Toward quantitative three-dimensional microvascular networks segmentation with multiview light-sheet fluorescence microscopy

Three-dimensional (3-D) large-scale imaging of microvascular networks is of interest in various areas of biology and medicine related to structural, functional, developmental, and pathological issues. Light-sheet fluorescence microscopy (LSFM) techniques are rapidly spreading and are now on the way to offer operational solutions for large-scale tissue imaging. This contribution describes how reliable vessel segmentation can be handled from LSFM data in very large tissue volumes using a suitable image analysis workflow. Since capillaries are tubular objects of a few microns scale radius, they represent challenging structures to reliably reconstruct without distortion and artifacts. We provide a systematic analysis of multiview deconvolution image processing workflow to control and evaluate the accuracy of the reconstructed vascular network using various low to high level, metrics. We show that even if low-level structural metrics are sensitive to isotropic imaging enhancement provided by a larger number of views, functional high-level metrics, including perfusion permeability, are less sensitive. Hence, combining deconvolution and registration onto a few number of views appears sufficient for a reliable quantitative 3-D vessel segmentation for their possible use for perfusion modeling

From whole-organ imaging to in-silico blood flow modeling: a new multi-scale network analysis for revisiting tissue functional anatomy

We present a multi-disciplinary image-based blood flow perfusion modeling of a whole organ vascular network for analyzing both its structural and functional properties. We show how the use of Light-Sheet Fluorescence Microscopy (LSFM) permits whole-organ micro- vascular imaging, analysis and modelling. By using adapted image post-treatment workflow, we could segment, vectorize and reconstruct the entire micro-vascular network composed of 1.7 million vessels, from the tissue-scale, inside a * 25 × 5 × 1 = 125mm 3 volume of the mouse fat pad, hundreds of times larger than previous studies, down to the cellular scale at micron resolution, with the entire blood perfusion modeled. Adapted network analysis revealed the structural and functional organization of meso-scale tissue as strongly connected communities of vessels. These communities share a distinct heterogeneous core region and a more homogeneous peripheral region, consistently with known biological functions of fat tissue. Graph clustering analysis also revealed two distinct robust meso-scale typical sizes (from 10 to several hundred times the cellular size), revealing, for the first time, strongly connected functional vascular communities. These community networks support heterogeneous micro-environments. This work provides the proof of concept that in-silico all-tissue perfusion modeling can reveal new structural and functional exchanges between micro-regions in tissues, found from community clusters in the vascular graph

Automatic road network extraction from high resolution satellite imagery using spectral classification methods

Road networks play an important role in a number of geospatial applications, such as cartographic, infrastructure planning and traffic routing software. Automatic and semi-automatic road network extraction techniques have significantly increased the extraction rate of road networks. Automated processes still yield some erroneous and incomplete results and costly human intervention is still required to evaluate results and correct errors. With the aim of improving the accuracy of road extraction systems, three objectives are defined in this thesis: Firstly, the study seeks to develop a flexible semi-automated road extraction system, capable of extracting roads from QuickBird satellite imagery. The second objective is to integrate a variety of algorithms within the road network extraction system. The benefits of using each of these algorithms within the proposed road extraction system, is illustrated. Finally, a fully automated system is proposed by incorporating a number of the algorithms investigated throughout the thesis. CopyrightDissertation (MSc)--University of Pretoria, 2010.Computer Scienceunrestricte

An Evolutionary Approach to Adaptive Image Analysis for Retrieving and Long-term Monitoring Historical Land Use from Spatiotemporally Heterogeneous Map Sources

