Electrical Engineering And Systems Science

For artificial intelligence-based image analysis methods to reach clinical applicability, the development of high-performance algorithms is crucial. For example, existent segmentation algorithms based on natural images are neither efficient in their parameter use nor optimized for medical imaging. Here we present MoNet, a highly optimized neural-network-based pancreatic segmentation algorithm focused on achieving high performance by efficient multi-scale image feature utilization.

Automatic detection and segmentation of objects in 2D and 3D microscopy data is important for countless biomedical applications. In the natural image domain, spatial embedding-based instance segmentation methods are known to yield high-quality results, but their utility for segmenting microscopy data is currently little researched. Here we introduce EmbedSeg, an embedding-based instance segmentation method which outperforms existing state-of-the-art baselines on 2D as well as 3D microscopy datasets. Additionally, we show that EmbedSeg has a GPU memory footprint small enough to train even on laptop GPUs, making it accessible to virtually everyone. Finally, we introduce four new 3D microscopy datasets, which we make publicly available alongside ground truth training labels. Our open-source implementation is available at this https URL.

We present a multi-stage 3D computer-aided detection and diagnosis (CAD) model for automated localization of clinically significant prostate cancer (csPCa) in bi-parametric MR imaging (bpMRI). Deep attention mechanisms drive its detection network, targeting salient structures and highly discriminative feature dimensions across multiple resolutions. Its goal is to accurately identify csPCa lesions from indolent cancer and the wide range of benign pathology that can afflict the prostate gland. Simultaneously, a decoupled residual classifier is used to achieve consistent false positive reduction, without sacrificing high sensitivity or computational efficiency. In order to guide model generalization with domain-specific clinical knowledge, a probabilistic anatomical prior is used to encode the spatial prevalence and zonal distinction of csPCa. Using a large dataset of 1950 prostate bpMRI paired with radiologically-estimated annotations, we hypothesize that such CNN-based models can be trained to detect biopsy-confirmed malignancies in an independent cohort. For 486 institutional testing scans, the 3D CAD system achieves 83.69 ± 5.22% and 93.19 ± 2.96% detection sensitivity at 0.50 and 1.46 false positive(s) per patient, respectively, with 0.882 ± 0.030 AUROC in patient-based diagnosis ??significantly outperforming four state-of-the-art baseline architectures (U-SEResNet, UNet++, nnU-Net, Attention U-Net) from recent literature. For 296 external biopsy-confirmed testing scans, the ensembled CAD system shares moderate agreement with a consensus of expert radiologists (76.69%; kappa = 0.51 ± 0.04) and independent pathologists (81.08%; kappa = 0.56 ± 0.06); demonstrating strong generalization to histologically-confirmed csPCa diagnosis.

In this paper, we propose an enhanced 3D myocardial strain estimation procedure, which combines complementary displacement information from multiple orientations of a single imaging modality (untagged CMR SSFP images). To estimate myocardial strain across the left ventricle, we register the sets of short-axis, four-chamber and two-chamber views via a 2D non-rigid registration algorithm implemented in a commercial software (Segment, Medviso). We then create a series of interpolating functions for the three orthogonal directions of motion and use them to deform a tetrahedral mesh representation of a patient-specific left ventricle. Additionally, we correct for overestimation of displacement by introducing a weighting scheme that is based on displacement along the long axis. The procedure was evaluated on the STACOM 2011 dataset containing CMR SSFP images for 16 healthy volunteers. We show increased accuracy in estimating the three strain components (radial, circumferential, longitudinal) compared to reported results in the challenge, for the imaging modality of interest (SSFP). Our peak strain estimates are also significantly closer to reported measurements from studies of a larger cohort in the literature and our own ground truth measurements using Segment Strain Analysis Module. Our proposed procedure provides a relatively fast and simple method to improve 2D tracking results, with the added flexibility in either deforming a reconstructed mesh model from other image modalities or using the built-in CMR mesh reconstruction procedure. Our, proposed scheme presents a deforming patient-specific model of the left ventricle, using the commonest imaging modality , routinely administered in clinical settings, without requiring additional or specialized imaging protocols.

A Magnetic Resonance Imaging (MRI) exam typically consists of the acquisition of multiple MR pulse sequences, which are required for a reliable diagnosis. Each sequence can be parameterized through multiple acquisition parameters affecting MR image contrast, signal-to-noise ratio, resolution, or scan time. With the rise of generative deep learning models, approaches for the synthesis of MR images are developed to either synthesize additional MR contrasts, generate synthetic data, or augment existing data for AI training. However, current generative approaches for the synthesis of MR images are only trained on images with a specific set of acquisition parameter values, limiting the clinical value of these methods as various sets of acquisition parameter settings are used in clinical practice. Therefore, we trained a generative adversarial network (GAN) to generate synthetic MR knee images conditioned on various acquisition parameters (repetition time, echo time, image orientation). This approach enables us to synthesize MR images with adjustable image contrast. In a visual Turing test, two experts mislabeled 40.5% of real and synthetic MR images, demonstrating that the image quality of the generated synthetic and real MR images is comparable. This work can support radiologists and technologists during the parameterization of MR sequences by previewing the yielded MR contrast, can serve as a valuable tool for radiology training, and can be used for customized data generation to support AI training.

