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Medical Image Analysis

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https://read.qxmd.com/read/30861443/predicting-breast-tumor-proliferation-from-whole-slide-images-the-tupac16-challenge
#1
Mitko Veta, Yujing J Heng, Nikolas Stathonikos, Babak Ehteshami Bejnordi, Francisco Beca, Thomas Wollmann, Karl Rohr, Manan A Shah, Dayong Wang, Mikael Rousson, Martin Hedlund, David Tellez, Francesco Ciompi, Erwan Zerhouni, David Lanyi, Matheus Viana, Vassili Kovalev, Vitali Liauchuk, Hady Ahmady Phoulady, Talha Qaiser, Simon Graham, Nasir Rajpoot, Erik Sjöblom, Jesper Molin, Kyunghyun Paeng, Sangheum Hwang, Sunggyun Park, Zhipeng Jia, Eric I-Chao Chang, Yan Xu, Andrew H Beck, Paul J van Diest, Josien P W Pluim
Tumor proliferation is an important biomarker indicative of the prognosis of breast cancer patients. Assessment of tumor proliferation in a clinical setting is a highly subjective and labor-intensive task. Previous efforts to automate tumor proliferation assessment by image analysis only focused on mitosis detection in predefined tumor regions. However, in a real-world scenario, automatic mitosis detection should be performed in whole-slide images (WSIs) and an automatic method should be able to produce a tumor proliferation score given a WSI as input...
February 27, 2019: Medical Image Analysis
https://read.qxmd.com/read/30836308/breast-mri-and-x-ray-mammography-registration-using-gradient-values
#2
Eloy García, Yago Diez, Oliver Diaz, Xavier Lladó, Albert Gubern-Mérida, Robert Martí, Joan Martí, Arnau Oliver
Breast magnetic resonance imaging (MRI) and X-ray mammography are two image modalities widely used for early detection and diagnosis of breast diseases in women. The combination of these modalities, traditionally done using intensity-based registration algorithms, leads to a more accurate diagnosis and treatment, due to the capability of co-localizing lesions and susceptibles areas between the two image modalities. In this work, we present the first attempt to register breast MRI and X-ray mammographic images using intensity gradients as the similarity measure...
February 26, 2019: Medical Image Analysis
https://read.qxmd.com/read/30856455/deep-learning-based-multiclass-retinal-fluid-segmentation-and-detection-in-optical-coherence-tomography-images-using-a-fully-convolutional-neural-network
#3
Donghuan Lu, Morgan Heisler, Sieun Lee, Gavin Weiguang Ding, Eduardo Navajas, Marinko V Sarunic, Mirza Faisal Beg
As a non-invasive imaging modality, optical coherence tomography (OCT) can provide micrometer-resolution 3D images of retinal structures. These images can help reveal disease-related alterations below the surface of the retina, such as the presence of edema, or accumulation of fluid which can distort vision, and are an indication of disruptions in the vasculature of the retina. In this paper, a new framework is proposed for multiclass fluid segmentation and detection in the retinal OCT images. Based on the intensity of OCT images and retinal layer segmentations provided by a graph-cut algorithm, a fully convolutional neural network was trained to recognize and label the fluid pixels...
February 22, 2019: Medical Image Analysis
https://read.qxmd.com/read/30818161/medical-image-classification-using-synergic-deep-learning
#4
Jianpeng Zhang, Yutong Xie, Qi Wu, Yong Xia
The classification of medical images is an essential task in computer-aided diagnosis, medical image retrieval and mining. Although deep learning has shown proven advantages over traditional methods that rely on the handcrafted features, it remains challenging due to the significant intra-class variation and inter-class similarity caused by the diversity of imaging modalities and clinical pathologies. In this paper, we propose a synergic deep learning (SDL) model to address this issue by using multiple deep convolutional neural networks (DCNNs) simultaneously and enabling them to mutually learn from each other...
