147 research outputs found
3D medical volume segmentation using hybrid multiresolution statistical approaches
This article is available through the Brunel Open Access Publishing Fund. Copyright Ā© 2010 S AlZuābi and A Amira.3D volume segmentation is the process of partitioning voxels into 3D regions (subvolumes) that represent meaningful physical entities which are more meaningful and easier to analyze and usable in future applications. Multiresolution Analysis (MRA) enables the preservation of an image according to certain levels of resolution or blurring. Because of multiresolution quality, wavelets have been deployed in image compression, denoising, and classification. This paper focuses on the implementation of efficient medical volume segmentation techniques. Multiresolution analysis including 3D wavelet and ridgelet has been used for feature extraction which can be modeled using Hidden Markov Models (HMMs) to segment the volume slices. A comparison study has been carried out to evaluate 2D and 3D techniques which reveals that 3D methodologies can accurately detect the Region Of Interest (ROI). Automatic segmentation has been achieved using HMMs where the ROI is detected accurately but suffers a long computation time for its calculations
Diffusion Models for Medical Image Analysis: A Comprehensive Survey
Denoising diffusion models, a class of generative models, have garnered
immense interest lately in various deep-learning problems. A diffusion
probabilistic model defines a forward diffusion stage where the input data is
gradually perturbed over several steps by adding Gaussian noise and then learns
to reverse the diffusion process to retrieve the desired noise-free data from
noisy data samples. Diffusion models are widely appreciated for their strong
mode coverage and quality of the generated samples despite their known
computational burdens. Capitalizing on the advances in computer vision, the
field of medical imaging has also observed a growing interest in diffusion
models. To help the researcher navigate this profusion, this survey intends to
provide a comprehensive overview of diffusion models in the discipline of
medical image analysis. Specifically, we introduce the solid theoretical
foundation and fundamental concepts behind diffusion models and the three
generic diffusion modelling frameworks: diffusion probabilistic models,
noise-conditioned score networks, and stochastic differential equations. Then,
we provide a systematic taxonomy of diffusion models in the medical domain and
propose a multi-perspective categorization based on their application, imaging
modality, organ of interest, and algorithms. To this end, we cover extensive
applications of diffusion models in the medical domain. Furthermore, we
emphasize the practical use case of some selected approaches, and then we
discuss the limitations of the diffusion models in the medical domain and
propose several directions to fulfill the demands of this field. Finally, we
gather the overviewed studies with their available open-source implementations
at
https://github.com/amirhossein-kz/Awesome-Diffusion-Models-in-Medical-Imaging.Comment: Second revision: including more papers and further discussion
Statistical Medial Model dor Cardiac Segmentation and Morphometry
In biomedical image analysis, shape information can be utilized for many purposes. For example, irregular shape features can help identify diseases; shape features can help match different instances of anatomical structures for statistical comparison; and prior knowledge of the mean and possible variation of an anatomical structure\u27s shape can help segment a new example of this structure in noisy, low-contrast images. A good shape representation helps to improve the performance of the above techniques. The overall goal of the proposed research is to develop and evaluate methods for representing shapes of anatomical structures. The medial model is a shape representation method that models a 3D object by explicitly defining its skeleton (medial axis) and deriving the object\u27s boundary via inverse-skeletonization . This model represents shape compactly, and naturally expresses descriptive global shape features like thickening , bending , and elongation . However, its application in biomedical image analysis has been limited, and it has not yet been applied to the heart, which has a complex shape. In this thesis, I focus on developing efficient methods to construct the medial model, and apply it to solve biomedical image analysis problems. I propose a new 3D medial model which can be efficiently applied to complex shapes. The proposed medial model closely approximates the medial geometry along medial edge curves and medial branching curves by soft-penalty optimization and local correction. I further develop a scheme to perform model-based segmentation using a statistical medial model which incorporates prior shape and appearance information. The proposed medial models are applied to a series of image analysis tasks. The 2D medial model is applied to the corpus callosum which results in an improved alignment of the patterns of commissural connectivity compared to a volumetric registration method. The 3D medial model is used to describe the myocardium of the left and right ventricles, which provides detailed thickness maps characterizing different disease states. The model-based myocardium segmentation scheme is tested in a heterogeneous adult MRI dataset. Our segmentation experiments demonstrate that the statistical medial model can accurately segment the ventricular myocardium and provide useful parameters to characterize heart function
Existing and Potential Statistical and Computational Approaches for the Analysis of 3D CT Images of Plant Roots
Scanning technologies based on X-ray Computed Tomography (CT) have been widely used in many scientific fields including medicine, nanosciences and materials research. Considerable progress in recent years has been made in agronomic and plant science research thanks to X-ray CT technology. X-ray CT image-based phenotyping methods enable high-throughput and non-destructive measuring and inference of root systems, which makes downstream studies of complex mechanisms of plants during growth feasible. An impressive amount of plant CT scanning data has been collected, but how to analyze these data efficiently and accurately remains a challenge. We review statistical and computational approaches that have been or may be effective for the analysis of 3D CT images of plant roots. We describe and comment on different approaches to aspects of the analysis of plant roots based on images, namely, (1) root segmentation, i.e., the isolation of root from non-root matter; (2) root-system reconstruction; and (3) extraction of higher-level phenotypes. As many of these approaches are novel and have yet to be applied to this context, we limit ourselves to brief descriptions of the methodologies. With the rapid development and growing use of X-ray CT scanning technologies to generate large volumes of data relevant to root structure, it is timely to review existing and potential quantitative and computational approaches to the analysis of such data. Summaries of several computational tools are included in the Appendix
Automated Extraction of Biomarkers for Alzheimer's Disease from Brain Magnetic Resonance Images
In this work, different techniques for the automated extraction of biomarkers for
Alzheimer's disease (AD) from brain magnetic resonance imaging (MRI) are proposed.
