. To do this, we design a novel conditional normalizing flow (CNF) that infers the signal component in the measurement operator's nullspace, which is later combined with measured data to form complete images. Using fastMRI brain and knee data, we demonstrate fast inference and accuracy that surpasses recent posterior sampling techniques for MRI. Code is available at https://github.com/jwen307/mri_cnf/

Abstract: We propose a novel algorithm called Unique Brain Network Identification Number (UBNIN) for encoding brain networks of individual subject. To realize this objective, we employed T1-weighted structural MRI of 180 Parkinson's disease (PD) patients from National Institute of Mental Health and Neurosciences, India. We parcellated each subject's brain volume and constructed individual adjacency matrix using correlation between grey matter (GM) volume of every pair of regions. The unique code is derived from values representing connections of every node (i), weighted by a factor of 2^-(i-1). The numerical representation UBNIN was observed to be distinct for each individual brain network, which may also be applied to other neuroimaging modalities. This model may be implemented as neural signature of a person's unique brain connectivity, thereby useful for brainprinting applications. Additionally, we segregated the above dataset into five age-cohorts: A:22-32years, B:33-42years, C:43-52years, D:53-62years and E:63-72years to study the variation in network topology over age. Sparsity was adopted as the threshold estimate to binarize each age-based correlation matrix. Connectivity metrics were obtained using Brain Connectivity toolbox-based MATLAB functions. For each age-cohort, a decreasing trend was observed in mean clustering coefficient with increasing sparsity. Significantly different clustering coefficient was noted between age-cohort B and C (sparsity: 0.63,0.66), C and E (sparsity: 0.66,0.69). Our findings suggest network connectivity patterns change with age, indicating network disruption due to the underlying neuropathology. Varying clustering coefficient for different cohorts indicate that information transfer between neighboring nodes change with age. This provides evidence on age-related brain shrinkage and network degeneration.