February 18, 2019: Medical Image Analysis
https://read.qxmd.com/read/30784956/evaluating-reinforcement-learning-agents-for-anatomical-landmark-detection
#5
Amir Alansary, Ozan Oktay, Yuanwei Li, Loic Le Folgoc, Benjamin Hou, Ghislain Vaillant, Konstantinos Kamnitsas, Athanasios Vlontzos, Ben Glocker, Bernhard Kainz, Daniel Rueckert
Automatic detection of anatomical landmarks is an important step for a wide range of applications in medical image analysis. Manual annotation of landmarks is a tedious task and prone to observer errors. In this paper, we evaluate novel deep reinforcement learning (RL) strategies to train agents that can precisely and robustly localize target landmarks in medical scans. An artificial RL agent learns to identify the optimal path to the landmark by interacting with an environment, in our case 3D images. Furthermore, we investigate the use of fixed- and multi-scale search strategies with novel hierarchical action steps in a coarse-to-fine manner...
February 14, 2019: Medical Image Analysis
https://read.qxmd.com/read/30851541/constrained-cnn-losses-for-weakly-supervised-segmentation
#6
Hoel Kervadec, Jose Dolz, Meng Tang, Eric Granger, Yuri Boykov, Ismail Ben Ayed
Weakly-supervised learning based on, e.g., partially labelled images or image-tags, is currently attracting significant attention in CNN segmentation as it can mitigate the need for full and laborious pixel/voxel annotations. Enforcing high-order (global) inequality constraints on the network output (for instance, to constrain the size of the target region) can leverage unlabeled data, guiding the training process with domain-specific knowledge. Inequality constraints are very flexible because they do not assume exact prior knowledge...
February 13, 2019: Medical Image Analysis
https://read.qxmd.com/read/30825805/an-image-interpolation-approach-for-acquisition-time-reduction-in-navigator-based-4d-mri
#7
Neerav Karani, Lin Zhang, Christine Tanner, Ender Konukoglu
Navigated 2D multi-slice dynamic Magnetic Resonance (MR) imaging enables high contrast 4D MR imaging during free breathing and provides in-vivo observations for treatment planning and guidance. Navigator slices are vital for retrospective stacking of 2D data slices in this method. However, they also prolong the acquisition sessions. Temporal interpolation of navigator slices can be used to reduce the number of navigator acquisitions without degrading specificity in stacking. In this work, we propose a convolutional neural network (CNN) based method for temporal interpolation, with motion field prediction as an intermediate step...
February 13, 2019: Medical Image Analysis
https://read.qxmd.com/read/30807894/obelisk-net-fewer-layers-to-solve-3d-multi-organ-segmentation-with-sparse-deformable-convolutions
#8
Mattias P Heinrich, Ozan Oktay, Nassim Bouteldja
Deep networks have set the state-of-the-art in most image analysis tasks by replacing handcrafted features with learned convolution filters within end-to-end trainable architectures. Still, the specifications of a convolutional network are subject to much manual design - the shape and size of the receptive field for convolutional operations is a very sensitive part that has to be tuned for different image analysis applications. 3D fully-convolutional multi-scale architectures with skip-connection that excel at semantic segmentation and landmark localisation have huge memory requirements and rely on large annotated datasets - an important limitation for wider adaptation in medical image analysis...
February 13, 2019: Medical Image Analysis
https://read.qxmd.com/read/30771712/iterative-fully-convolutional-neural-networks-for-automatic-vertebra-segmentation-and-identification
#9
Nikolas Lessmann, Bram van Ginneken, Pim A de Jong, Ivana Išgum
Precise segmentation and anatomical identification of the vertebrae provides the basis for automatic analysis of the spine, such as detection of vertebral compression fractures or other abnormalities. Most dedicated spine CT and MR scans as well as scans of the chest, abdomen or neck cover only part of the spine. Segmentation and identification should therefore not rely on the visibility of certain vertebrae or a certain number of vertebrae. We propose an iterative instance segmentation approach that uses a fully convolutional neural network to segment and label vertebrae one after the other, independently of the number of visible vertebrae...
February 12, 2019: Medical Image Analysis
https://read.qxmd.com/read/30836307/optimal-surface-segmentation-with-convex-priors-in-irregularly-sampled-space
#10
Abhay Shah, Michael D Abámoff, Xiaodong Wu
Optimal surface segmentation is a state-of-the-art method used for segmentation of multiple globally optimal surfaces in volumetric datasets. The method is widely used in numerous medical image segmentation applications. However, nodes in the graph based optimal surface segmentation method typically encode uniformly distributed orthogonal voxels of the volume. Thus the segmentation cannot attain an accuracy greater than a single unit voxel, i.e. the distance between two adjoining nodes in graph space. Segmentation accuracy higher than a unit voxel is achievable by exploiting partial volume information in the voxels which shall result in non-equidistant spacing between adjoining graph nodes...