The described work forms part of PredictAD (www.predictad.eu), a joined
European research project aiming at the identification of a unified biomarker for AD
combining different clinical and imaging measurements. Two different approaches are
followed in this thesis towards the extraction of MRI-based biomarkers: (I) the extraction
of traditional morphological biomarkers based on neuronatomical structures
and (II) the extraction of data-driven biomarkers applying machine-learning techniques.
A novel method for a unified and automated estimation of structural volumes
and volume changes is proposed. Furthermore, a new technique that allows the low-dimensional
representation of a high-dimensional image population for data analysis
and visualization is described. All presented methods are evaluated on images from
the Alzheimer's Disease Neuroimaging Initiative (ADNI), providing a large and diverse
clinical database. A rigorous evaluation of the power of all identified biomarkers to
discriminate between clinical subject groups is presented. In addition, the agreement
of automatically derived volumes with reference labels as well as the power of the
proposed method to measure changes in a subject's atrophy rate are assessed. The
proposed methods compare favorably to state-of-the art techniques in neuroimaging
in terms of accuracy, robustness and run-time
Role of deep learning in infant brain MRI analysis
Deep learning algorithms and in particular convolutional networks have shown tremendous success in medical image analysis applications, though relatively few methods have been applied to infant MRI data due numerous inherent challenges such as inhomogenous tissue appearance across the image, considerable image intensity variability across the first year of life, and a low signal to noise setting. This paper presents methods addressing these challenges in two selected applications, specifically infant brain tissue segmentation at the isointense stage and presymptomatic disease prediction in neurodevelopmental disorders. Corresponding methods are reviewed and compared, and open issues are identified, namely low data size restrictions, class imbalance problems, and lack of interpretation of the resulting deep learning solutions. We discuss how existing solutions can be adapted to approach these issues as well as how generative models seem to be a particularly strong contender to address them
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3D multiresolution statistical approaches for accelerated medical image and volume segmentation
This thesis was submitted for the degree of Doctor of Philosophy and awarded by Brunel University.Medical volume segmentation got the attraction of many researchers; therefore, many techniques have been implemented in terms of medical imaging including segmentations and other imaging processes. This research focuses on an implementation of segmentation system which uses several techniques together or on their own to segment medical volumes, the system takes a stack of 2D slices or a full 3D volumes acquired from medical scanners as a data input.
Two main approaches have been implemented in this research for segmenting medical volume which are multi-resolution analysis and statistical modeling. Multi-resolution analysis has been mainly employed in this research for extracting the features. Higher dimensions of discontinuity (line or curve singularity) have been extracted in medical images using a modified multi-resolution analysis transforms such as ridgelet and curvelet transforms.
The second implemented approach in this thesis is the use of statistical modeling in medical image segmentation; Hidden Markov models have been enhanced here to segment medical slices automatically, accurately, reliably and with lossless results. But the problem with using Markov models here is the computational time which is too long. This has been addressed by using feature reduction techniques which has also been implemented in this thesis. Some feature reduction and dimensionality reduction techniques have been used to accelerate the slowest block in the proposed system. This includes Principle Components Analysis, Gaussian Pyramids and other methods. The feature reduction techniques have been employed efficiently with the 3D volume segmentation techniques such as 3D wavelet and 3D Hidden Markov models.
The system has been tested and validated using several procedures starting at a comparison with the predefined results, crossing the specialistsā validations, and ending by validating the system using a survey filled by the end users explaining the techniques and the results. This concludes that Markovian models segmentation results has overcome all other techniques in most patientsā cases. Curvelet transform has been also proved promising segmentation results; the end users rate it better than Markovian models due to the long time required with Hidden Markov models
Computer Vision Techniques for Transcatheter Intervention
Minimally invasive transcatheter technologies have demonstrated substantial promise for the diagnosis and treatment of cardiovascular diseases. For example, TAVI is an alternative to AVR for the treatment of severe aortic stenosis and TAFA is widely used for the treatment and cure of atrial fibrillation. In addition, catheter-based IVUS and OCT imaging of coronary arteries provides important information about the coronary lumen, wall and plaque characteristics. Qualitative and quantitative analysis of these cross-sectional image data will be beneficial for the evaluation and treatment of coronary artery diseases such as atherosclerosis. In all the phases (preoperative, intraoperative, and postoperative) during the transcatheter intervention procedure, computer vision techniques (e.g., image segmentation, motion tracking) have been largely applied in the field to accomplish tasks like annulus measurement, valve selection, catheter placement control, and vessel centerline extraction. This provides beneficial guidance for the clinicians in surgical planning, disease diagnosis, and treatment assessment. In this paper, we present a systematical review on these state-of-the-art methods.We aim to give a comprehensive overview for researchers in the area of computer vision on the subject of transcatheter intervention. Research in medical computing is multi-disciplinary due to its nature, and hence it is important to understand the application domain, clinical background, and imaging modality so that methods and quantitative measurements derived from analyzing the imaging data are appropriate and meaningful. We thus provide an overview on background information of transcatheter intervention procedures, as well as a review of the computer vision techniques and methodologies applied in this area
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