There is increasing interest in identifying changes in the underlying states of brain networks. The availability of large scale neuroimaging data creates a strong need to develop fast, scalable methods for detecting and localizing in time such changes and also identify their drivers, thus enabling neuroscientists to hypothesize about potential mechanisms. This paper presents a fast method for detecting

The minimum histological criterion for the diagnostics of Alzheimer's disease (AD) in tissue is the presence of senile plaques and neurofibrillary tangles in specific brain locations. The routine procedure of morphological analysis implies time-consuming and laborious steps including sectioning and staining of formalin-fixed paraffin-embedded (FFPE) tissue. We developed a multispectral Stokes polarimetric

While Electrical Impedance Tomography (EIT) has found many biomedicine applications, better image quality is needed to provide quantitative analysis for tissue engineering and regenerative medicine. This paper reports an impedance-optical dual-modal imaging framework that primarily targets at high-quality 3D cell culture imaging and can be extended to other tissue engineering applications. The framework

Machine learning and deep learning methods have become essential for computer-assisted prediction in medicine, with a growing number of applications also in the field of mammography. Typically these algorithms are trained for a specific task, e.g., the classification of lesions or the prediction of a mammogram's pathology status. To obtain a comprehensive view of a patient, models which were all trained

Image-guided radiation therapy (IGRT) is the most effective treatment for head and neck cancer. The successful implementation of IGRT requires accurate delineation of organ-at-risk (OAR) in the computed tomography (CT) images. In routine clinical practice, OARs are manually segmented by oncologists, which is time-consuming, laborious, and subjective. To assist oncologists in OAR contouring, we proposed

Computed tomography (CT) images are often impaired by unfavorable artifacts caused by metallic implants within patients, which would adversely affect the subsequent clinical diagnosis and treatment. Although the existing deep-learning-based approaches have achieved promising success on metal artifact reduction (MAR) for CT images, most of them treated the task as a general image restoration problem

Dark-field radiography of the human chest is a promising novel imaging technique with the potential of becoming a valuable tool for the early diagnosis of chronic obstructive pulmonary disease and other diseases of the lung. The large field-of-view needed for clinical purposes could recently be achieved by a scanning system. While this approach overcomes the limited availability of large area grating

We propose a method for human embryo grading with its images. This grading has been achieved by positive-negative classification (i.e., live birth or non-live birth). However, negative (non-live birth) labels collected in clinical practice are unreliable because the visual features of negative images are equal to those of positive (live birth) images if these non-live birth embryos have chromosome

Digital reconstruction of neuronal morphologies in 3D microscopy images is critical in the field of neuroscience. However, most existing automatic tracing algorithms cannot obtain accurate neuron reconstruction when processing 3D neuron images contaminated by strong background noises or containing weak filament signals. In this paper, we present a 3D neuron segmentation network named Structure-Guided

Deep learning-based histopathology image classification is a key technique to help physicians in improving the accuracy and promptness of cancer diagnosis. However, the noisy labels are often inevitable in the complex manual annotation process, and thus mislead the training of the classification model. In this work, we introduce a novel hard sample aware noise robust learning method for histopathology

Spherical matrix arrays represent an advantageous tomographic detection geometry for non-invasive deep tissue mapping of vascular networks and oxygenation with volumetric photoacoustic tomography (VPT). Hybridization of VPT with ultrasound (US) imaging remains difficult with this configuration due to the relatively large inter-element pitch of spherical arrays. We suggest a new approach for combining

Coronary calcification is a strong indicator of coronary artery disease and a key determinant of the outcome of percutaneous coronary intervention. We propose a fully automated method to segment and quantify coronary calcification in intravascular OCT (IVOCT) images based on convolutional neural networks (CNN). All possible calcified plaques were segmented from IVOCT pullbacks using a spatial-temporal

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As a follow-up to the first IEEE Transactions on Medical Imaging (TMI) special issue on the theme of deep tomographic reconstruction, the second special issue is assembled to reflect the status and momentum of this rapidly emerging field. In this editorial, we provide a brief background illustrating the motivation for the development of network-based, data-driven, and learning-oriented reconstruction

Precise segmentation of teeth from intra-oral scanner images is an essential task in computer-aided orthodontic surgical planning. The state-of-the-art deep learning-based methods often simply concatenate the raw geometric attributes (i.e., coordinates and normal vectors) of mesh cells to train a single-stream network for automatic intra-oral scanner image segmentation. However, since different raw