Land use changes have become a major contributor to the anthropogenic global change. The ongoing dispersion and concentration of the human species, being at their orders unprecedented, have indisputably altered Earth’s surface and atmosphere. The effects are so salient and irreversible that a new geological epoch, following the interglacial Holocene, has been announced: the Anthropocene. While its onset is by some scholars dated back to the Neolithic revolution, it is commonly referred to the late 18th century. The rapid development since the industrial revolution and its implications gave rise to an increasing awareness of the extensive anthropogenic land change and led to an urgent need for sustainable strategies for land use and land management. By preserving of landscape and settlement patterns at discrete points in time, archival geospatial data sources such as remote sensing imagery and historical geotopographic maps, in particular, could give evidence of the dynamic land use change during this crucial period. In this context, this thesis set out to explore the potentials of retrospective geoinformation for monitoring, communicating, modeling and eventually understanding the complex and gradually evolving processes of land cover and land use change. Currently, large amounts of geospatial data sources such as archival maps are being worldwide made online accessible by libraries and national mapping agencies. Despite their abundance and relevance, the usage of historical land use and land cover information in research is still often hindered by the laborious visual interpretation, limiting the temporal and spatial coverage of studies. Thus, the core of the thesis is dedicated to the computational acquisition of geoinformation from archival map sources by means of digital image analysis. Based on a comprehensive review of literature as well as the data and proposed algorithms, two major challenges for long-term retrospective information acquisition and change detection were identified: first, the diversity of geographical entity representations over space and time, and second, the uncertainty inherent to both the data source itself and its utilization for land change detection. To address the former challenge, image segmentation is considered a global non-linear optimization problem. The segmentation methods and parameters are adjusted using a metaheuristic, evolutionary approach. For preserving adaptability in high level image analysis, a hybrid model- and data-driven strategy, combining a knowledge-based and a neural net classifier, is recommended. To address the second challenge, a probabilistic object- and field-based change detection approach for modeling the positional, thematic, and temporal uncertainty adherent to both data and processing, is developed. Experimental results indicate the suitability of the methodology in support of land change monitoring. In conclusion, potentials of application and directions for further research are given

Semi-automatic Road Extraction from Very High Resolution Remote Sensing Imagery by RoadModeler

Accurate and up-to-date road information is essential for both effective urban planning and disaster management. Today, very high resolution (VHR) imagery acquired by airborne and spaceborne imaging sensors is the primary source for the acquisition of spatial information of increasingly growing road networks. Given the increased availability of the aerial and satellite images, it is necessary to develop computer-aided techniques to improve the efficiency and reduce the cost of road extraction tasks. Therefore, automation of image-based road extraction is a very active research topic. This thesis deals with the development and implementation aspects of a semi-automatic road extraction strategy, which includes two key approaches: multidirectional and single-direction road extraction. It requires a human operator to initialize a seed circle on a road and specify a extraction approach before the road is extracted by automatic algorithms using multiple vision cues. The multidirectional approach is used to detect roads with different materials, widths, intersection shapes, and degrees of noise, but sometimes it also interprets parking lots as road areas. Different from the multidirectional approach, the single-direction approach can detect roads with few mistakes, but each seed circle can only be used to detect one road. In accordance with this strategy, a RoadModeler prototype was developed. Both aerial and GeoEye-1 satellite images of seven different types of scenes with various road shapes in rural, downtown, and residential areas were used to evaluate the performance of the RoadModeler. The experimental results demonstrated that the RoadModeler is reliable and easy-to-use by a non-expert operator. Therefore, the RoadModeler is much better than the object-oriented classification. Its average road completeness, correctness, and quality achieved 94%, 97%, and 94%, respectively. These results are higher than those of Hu et al. (2007), which are 91%, 90%, and 85%, respectively. The successful development of the RoadModeler suggests that the integration of multiple vision cues potentially offers a solution to simple and fast acquisition of road information. Recommendations are given for further research to be conducted to ensure that this progress goes beyond the prototype stage and towards everyday use

Automated 3D scene reconstruction from open geospatial data sources: airborne laser scanning and a 2D topographic database

Open geospatial data sources provide opportunities for low cost 3D scene reconstruction. In this study, based on a sparse airborne laser scanning (ALS) point cloud (0.8 points/m2) obtained from open source databases, a building reconstruction pipeline for CAD building models was developed. The pipeline includes voxel-based roof patch segmentation, extraction of the key-points representing the roof patch outline, step edge identification and adjustment, and CAD building model generation. The advantages of our method lie in generating CAD building models without the step of enforcing the edges to be parallel or building regularization. Furthermore, although it has been challenging to use sparse datasets for 3D building reconstruction, our result demonstrates the great potential in such applications. In this paper, we also investigated the applicability of open geospatial datasets for 3D road detection and reconstruction. Road central lines were acquired from an open source 2D topographic database. ALS data were utilized to obtain the height and width of the road. A constrained search method (CSM) was developed for road width detection. The CSM method was conducted by splitting a given road into patches according to height and direction criteria. The road edges were detected patch by patch. The road width was determined by the average distance from the edge points to the central line. As a result, 3D roads were reconstructed from ALS and a topographic database