February 8, 2019: Medical Image Analysis
https://read.qxmd.com/read/30798117/frequency-splitting-dynamic-mri-reconstruction-using-multi-scale-3d-convolutional-sparse-coding-and-automatic-parameter-selection
#11
Thanh Nguyen-Duc, Tran Minh Quan, Won-Ki Jeong
In this paper, we propose a novel image reconstruction algorithm using multi-scale 3D convolutional sparse coding and a spectral decomposition technique for highly undersampled dynamic Magnetic Resonance Imaging (MRI) data. The proposed method recovers high-frequency information using a shared 3D convolution-based dictionary built progressively during the reconstruction process in an unsupervised manner, while low-frequency information is recovered using a total variation-based energy minimization method that leverages temporal coherence in dynamic MRI...
February 7, 2019: Medical Image Analysis
https://read.qxmd.com/read/30772666/multiple-correlation-similarity-for-block-matching-based-fast-ct-to-ultrasound-registration-in-liver-interventions
#12
Jyotirmoy Banerjee, Yuanyuan Sun, Camiel Klink, Renske Gahrmann, Wiro J Niessen, Adriaan Moelker, Theo van Walsum
In this work we present a fast approach to perform registration of computed tomography to ultrasound volumes for image guided intervention applications. The method is based on a combination of block-matching and outlier rejection. The block-matching uses a correlation based multimodal similarity metric, where the intensity and the gradient of the computed tomography images along with the ultrasound volumes are the input images to find correspondences between blocks in the computed tomography and the ultrasound volumes...
February 7, 2019: Medical Image Analysis
https://read.qxmd.com/read/30769327/adversarial-training-with-cycle-consistency-for-unsupervised-super-resolution-in-endomicroscopy
#13
Daniele Ravì, Agnieszka Barbara Szczotka, Stephen P Pereira, Tom Vercauteren
In recent years, endomicroscopy has become increasingly used for diagnostic purposes and interventional guidance. It can provide intraoperative aids for real-time tissue characterization and can help to perform visual investigations aimed for example to discover epithelial cancers. Due to physical constraints on the acquisition process, endomicroscopy images, still today have a low number of informative pixels which hampers their quality. Post-processing techniques, such as Super-Resolution (SR), are a potential solution to increase the quality of these images...
February 2, 2019: Medical Image Analysis
https://read.qxmd.com/read/30763829/automatic-needle-detection-and-real-time-bi-planar-needle-visualization-during-3d-ultrasound-scanning-of-the-liver
#14
Muhammad Arif, Adriaan Moelker, Theo van Walsum
2D ultrasound (US) image guidance is used in minimally invasive procedures in the liver to visualize the target and the needle. Needle insertion using 2D ultrasound keeping the transducer position to view needle and reach target is challenging. Dedicated needle holders attached to the US transducer help to target in plane and at a specific angle. A drawback of this is that, the probe is fixed to the needle and cannot be rotated to assess the position of the needle in a perpendicular plane. In this study, we propose an automatic needle detection and tracking method using 3D US imaging to improve image guidance and visualization of the target in the liver with respect to the needle during these interventional procedures...
February 2, 2019: Medical Image Analysis
https://read.qxmd.com/read/30831356/f-anogan-fast-unsupervised-anomaly-detection-with-generative-adversarial-networks
#15
Thomas Schlegl, Philipp Seeböck, Sebastian M Waldstein, Georg Langs, Ursula Schmidt-Erfurth
Obtaining expert labels in clinical imaging is difficult since exhaustive annotation is time-consuming. Furthermore, not all possibly relevant markers may be known and sufficiently well described a priori to even guide annotation. While supervised learning yields good results if expert labeled training data is available, the visual variability, and thus the vocabulary of findings, we can detect and exploit, is limited to the annotated lesions. Here, we present fast AnoGAN (f-AnoGAN), a generative adversarial network (GAN) based unsupervised learning approach capable of identifying anomalous images and image segments, that can serve as imaging biomarker candidates...