Segmentation is a fundamental task in biomedical image analysis. Unlike the existing region-based dense pixel classification methods or boundary-based polygon regression methods, we build a novel graph neural network (GNN) based deep learning framework with multiple graph reasoning modules to explicitly leverage both region and boundary features in an end-to-end manner. The mechanism extracts discriminative

Uniquely capable of simultaneous imaging of the hemoglobin concentration, blood oxygenation, and flow speed at the microvascular level in vivo, multi-parametric photoacoustic microscopy (PAM) has shown considerable impact in biomedicine. However, the multi-parametric PAM acquisition requires dense sampling and thus a high laser pulse repetition rate (up to MHz), which sets a strict limit on the applicable

An increased pulse pressure, due to arteries stiffening with age and cardiovascular disease, may lead to downstream brain damage in microvessels and cognitive decline. Brain-wide imaging of the pulsatility propagation from main feeding arteries to capillaries in small animals could improve our understanding of the link between pulsatility and cognitive decline. However, it requires higher spatiotemporal

Lung cancer is the leading cause of cancer deaths worldwide. Accurately diagnosing the malignancy of suspected lung nodules is of paramount clinical importance. However, to date, the pathologically-proven lung nodule dataset is largely limited and is highly imbalanced in benign and malignant distributions. In this study, we proposed a Semi-supervised Deep Transfer Learning (SDTL) framework for benign-malignant

Despite the promise of Convolutional neural network (CNN) based classification models for histopathological images, it is infeasible to quantify its uncertainties. Moreover, CNNs may suffer from overfitting when the data is biased. We show that Bayesian-CNN can overcome these limitations by regularizing automatically and by quantifying the uncertainty. We have developed a novel technique to utilize

Prior studies have reported that breast thermography is a potential adjunct tool to mammography in early cancer detection, especially in developing countries with limited medical facilities. This non-invasive, safe, and painless screening tool can reduce the mortality due to cancer by early detection and monitoring. This prospective study aims to analyze changes in static breast thermograms of a BIRADS

Dual-modal ultrasound (US) and photoacoustic (PA) imaging has tremendous advantages in biomedical applications, such as pharmacokinetics, cancer screening, and imaging-guided therapy. Compared with ring-shaped arrays, a linear piezoelectric transducer array applies to more anatomical sites and has been widely used in US/PA imaging. However, the linear array may limit the imaging quality due to narrow

Tucker decomposition can provide an intuitive summary to understand brain function by decomposing multi-subject fMRI data into a core tensor and multiple factor matrices, and was mostly used to extract functional connectivity patterns across time/subjects using orthogonality constraints. However, these algorithms are unsuitable for extracting common spatial and temporal patterns across subjects due

Unsupervised domain adaptation (UDA), aiming to adapt the model to an unseen domain without annotations, has drawn sustained attention in surgical instrument segmentation. Existing UDA methods neglect the domain-common knowledge of two datasets, thus failing to grasp the inter-category relationship in the target domain and leading to poor performance. To address these issues, we propose a graph-based

The traditional finite element method-based fluorescence molecular tomography (FMT)/ X-ray computed tomography (XCT) imaging reconstruction suffers from complicated mesh generation and dual-modality image data fusion, which limits the application of in vivo imaging. To solve this problem, a novel standardized imaging space reconstruction (SISR) method for the quantitative determination of fluorescent

For interpretation of electroencephalography (EEG) and magnetoencephalography (MEG) data, multiple solutions of the respective forward problems are needed. In this paper, we assess performance of the mixed-hybrid finite element method (MHFEM) applied to EEG and MEG modeling. The method provides an approximate potential and induced currents and results in a system with a positive semi-definite matrix

Multimodal learning usually requires a complete set of modalities during inference to maintain performance. Although training data can be well-prepared with high-quality multiple modalities, in many cases of clinical practice, only one modality can be acquired and important clinical evaluations have to be made based on the limited single modality information. In this work, we propose a privileged knowledge

Medical images from multicentres often suffer from the domain shift problem, which makes the deep learning models trained on one domain usually fail to generalize well to another. One of the potential solutions for the problem is the generative adversarial network (GAN), which has the capacity to translate images between different domains. Nevertheless, the existing GAN-based approaches are prone to

In semi-supervised medical image segmentation, most previous works draw on the common assumption that higher entropy means higher uncertainty. In this paper, we investigate a novel method of estimating uncertainty. We observe that, when assigned different misclassification costs in a certain degree, if the segmentation result of a pixel becomes inconsistent, this pixel shows a relative uncertainty

