Inter-Modal Selective 3D Coding of PET-CT Datasets

In this work we introduce a new selective coding approach suitable for co-registered multi-modal medical images and we apply it to large PET-CT volumes. Salience information guiding a space variant reconstruction quality of the anatomical volume (CT) is generated through an automatic analysis of the functional volume (PET). This allows a versatile multiple volume-of-interest coding with arbitrary 3D-shape and scaling-factors and without the need of side information to be transmitted. The proposed solutions are suitable for critical applications where high and optimized compression ratio, minimization of human intervention and full diagnostic quality preservation are all required

ISA-Net: Improved spatial attention network for PET-CT tumor segmentation

Achieving accurate and automated tumor segmentation plays an important role in both clinical practice and radiomics research. Segmentation in medicine is now often performed manually by experts, which is a laborious, expensive and error-prone task. Manual annotation relies heavily on the experience and knowledge of these experts. In addition, there is much intra- and interobserver variation. Therefore, it is of great significance to develop a method that can automatically segment tumor target regions. In this paper, we propose a deep learning segmentation method based on multimodal positron emission tomography-computed tomography (PET-CT), which combines the high sensitivity of PET and the precise anatomical information of CT. We design an improved spatial attention network(ISA-Net) to increase the accuracy of PET or CT in detecting tumors, which uses multi-scale convolution operation to extract feature information and can highlight the tumor region location information and suppress the non-tumor region location information. In addition, our network uses dual-channel inputs in the coding stage and fuses them in the decoding stage, which can take advantage of the differences and complementarities between PET and CT. We validated the proposed ISA-Net method on two clinical datasets, a soft tissue sarcoma(STS) and a head and neck tumor(HECKTOR) dataset, and compared with other attention methods for tumor segmentation. The DSC score of 0.8378 on STS dataset and 0.8076 on HECKTOR dataset show that ISA-Net method achieves better segmentation performance and has better generalization. Conclusions: The method proposed in this paper is based on multi-modal medical image tumor segmentation, which can effectively utilize the difference and complementarity of different modes. The method can also be applied to other multi-modal data or single-modal data by proper adjustment

ResViT: Residual vision transformers for multi-modal medical image synthesis

Multi-modal imaging is a key healthcare technology that is often underutilized due to costs associated with multiple separate scans. This limitation yields the need for synthesis of unacquired modalities from the subset of available modalities. In recent years, generative adversarial network (GAN) models with superior depiction of structural details have been established as state-of-the-art in numerous medical image synthesis tasks. GANs are characteristically based on convolutional neural network (CNN) backbones that perform local processing with compact filters. This inductive bias in turn compromises learning of contextual features. Here, we propose a novel generative adversarial approach for medical image synthesis, ResViT, to combine local precision of convolution operators with contextual sensitivity of vision transformers. ResViT employs a central bottleneck comprising novel aggregated residual transformer (ART) blocks that synergistically combine convolutional and transformer modules. Comprehensive demonstrations are performed for synthesizing missing sequences in multi-contrast MRI, and CT images from MRI. Our results indicate superiority of ResViT against competing methods in terms of qualitative observations and quantitative metrics

A Survey on Deep Learning in Medical Image Analysis

Deep learning algorithms, in particular convolutional networks, have rapidly become a methodology of choice for analyzing medical images. This paper reviews the major deep learning concepts pertinent to medical image analysis and summarizes over 300 contributions to the field, most of which appeared in the last year. We survey the use of deep learning for image classification, object detection, segmentation, registration, and other tasks and provide concise overviews of studies per application area. Open challenges and directions for future research are discussed.Comment: Revised survey includes expanded discussion section and reworked introductory section on common deep architectures. Added missed papers from before Feb 1st 201

Computational methods for the analysis of functional 4D-CT chest images.

