1,103 research outputs found
Robust semi-automatic vessel tracing in the human retinal image by an instance segmentation neural network
The morphology and hierarchy of the vascular systems are essential for
perfusion in supporting metabolism. In human retina, one of the most
energy-demanding organs, retinal circulation nourishes the entire inner retina
by an intricate vasculature emerging and remerging at the optic nerve head
(ONH). Thus, tracing the vascular branching from ONH through the vascular tree
can illustrate vascular hierarchy and allow detailed morphological
quantification, and yet remains a challenging task. Here, we presented a novel
approach for a robust semi-automatic vessel tracing algorithm on human fundus
images by an instance segmentation neural network (InSegNN). Distinct from
semantic segmentation, InSegNN separates and labels different vascular trees
individually and therefore enable tracing each tree throughout its branching.
We have built-in three strategies to improve robustness and accuracy with
temporal learning, spatial multi-sampling, and dynamic probability map. We
achieved 83% specificity, and 50% improvement in Symmetric Best Dice (SBD)
compared to literature, and outperformed baseline U-net. We have demonstrated
tracing individual vessel trees from fundus images, and simultaneously retain
the vessel hierarchy information. InSegNN paves a way for any subsequent
morphological analysis of vascular morphology in relation to retinal diseases
Geospatial Information Research: State of the Art, Case Studies and Future Perspectives
Geospatial information science (GI science) is concerned with the development and application of geodetic and information science methods for modeling, acquiring, sharing, managing, exploring, analyzing, synthesizing, visualizing, and evaluating data on spatio-temporal phenomena related to the Earth. As an interdisciplinary scientific discipline, it focuses on developing and adapting information technologies to understand processes on the Earth and human-place interactions, to detect and predict trends and patterns in the observed data, and to support decision making. The authors – members of DGK, the Geoinformatics division, as part of the Committee on Geodesy of the Bavarian Academy of Sciences and Humanities, representing geodetic research and university teaching in Germany – have prepared this paper as a means to point out future research questions and directions in geospatial information science. For the different facets of geospatial information science, the state of art is presented and underlined with mostly own case studies. The paper thus illustrates which contributions the German GI community makes and which research perspectives arise in geospatial information science. The paper further demonstrates that GI science, with its expertise in data acquisition and interpretation, information modeling and management, integration, decision support, visualization, and dissemination, can help solve many of the grand challenges facing society today and in the future
Unsupervised image registration towards enhancing performance and explainability in cardiac and brain image analysis
Magnetic Resonance Imaging (MRI) typically recruits multiple sequences (defined here as “modalities”). As each modality is designed to offer different anatomical and functional clinical information, there are evident disparities in the imaging content across modalities. Inter- and intra-modality affine and non-rigid image registration is an essential medical image analysis process in clinical imaging, as for example before imaging biomarkers need to be derived and clinically evaluated across different MRI modalities, time phases and slices. Although commonly needed in real clinical scenarios, affine and non-rigid image registration is not extensively investigated using a single unsupervised model architecture. In our work, we present an unsupervised deep learning registration methodology that can accurately model affine and non-rigid transformations, simultaneously. Moreover, inverse-consistency is a fundamental inter-modality registration property that is not considered in deep learning registration algorithms. To address inverse consistency, our methodology performs bi-directional cross-modality image synthesis to learn modality-invariant latent representations, and involves two factorised transformation networks (one per each encoder-decoder channel) and an inverse-consistency loss to learn topology-preserving anatomical transformations. Overall, our model (named “FIRE”) shows improved performances against the reference standard baseline method (i.e., Symmetric Normalization implemented using the ANTs toolbox) on multi-modality brain 2D and 3D MRI and intra-modality cardiac 4D MRI data experiments. We focus on explaining model-data components to enhance model explainability in medical image registration. On computational time experiments, we show that the FIRE model performs on a memory-saving mode, as it can inherently learn topology-preserving image registration directly in the training phase. We therefore demonstrate an efficient and versatile registration technique that can have merit in multi-modal image registrations in the clinical setting
Repurposing existing skeletal spatial structure (SkS) system designs using the Field Information Modeling (FIM) framework for generative decision-support in future construction projects
Skeletal spatial structure (SkS) systems are modular systems which have shown promise to support mass customization, and sustainability in construction. SkS have been used extensively in the reconstruction efforts since World War II, particularly to build geometrically flexible and free-form structures. By employing advanced digital engineering and construction practices, the existing SkS designs may be repurposed to generate new optimal designs that satisfy current construction demands of contemporary societies. To this end, this study investigated the application of point cloud processing using the Field Information Modeling (FIM) framework for the digital documentation and generative redesign of existing SkS systems. Three new algorithms were proposed to (i) expand FIM to include generative decision-support; (ii) generate as-built building information modeling (BIM) for SkS; and (iii) modularize SkS designs with repeating patterns for optimal production and supply chain management. These algorithms incorporated a host of new AI-inspired methods, including support vector machine (SVM) for decision support; Bayesian optimization for neighborhood definition; Bayesian Gaussian mixture clustering for modularization; and Monte Carlo stochastic multi-criteria decision making (MCDM) for selection of the top Pareto front solutions obtained by the non-dominant sorting Genetic Algorithm (NSGA II). The algorithms were tested and validated on four real-world point cloud datasets to solve two generative modeling problems, namely, engineering design optimization and facility location optimization. It was observed that the proposed Bayesian neighborhood definition outperformed particle swarm and uniform sampling by 34% and 27%, respectively. The proposed SVM-based linear feature detection outperformed k-means and spectral clustering by 56% and 9%, respectively. Finally, the NSGA II algorithm combined with the stochastic MCDM produced diverse “top four” solutions based on project-specific criteria. The results indicate promise for future utilization of the framework to produce training datasets for generative adversarial networks that generate new designs based only on stakeholder requirements
Computerized Analysis of Magnetic Resonance Images to Study Cerebral Anatomy in Developing Neonates
The study of cerebral anatomy in developing neonates is of great importance for
the understanding of brain development during the early period of life. This
dissertation therefore focuses on three challenges in the modelling of cerebral
anatomy in neonates during brain development. The methods that have been
developed all use Magnetic Resonance Images (MRI) as source data.
To facilitate study of vascular development in the neonatal period, a set of image
analysis algorithms are developed to automatically extract and model cerebral
vessel trees. The whole process consists of cerebral vessel tracking from
automatically placed seed points, vessel tree generation, and vasculature
registration and matching. These algorithms have been tested on clinical Time-of-
Flight (TOF) MR angiographic datasets.
To facilitate study of the neonatal cortex a complete cerebral cortex segmentation
and reconstruction pipeline has been developed. Segmentation of the neonatal
cortex is not effectively done by existing algorithms designed for the adult brain
because the contrast between grey and white matter is reversed. This causes pixels
containing tissue mixtures to be incorrectly labelled by conventional methods. The
neonatal cortical segmentation method that has been developed is based on a novel
expectation-maximization (EM) method with explicit correction for mislabelled
partial volume voxels. Based on the resulting cortical segmentation, an implicit
surface evolution technique is adopted for the reconstruction of the cortex in
neonates. The performance of the method is investigated by performing a detailed
landmark study.
To facilitate study of cortical development, a cortical surface registration algorithm
for aligning the cortical surface is developed. The method first inflates extracted
cortical surfaces and then performs a non-rigid surface registration using free-form
deformations (FFDs) to remove residual alignment. Validation experiments using
data labelled by an expert observer demonstrate that the method can capture local
changes and follow the growth of specific sulcus
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