Although atrial fibrillation (AF) is the most common sustained atrial arrhythmia, treatment success for this condition remains suboptimal. Information from magnetic resonance imaging (MRI) has the potential to improve treatment efficacy, but there are currently few automatic tools for the segmentation of the atria in MR images. In the study, we propose a LA-Net, a multi-task network optimised to simultaneously

Diffuse optical tomography (DOT) leverages near-infrared light propagation through tissue to assess its optical properties and identify abnormalities. DOT image reconstruction is an ill-posed problem due to the highly scattered photons in the medium and the smaller number of measurements compared to the number of unknowns. Limited-angle DOT reduces probe complexity at the cost of increased reconstruction

The early detection and timely treatment of breast cancer can save lives. Mammography is one of the most efficient approaches to screening early breast cancer. An automatic mammographic image classification method could improve the work efficiency of radiologists. Current deep learning-based methods typically use the traditional softmax loss to optimize the feature extraction part, which aims to learn

Lung ultrasound (LUS) is a cheap, safe and non-invasive imaging modality that can be performed at patient bed-side. However, to date LUS is not widely adopted due to lack of trained personnel required for interpreting the acquired LUS frames. In this work we propose a framework for training deep artificial neural networks for interpreting LUS, which may promote broader use of LUS. When using LUS to

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Annotation-efficient deep learning refers to methods and practices that yield high-performance deep learning models without the use of massive carefully labeled training datasets. This paradigm has recently attracted attention from the medical imaging research community because (1) it is difficult to collect large, representative medical imaging datasets given the diversity of imaging protocols, imaging

With self-supervised learning, both labeled and unlabeled data can be used for representation learning and model pretraining. This is particularly relevant when automating the selection of a patient's fertilized eggs (embryos) during a fertility treatment, in which only the embryos that were transferred to the female uterus may have labels of pregnancy. In this paper, we apply a self-supervised video

We introduce a strategy for learning image registration without acquired imaging data, producing powerful networks agnostic to contrast introduced by magnetic resonance imaging (MRI). While classical registration methods accurately estimate the spatial correspondence between images, they solve an optimization problem for every new image pair. Learning-based techniques are fast at test time but limited

Deep learning methods, especially convolutional neural networks, have been successfully applied to lesion segmentation in breast ultrasound (BUS) images. However, pattern complexity and intensity similarity between the surrounding tissues (i.e., background) and lesion regions (i.e., foreground) bring challenges for lesion segmentation. Considering that such rich texture information is contained in

This work presents the first quantitative ultrasonic sound speed images of ex vivo limb cross-sections containing both soft tissue and bone using Full Waveform Inversion (FWI) with level set (LS) and travel time regularization. The estimated bulk sound speed of bone and soft tissue are within 10% and 1%, respectively, of ground truth estimates. The sound speed imagery shows muscle, connective tissue

Many biological tissues contain an underlying fibrous microstructure that is optimized to suit a physiological function. The fiber architecture dictates physical characteristics such as stiffness, diffusivity, and electrical conduction. Abnormal deviations of fiber architecture are often associated with disease. Thus, it is useful to characterize fiber network organization from image data in order

Automatic medical image segmentation plays a crucial role in many medical applications, such as disease diagnosis and treatment planning. Existing deep learning based models usually regarded the segmentation task as pixel-wise classification and neglected the semantic correlations of pixels across different images, leading to vague feature distribution. Moreover, pixel-wise annotated data is rare in

Although deep networks have been shown to perform very well on a variety of medical imaging tasks, inference in the presence of pathology presents several challenges to common models. These challenges impede the integration of deep learning models into real clinical workflows, where the customary process of cascading deterministic outputs from a sequence of image-based inference steps (e.g. registration

Semi-supervised learning provides great significance in left atrium (LA) segmentation model learning with insufficient labelled data. Generalising semi-supervised learning to cross-domain data is of high importance to further improve model robustness. However, the widely existing distribution difference and sample mismatch between different data domains hinder the generalisation of semi-supervised

Medical imaging denoising faces great challenges, yet is in great demand. With its distinctive characteristics, medical imaging denoising in the image domain requires innovative deep learning strategies. In this study, we propose a simple yet effective strategy, the content-noise complementary learning (CNCL) strategy, in which two deep learning predictors are used to learn the respective content and

Ciliary movements within the human airway are essential for maintaining a clean lung environment. Motile cilia have a characteristic ciliary beat frequency (CBF). However, CBF measurement with current video microscopic techniques can be error-prone due to the use of the single-point Fourier transformation, which is often biased for ciliary measurements. Herein, we describe a new video microscopy technique

