Volume 39, Issue 5

Generalized nucleus segmentation techniques can contribute greatly to reducing the time to develop and validate visual biomarkers for new digital pathology datasets. We summarize the results of MoNuSeg 2018 Challenge whose objective was to develop generalizable nuclei segmentation techniques in digital pathology. The challenge was an official satellite event of the MICCAI 2018 conference in which 32 teams with more than 80 participants from geographically diverse institutes participated. Contestants were given a training set with 30 images from seven organs with annotations of 21,623 individual nuclei. A test dataset with 14 images taken from seven organs, including two organs that did not appear in the training set was released without annotations. Entries were evaluated based on average aggregated Jaccard index (AJI) on the test set to prioritize accurate instance segmentation as opposed to mere semantic segmentation. More than half the teams that completed the challenge outperformed a previous baseline. Among the trends observed that contributed to increased accuracy were the use of color normalization as well as heavy data augmentation. Additionally, fully convolutional networks inspired by variants of U-Net, FCN, and Mask-RCNN were popularly used, typically based on ResNet or VGG base architectures. Watershed segmentation on predicted semantic segmentation maps was a popular post-processing strategy. Several of the top techniques compared favorably to an individual human annotator and can be used with confidence for nuclear morphometrics.

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Diabetic retinopathy (DR) and diabetic macular edema (DME) are the leading causes of permanent blindness in the working-age population. Automatic grading of DR and DME helps ophthalmologists design tailored treatments to patients, thus is of vital importance in the clinical practice. However, prior works either grade DR or DME, and ignore the correlation between DR and its complication, i.e., DME....

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Segmentation of livers and liver tumors is one of the most important steps in radiation therapy of hepatocellular carcinoma. The segmentation task is often done manually, making it tedious, labor intensive, and subject to intra-/inter- operator variations. While various algorithms for delineating organ-at-risks (OARs) and tumor targets have been proposed, automatic segmentation of livers and liver...

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We introduce a new computer aided detection and diagnosis system for lung cancer screening with low-dose CT scans that produces meaningful probability assessments. Our system is based entirely on 3D convolutional neural networks and achieves state-of-the-art performance for both lung nodule detection and malignancy classification tasks on the publicly available LUNA16 and Kaggle Data Science Bowl ...

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We present a self-supervised approach to training convolutional neural networks for dense depth estimation from monocular endoscopy data without a priori modeling of anatomy or shading. Our method only requires monocular endoscopic videos and a multi-view stereo method, e.g., structure from motion, to supervise learning in a sparse manner. Consequently, our method requires neither manual labeling ...

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An attention guided convolutional neural network (CNN) for the classification of breast cancer histopathology images is proposed. Neural networks are generally applied as black box models and often the network’s decisions are difficult to interpret. Making the decision process transparent, and hence reliable is important for a computer-assisted diagnosis (CAD) system. Moreover, it is crucial that ...

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The detection of retinal vessel is of great importance in the diagnosis and treatment of many ocular diseases. Many methods have been proposed for vessel detection. However, most of the algorithms neglect the connectivity of the vessels, which plays an important role in the diagnosis. In this paper, we propose a novel method for retinal vessel detection. The proposed method includes a dense dilate...

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Recently, a hypergraph constructed from functional magnetic resonance imaging (fMRI) was utilized to explore brain functional connectivity networks (FCNs) for the classification of neurodegenerative diseases. Each edge of a hypergraph (called hyperedge) can connect any number of brain regions-of-interest (ROIs) instead of only two ROIs, and thus characterizes high-order relations among multiple RO...

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Intracoronary imaging is a crucial imaging technology in coronary disease diagnosis as it visualizes the internal tissue morphologies of coronary arteries. Vessel border detection in intracoronary images (VBDI) is desired because it can help the succeeding procedures of computer-aided disease diagnosis. However, existing VDBI methods suffer from the challenge of vessel-environment variability (i.e...

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In patients with obstructive coronary artery disease, the functional significance of a coronary artery stenosis needs to be determined to guide treatment. This is typically established through fractional flow reserve (FFR) measurement, performed during invasive coronary angiography (ICA). We present a method for automatic and non-invasive detection of patients requiring ICA, employing deep unsuper...

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3D optical coherence tomography angiography (OCT-A) is a novel and non-invasive imaging modality for analyzing retinal diseases. The studies of microvasculature in 2D en face projection images have been widely implemented, but comprehensive 3D analysis of OCT-A images with rich depth-resolved microvascular information is rarely considered. In this paper, we propose a robust, effective, and automat...