January 31, 2019: Medical Image Analysis
https://read.qxmd.com/read/30743192/novel-and-facile-criterion-to-assess-the-accuracy-of-wss-estimation-by-4d-flow-mri
#16
Seungbin Ko, Byungkuen Yang, Jee-Hyun Cho, Jeesoo Lee, Simon Song
Four-dimensional flow magnetic resonance imaging (4D flow MRI) is a versatile tool to obtain hemodynamic information and anatomic information simultaneously. The wall shear stress (WSS), a force exerted on a vessel wall in parallel, is one of the hemodynamic parameters available with 4D flow MRI and is thought to play an important role in clinical applications such as assessing the development of atherosclerosis. Nevertheless, the accuracy of WSS obtained with 4D flow MRI is rarely evaluated or reported in literature, especially in the in vivo studies...
January 31, 2019: Medical Image Analysis
https://read.qxmd.com/read/30763830/multi-task-exclusive-relationship-learning-for-alzheimer-s-disease-progression-prediction-with-longitudinal-data
#17
Mingliang Wang, Daoqiang Zhang, Dinggang Shen, Mingxia Liu
Alzheimer's disease (AD) is a neurodegenerative disorder characterized by progressive impairment of memory and other cognitive functions. Currently, many multi-task learning approaches have been proposed to predict the disease progression at the early stage using longitudinal data, with each task corresponding to a particular time point. However, the underlying association among different time points in disease progression is still under-explored in previous studies. To this end, we propose a multi-task exclusive relationship learning model to automatically capture the intrinsic relationship among tasks at different time points for estimating clinical measures based on longitudinal imaging data...
January 30, 2019: Medical Image Analysis
https://read.qxmd.com/read/30831357/aar-rt-a-system-for-auto-contouring-organs-at-risk-on-ct-images-for-radiation-therapy-planning-principles-design-and-large-scale-evaluation-on-head-and-neck-and-thoracic-cancer-cases
#18
Xingyu Wu, Jayaram K Udupa, Yubing Tong, Dewey Odhner, Gargi V Pednekar, Charles B Simone, David McLaughlin, Chavanon Apinorasethkul, Ontida Apinorasethkul, John Lukens, Dimitris Mihailidis, Geraldine Shammo, Paul James, Akhil Tiwari, Lisa Wojtowicz, Joseph Camaratta, Drew A Torigian
Contouring (segmentation) of Organs at Risk (OARs) in medical images is required for accurate radiation therapy (RT) planning. In current clinical practice, OAR contouring is performed with low levels of automation. Although several approaches have been proposed in the literature for improving automation, it is difficult to gain an understanding of how well these methods would perform in a realistic clinical setting. This is chiefly due to three key factors - small number of patient studies used for evaluation, lack of performance evaluation as a function of input image quality, and lack of precise anatomic definitions of OARs...
January 29, 2019: Medical Image Analysis
https://read.qxmd.com/read/30703580/noise-reduction-in-diffusion-mri-using-non-local-self-similar-information-in-joint-x-q-space
#19
Geng Chen, Yafeng Wu, Dinggang Shen, Pew-Thian Yap
Diffusion MRI affords valuable insights into white matter microstructures, but suffers from low signal-to-noise ratio (SNR), especially at high diffusion weighting (i.e., b-value). To avoid time-intensive repeated acquisition, post-processing algorithms are often used to reduce noise. Among existing methods, non-local means (NLM) has been shown to be particularly effective. However, most NLM algorithms for diffusion MRI focus on patch matching in the spatial domain (i.e., x-space) and disregard the fact that the data live in a combined 6D space covering both spatial domain and diffusion wavevector domain (i...
January 21, 2019: Medical Image Analysis
https://read.qxmd.com/read/30703579/recurrent-inference-machines-for-reconstructing-heterogeneous-mri-data
#20
Kai Lønning, Patrick Putzky, Jan-Jakob Sonke, Liesbeth Reneman, Matthan W A Caan, Max Welling
Deep learning allows for accelerated magnetic resonance image (MRI) reconstruction, thereby shortening measurement times. Rather than using sparsifying transforms, a prerequisite in Compressed Sensing (CS), suitable MRI prior distributions are learned from data. In clinical practice, both the underlying anatomy as well as image acquisition settings vary. For this reason, deep neural networks must be able to reapply what they learn across different measurement conditions. We propose to use Recurrent Inference Machines (RIM) as a framework for accelerated MRI reconstruction...
January 18, 2019: Medical Image Analysis
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