Biomedical microscopy images with high-resolution (HR) and axial information can help analysis and diagnosis. However, obtaining such images usually takes more time and economic costs, which makes it impractical in most scenarios. In this paper, we first propose a novel Self-texture Transfer Super-resolution and Refocusing Network (STSRNet) to reconstruct HR multi-focal plane (MFP) images from a single

The MR-Linac is a combination of an MR-scanner and radiotherapy linear accelerator (Linac) which holds the promise to increase the precision of radiotherapy treatments with MR-guided radiotherapy by monitoring motion during radiotherapy with MRI, and adjusting the radiotherapy plan accordingly. Optimal MR-guidance for respiratory motion during radiotherapy requires MR-based 3D motion estimation with

68Ga-DOTATATE PET-CT is routinely used for imaging neuroendocrine tumor (NET) somatostatin receptor subtype 2 (SSTR2) density in patients, and is complementary to FDG PET-CT for improving the accuracy of NET detection, characterization, grading, staging, and predicting/monitoring NET responses to treatment. Performing sequential 18F-FDG and 68Ga-DOTATATE PET scans would require 2 or more days and can

Drusen is considered as the landmark for diagnosis of AMD and important risk factor for the development of AMD. Therefore, accurate segmentation of drusen in retinal OCT images is crucial for early diagnosis of AMD. However, drusen segmentation in retinal OCT images is still very challenging due to the large variations in size and shape of drusen, blurred boundaries, and speckle noise interference

Diffusion kurtosis imaging (DKI) has been shown to be valuable in a wide range of neuroscientific and clinical applications. However, reliable estimation of DKI tensors is often compromised by noise, especially for the kurtosis tensor (KT). Here, we propose a joint denoising and estimating framework that integrates multiple sources of prior information, including nonlocal structural self-similarity

Recently, many methods based on hand-designed convolutional neural networks (CNNs) have achieved promising results in automatic retinal vessel segmentation. However, these CNNs remain constrained in capturing retinal vessels in complex fundus images. To improve their segmentation performance, these CNNs tend to have many parameters, which may lead to overfitting and high computational complexity. Moreover

Recent proposals of deep learning-based beamformers for ultrasound imaging (US) have attracted significant attention as computational efficient alternatives to adaptive and compressive beamformers. Moreover, deep beamformers are versatile in that image post-processing algorithms can be readily combined. Unfortunately, with the existing technology, a large number of beamformers need to be trained and

Dynamic functional connectivity (dFC) network inferred from resting-state fMRI reveals macroscopic dynamic neural activity patterns for brain disease identification. However, dFC methods ignore the causal influence between the brain regions. Furthermore, due to the complex non-Euclidean structure of brain networks, advanced deep neural networks are difficult to be applied for learning high-dimensional

Automatic angle-closure assessment in Anterior Segment OCT (AS-OCT) images is an important task for the screening and diagnosis of glaucoma, and the most recent computer-aided models focus on a binary classification of anterior chamber angles (ACA) in AS-OCT, i.e., open-angle and angle-closure. In order to assist clinicians who seek better to understand the development of the spectrum of glaucoma types

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Our objective is to show the feasibility of using simulated mammograms to detect mammographically-occult (MO) cancer in women with dense breasts and a normal screening mammogram who could be triaged for additional screening with magnetic resonance imaging (MRI) or ultrasound. We developed a Conditional Generative Adversarial Network (CGAN) to simulate a mammogram with normal appearance using the opposite

Deep learning can provide rapid brain age estimation based on brain magnetic resonance imaging (MRI). However, most studies use one neural network to extract the global information from the whole input image, ignoring the local fine-grained details. In this paper, we propose a global-local transformer, which consists of a global-pathway to extract the global-context information from the whole input

The integrative analysis of complementary phenotype information contained in multi-modality data (e.g., histopathological images and genomic data) has advanced the prognostic evaluation of cancers. However, multi-modality based prognosis analysis confronts two challenges: (1) how to explore underlying relations inherent in different modalities data for learning compact and discriminative multi-modality

Functional MRI (fMRI) is widely used to study the functional organization of normal and pathological brains. However, the fMRI signal may be contaminated by subject motion artifacts that are only partially mitigated by motion correction strategies. These artifacts lead to distance-dependent biases in the inferred signal correlations. To mitigate these spurious effects, motion-corrupted volumes are

Conventional delay-and-sum (DAS) beamforming is highly efficient but also suffers from various sources of image degradation. Several adaptive beamformers have been proposed to address this problem, including more recently proposed deep learning methods. With deep learning, adaptive beamforming is typically framed as a regression problem, where clean ground-truth physical information is used for training