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Deep learning-based methods for deformable image registration are attractive alternatives to conventional registration methods because of their short registration times. However, these methods often fail to estimate larger displacements in complex deformation fields, for which a multi-resolution strategy is required. In this article, we propose to train neural networks progressively to address thi...

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Timely and accurate auxiliary diagnosis of intracranial aneurysm can help radiologist make treatment plans quickly, saving lives and cutting costs at the same time. At present, Digital Subtraction Angiography (DSA) is the gold standard for the diagnosis of intracranial aneurysm, but as radiologists interpret those imaging sequences frame by frame, misdiagnosis might occur. The utilization of compu...

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The integration of segmentation and direct quantification on the left ventricle (LV) from the paired apical views(i.e., apical 4-chamber and 2-chamber together) echo sequence clinically achieves the comprehensive cardiac assessment: multiview segmentation for anatomical morphology, and multidimensional quantification for contractile function. Direct quantification of LV, i.e., to automatically qua...

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Magnetic Particle Imaging is an emerging tracer imaging modality with zero background signal and zero ionizing radiation, high contrast and high sensitivity with quantitative images. While there is recent work showing that the low amplitude or low frequency drive parameters can improve MPI’s spatial resolution by mitigating relaxation losses, the concomitant decrease of the MPI’s tracer sensitivit...

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Electrical impedance tomography (EIT) is an attractive technique that aims to reconstruct the unknown electrical property in a domain from the surface electrical measurements. In this work, the induced-current learning method (ICLM) is proposed to solve nonlinear electrical impedance tomography (EIT) problems. Specifically, the cascaded end-to-end convolutional neural network (CEE-CNN) architectur...

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Surgical smoke removal algorithms can improve the quality of intra-operative imaging and reduce hazards in image-guided surgery, a highly desirable post-process for many clinical applications. These algorithms also enable effective computer vision tasks for future robotic surgery. In this article, we present a new unsupervised learning framework for high-quality pixel-wise smoke detection and remo...

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Ultrasound, alone or in concert with circulating microbubble contrast agents, has emerged as a promising modality for therapy and imaging of brain diseases. While this has become possible due to advancements in aberration correction methods, a range of applications, including adaptive focusing and tracking of the microbubble dynamics through the human skull, may benefit from even more computationa...

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Since age is the most significant risk factor for the development of Alzheimer's disease (AD), it is important to understand the effect of normal ageing on brain network characteristics before we can accurately diagnose the condition based on information derived from resting state electroencephalogram (EEG) recordings, aiming to detect brain network disruption. This article proposes a novel brain ...

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Radiofrequency ablation (RFA) is now a widely used minimally invasive treatment method for hepatic tumors. Preoperative planning plays a vital role in RFA therapy. With increasing tumor size, multiple overlapping ablations are needed, which are challenging to optimize while considering clinical constraints. In this paper, we present a new automatic RFA planning method. First, a 2-steps set cover-b...

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We propose a k-space preconditioning formulation for accelerating the convergence of iterative Magnetic Resonance Imaging (MRI) reconstructions from non-uniformly sampled k-space data. Existing methods either use sampling density compensations which sacrifice reconstruction accuracy, or circulant preconditioners which increase per-iteration computation. Our approach overcomes both shortcomings. Co...

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Laser speckle contrast imaging (LSCI) is a wide-field and noncontact imaging technology for mapping blood flow. Although the denoising method based on block-matching and three-dimensional transform-domain collaborative filtering (BM3D) was proposed to improve its signal-to-noise ratio (SNR) significantly, the processing time makes it difficult to realize real-time denoising. Furthermore, it is sti...

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The tomographic imaging method magnetic particle imaging (MPI) requires a multi-patch approach for capturing large field of views. This approach consists of a continuous or stepwise spatial shift of a small sub-volume of only few cubic centimeters size, which is scanned using one or multiple excitation fields in the kHz range. Under the assumption of ideal magnetic fields, the MPI system matrix is...

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This work introduces a 4D flow magnetic resonance imaging (MRI) pressure reconstruction method which employs weighted least-squares (WLS) for pressure integration. Pressure gradients are calculated from the velocity fields, and velocity errors are estimated from the velocity divergence for incompressible flow. Pressure gradient errors are estimated by propagating the velocity errors through Navier...

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Quantitative DCE-MRI provides voxel-wise estimates of tracer-kinetic parameters that are valuable in the assessment of health and disease. These maps suffer from many known sources of variability. This variability is expensive to compute using current methods, and is typically not reported. Here, we demonstrate a novel approach for simultaneous estimation of tracer-kinetic parameters and their unc...

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