To enhance image compression performance, recent deep neural network-based research can be divided into three categories: a learnable codec, a postprocessing network, and a compact representation network. The learnable codec has been designed for an end-to-end learning beyond the conventional compression modules. The postprocessing network increases the quality of decoded images using an example-based learning. The compact representation network is learned to reduce the capacity of an input image to reduce the bitrate while keeping the quality of the decoded image. However, these approaches are not compatible with the existing codecs or not optimal to increase the coding efficiency. Specifically, it is difficult to achieve optimal learning in the previous studies using the compact representation network, due to the inaccurate consideration of the codecs. In this paper, we propose a novel standard compatible image compression framework based on Auxiliary Codec Networks (ACNs). ACNs are designed to imitate image degradation operations of the existing codec, which delivers more accurate gradients to the compact representation network. Therefore, the compact representation and the postprocessing networks can be learned effectively and optimally. We demonstrate that our proposed framework based on JPEG and High Efficiency Video Coding (HEVC) standard substantially outperforms existing image compression algorithms in a standard compatible manner.

Brain tumor segmentation plays an essential role in medical image analysis. In recent studies, deep convolution neural networks (DCNNs) are extremely powerful to tackle tumor segmentation tasks. We propose in this paper a novel training method that enhances the segmentation results by adding an additional classification branch to the network. The whole network was trained end-to-end on the Multimodal Brain Tumor Segmentation Challenge (BraTS) 2020 training dataset. On the BraTS's validation set, it achieved an average Dice score of 78.43%, 89.99%, and 84.22% respectively for the enhancing tumor, the whole tumor, and the tumor core.

Recent studies on learning-based image denoising have achieved promising performance on various noise reduction tasks. Most of these deep denoisers are trained either under the supervision of clean references, or unsupervised on synthetic noise. The assumption with the synthetic noise leads to poor generalization when facing real photographs. To address this issue, we propose a novel deep image-denoising method by regarding the noise reduction task as a special case of the noise transference task. Learning noise transference enables the network to acquire the denoising ability by observing the corrupted samples. The results on real-world denoising benchmarks demonstrate that our proposed method achieves promising performance on removing realistic noises, making it a potential solution to practical noise reduction problems.

In recent years, hyperspectral anomaly detection (HAD) has become an active topic and plays a significant role in military and civilian fields. As a classic HAD method, the collaboration representation-based detector (CRD) has attracted extensive attention and in-depth research. Despite the good performance of CRD method, its computational cost is too high for the widely demanded real-time applications. To alleviate this problem, a novel ensemble and random collaborative representation-based detector (ERCRD) is proposed for HAD. This approach comprises two main steps. Firstly, we propose a random background modeling to replace the sliding dual window strategy used in the original CRD method. Secondly, we can obtain multiple detection results through multiple random background modeling, and these results are further refined to final detection result through ensemble learning. Experiments on four real hyperspectral datasets exhibit the accuracy and efficiency of this proposed ERCRD method compared with ten state-of-the-art HAD methods.

Pneumonia is a lung infection that causes 15% of childhood mortality, over 800,000 children under five every year, all over the world. This pathology is mainly caused by viruses or bacteria. X-rays imaging analysis is one of the most used methods for pneumonia diagnosis. These clinical images can be analyzed using machine learning methods such as convolutional neural networks (CNN), which learn to extract critical features for the classification. However, the usability of these systems is limited in medicine due to the lack of interpretability, because of these models cannot be used to generate an understandable explanation (from a human-based perspective), about how they have reached those results. Another problem that difficults the impact of this technology is the limited amount of labeled data in many medicine domains. The main contributions of this work are two fold: the first one is the design of a new explainable artificial intelligence (XAI) technique based on combining the individual heatmaps obtained from each model in the ensemble. This allows to overcome the explainability and interpretability problems of the CNN "black boxes", highlighting those areas of the image which are more relevant to generate the classification. The second one is the development of new ensemble deep learning models to classify chest X-rays that allow highly competitive results using small datasets for training. We tested our ensemble model using a small dataset of pediatric X-rays (950 samples) with low quality and anatomical variability (which represents one of the biggest challenges). We also tested other strategies such as single CNNs trained from scratch and transfer learning using CheXNet. Our results show that our ensemble model outperforms these strategies obtaining highly competitive results. Finally, we confirmed the robustness of our approach using another pneumonia diagnosis dataset [1].