Medical imaging is an important emerging technology that has been intensively used in the last few decades for disease diagnosis and monitoring as well as for the assessment of treatment effectiveness. Medical images provide a very large amount of valuable information that is too huge to be exploited by radiologists and physicians. Therefore, the design of computer-aided diagnostic (CAD) system, which can be used as an assistive tool for the medical community, is of a great importance. This dissertation deals with the development of a complete CAD system for lung cancer patients, which remains the leading cause of cancer-related death in the USA. In 2014, there were approximately 224,210 new cases of lung cancer and 159,260 related deaths. The process begins with the detection of lung cancer which is detected through the diagnosis of lung nodules (a manifestation of lung cancer). These nodules are approximately spherical regions of primarily high density tissue that are visible in computed tomography (CT) images of the lung. The treatment of these lung cancer nodules is complex, nearly 70% of lung cancer patients require radiation therapy as part of their treatment. Radiation-induced lung injury is a limiting toxicity that may decrease cure rates and increase morbidity and mortality treatment. By finding ways to accurately detect, at early stage, and hence prevent lung injury, it will have significant positive consequences for lung cancer patients. The ultimate goal of this dissertation is to develop a clinically usable CAD system that can improve the sensitivity and specificity of early detection of radiation-induced lung injury based on the hypotheses that radiated lung tissues may get affected and suffer decrease of their functionality as a side effect of radiation therapy treatment. These hypotheses have been validated by demonstrating that automatic segmentation of the lung regions and registration of consecutive respiratory phases to estimate their elasticity, ventilation, and texture features to provide discriminatory descriptors that can be used for early detection of radiation-induced lung injury. The proposed methodologies will lead to novel indexes for distinguishing normal/healthy and injured lung tissues in clinical decision-making. To achieve this goal, a CAD system for accurate detection of radiation-induced lung injury that requires three basic components has been developed. These components are the lung fields segmentation, lung registration, and features extraction and tissue classification. This dissertation starts with an exploration of the available medical imaging modalities to present the importance of medical imaging in today’s clinical applications. Secondly, the methodologies, challenges, and limitations of recent CAD systems for lung cancer detection are covered. This is followed by introducing an accurate segmentation methodology of the lung parenchyma with the focus of pathological lungs to extract the volume of interest (VOI) to be analyzed for potential existence of lung injuries stemmed from the radiation therapy. After the segmentation of the VOI, a lung registration framework is introduced to perform a crucial and important step that ensures the co-alignment of the intra-patient scans. This step eliminates the effects of orientation differences, motion, breathing, heart beats, and differences in scanning parameters to be able to accurately extract the functionality features for the lung fields. The developed registration framework also helps in the evaluation and gated control of the radiotherapy through the motion estimation analysis before and after the therapy dose. Finally, the radiation-induced lung injury is introduced, which combines the previous two medical image processing and analysis steps with the features estimation and classification step. This framework estimates and combines both texture and functional features. The texture features are modeled using the novel 7th-order Markov Gibbs random field (MGRF) model that has the ability to accurately models the texture of healthy and injured lung tissues through simultaneously accounting for both vertical and horizontal relative dependencies between voxel-wise signals. While the functionality features calculations are based on the calculated deformation fields, obtained from the 4D-CT lung registration, that maps lung voxels between successive CT scans in the respiratory cycle. These functionality features describe the ventilation, the air flow rate, of the lung tissues using the Jacobian of the deformation field and the tissues’ elasticity using the strain components calculated from the gradient of the deformation field. Finally, these features are combined in the classification model to detect the injured parts of the lung at an early stage and enables an earlier intervention

Data efficient deep learning for medical image analysis: A survey

The rapid evolution of deep learning has significantly advanced the field of medical image analysis. However, despite these achievements, the further enhancement of deep learning models for medical image analysis faces a significant challenge due to the scarcity of large, well-annotated datasets. To address this issue, recent years have witnessed a growing emphasis on the development of data-efficient deep learning methods. This paper conducts a thorough review of data-efficient deep learning methods for medical image analysis. To this end, we categorize these methods based on the level of supervision they rely on, encompassing categories such as no supervision, inexact supervision, incomplete supervision, inaccurate supervision, and only limited supervision. We further divide these categories into finer subcategories. For example, we categorize inexact supervision into multiple instance learning and learning with weak annotations. Similarly, we categorize incomplete supervision into semi-supervised learning, active learning, and domain-adaptive learning and so on. Furthermore, we systematically summarize commonly used datasets for data efficient deep learning in medical image analysis and investigate future research directions to conclude this survey.Comment: Under Revie

Neurophysiological consequences of synapse loss in progressive supranuclear palsy

Synaptic loss occurs early in many neurodegenerative diseases and contributes to cognitive impairment even in the absence of gross atrophy. Currently, for human disease there are few formal models to explain how cortical networks underlying cognition are affected by synaptic loss. We advocate that biophysical models of neurophysiology offer both a bridge from clinical to preclinical models of pathology, and quantitative assays for experimental medicine. Such biophysical models can also disclose hidden neuronal dynamics generating neurophysiological observations like electro- and magneto-encephalography. Here, we augment a biophysically informed mesoscale model of human cortical function by inclusion of synaptic density estimates as captured by [11C]UCB-J positron emission tomography, and provide insights into how regional synapse loss affects neurophysiology. We use the primary tauopathy of progressive supranuclear palsy (Richardson's syndrome) as an exemplar condition, with high clinicopathological correlations. Progressive supranuclear palsy causes a marked change in cortical neurophysiology in the presence of mild cortical atrophy and is associated with a decline in cognitive functions associated with the frontal lobe. Using parametric empirical Bayesian inversion of a conductance-based canonical microcircuit model of magnetoencephalography data, we show that the inclusion of regional synaptic density-as a subject-specific prior on laminar specific neuronal populations-markedly increases model evidence. Specifically, model comparison suggests that a reduction in synaptic density in inferior frontal cortex affects superficial and granular layer glutamatergic excitation. This predicted individual differences in behaviour, demonstrating the link between synaptic loss, neurophysiology, and cognitive deficits. The method we demonstrate is not restricted to progressive supranuclear palsy or the effects of synaptic loss: such pathology-enriched dynamic causal models can be used to assess the mechanisms of other neurological disorders, with diverse non-invasive measures of pathology, and is suitable to test the effects of experimental pharmacology