Procedures of quality control and data analysis of multi-site ground-based observations for the absolute flux calibration of Gaia

The Gaia space mission is a major project for the European astronomical community. As challenging as it is, the processing and analysis of the huge data-flow incoming from Gaia is the subject of thorough study and preparatory work by the DPAC (Data Processing and Analysis Consortium), in charge of all aspects of the Gaia data reduction. This PhD Thesis was carried out in the framework of the DPAC, within the team based in Bologna. The task of the Bologna team is to define the calibration model and to build a grid of spectro-photometric standard stars (SPSS) suitable for the absolute flux calibration of the Gaia G-band photometry and the BP/RP spectrophotometry. Such a flux calibration can be performed by repeatedly observing each SPSS during the life-time of the Gaia mission and by comparing the observed Gaia spectra to the spectra obtained by our ground-based observations. Due to both the different observing sites involved and the huge amount of frames expected (≃100000), it is essential to maintain the maximum homogeneity in data quality, acquisition and treatment, and a particular care has to be used to test the capabilities of each telescope/instrument combination (through the “instrument familiarization plan”), to devise methods to keep under control, and eventually to correct for, the typical instrumental effects that can affect the high precision required for the Gaia SPSS grid (a few % with respect to Vega). I contributed to the ground-based survey of Gaia SPSS in many respects: with the observations, the instrument familiarization plan, the data reduction and analysis activities (both photometry and spectroscopy), and to the maintenance of the data archives. However, the field I was personally responsible for was photometry and in particular relative photometry for the production of short-term light curves. In this context I defined and tested a semi-automated pipeline which allows for the pre-reduction of imaging SPSS data and the production of aperture photometry catalogues ready to be used for further analysis. A series of semi-automated quality control criteria are included in the pipeline at various levels, from pre-reduction, to aperture photometry, to light curves production and analysis.

Digitale Einstrahl-Holographie atmosphärischer Eiskristalle

Es wurde ein für bodengebundene Feldmessungen geeignetes System zur digital-holographischen Abbildung luftgetragener Objekte entwickelt und konstruiert. Es ist, abhängig von der Tiefenposition, geeignet zur direkten Bestimmung der Größe luftgetragener Objekte oberhalb von ca. 20 µm, sowie ihrer Form bei Größen oberhalb von ca. 100µm bis in den Millimeterbereich. Die Entwicklung umfaßte zusätzlich einen Algorithmus zur automatisierten Verbesserung der Hologrammqualität und zur semiautomatischen Entfernungsbestimmung großer Objekte entwickelt. Eine Möglichkeit zur intrinsischen Effizienzsteigerung der Bestimmung der Tiefenposition durch die Berechnung winkelgemittelter Profile wurde vorgestellt. Es wurde weiterhin ein Verfahren entwickelt, das mithilfe eines iterativen Ansatzes für isolierte Objekte die Rückgewinnung der Phaseninformation und damit die Beseitigung des Zwillingsbildes erlaubt. Weiterhin wurden mithilfe von Simulationen die Auswirkungen verschiedener Beschränkungen der digitalen Holographie wie der endlichen Pixelgröße untersucht und diskutiert. Die geeignete Darstellung der dreidimensionalen Ortsinformation stellt in der digitalen Holographie ein besonderes Problem dar, da das dreidimensionale Lichtfeld nicht physikalisch rekonstruiert wird. Es wurde ein Verfahren entwickelt und implementiert, das durch Konstruktion einer stereoskopischen Repräsentation des numerisch rekonstruierten Meßvolumens eine quasi-dreidimensionale, vergrößerte Betrachtung erlaubt. Es wurden ausgewählte, während Feldversuchen auf dem Jungfraujoch aufgenommene digitale Hologramme rekonstruiert. Dabei ergab sich teilweise ein sehr hoher Anteil an irregulären Kristallformen, insbesondere infolge massiver Bereifung. Es wurden auch in Zeiträumen mit formal eisuntersättigten Bedingungen Objekte bis hinunter in den Bereich ≤20µm beobachtet. Weiterhin konnte in Anwendung der hier entwickelten Theorie des ”Phasenrandeffektes“ ein Objekt von nur ca. 40µm Größe als Eisplättchen identifiziert werden. Größter Nachteil digitaler Holographie gegenüber herkömmlichen photographisch abbildenden Verfahren ist die Notwendigkeit der aufwendigen numerischen Rekonstruktion. Es ergibt sich ein hoher rechnerischer Aufwand zum Erreichen eines einer Photographie vergleichbaren Ergebnisses. Andererseits weist die digitale Holographie Alleinstellungsmerkmale auf. Der Zugang zur dreidimensionalen Ortsinformation kann der lokalen Untersuchung der relativen Objektabstände dienen. Allerdings zeigte sich, dass die Gegebenheiten der digitalen Holographie die Beobachtung hinreichend großer Mengen von Objekten auf der Grundlage einzelner Hologramm gegenwärtig erschweren. Es wurde demonstriert, dass vollständige Objektgrenzen auch dann rekonstruiert werden konnten, wenn ein Objekt sich teilweise oder ganz außerhalb des geometrischen Meßvolumens befand. Weiterhin wurde die zunächst in Simulationen demonstrierte Sub-Bildelementrekonstruktion auf reale Hologramme angewandt. Dabei konnte gezeigt werden, dass z.T. quasi-punktförmige Objekte mit Sub-Pixelgenauigkeit lokalisiert, aber auch bei ausgedehnten Objekten zusätzliche Informationen gewonnen werden konnten. Schließlich wurden auf rekonstruierten Eiskristallen Interferenzmuster beobachtet und teilweise zeitlich verfolgt. Gegenwärtig erscheinen sowohl kristallinterne Reflexion als auch die Existenz einer (quasi-)flüssigen Schicht als Erklärung möglich, wobei teilweise in Richtung der letztgenannten Möglichkeit argumentiert werden konnte. Als Ergebnis der Arbeit steht jetzt ein System zur Verfügung, das ein neues Meßinstrument und umfangreiche Algorithmen umfaßt. S. M. F. Raupach, H.-J. Vössing, J. Curtius und S. Borrmann: Digital crossed-beam holography for in-situ imaging of atmospheric particles, J. Opt. A: Pure Appl. Opt. 8, 796-806 (2006) S. M. F. Raupach: A cascaded adaptive mask algorithm for twin image removal and its application to digital holograms of ice crystals, Appl. Opt. 48, 287-301 (2009) S. M. F. Raupach: Stereoscopic 3D visualization of particle fields reconstructed from digital inline holograms, (zur Veröffentlichung angenommen, Optik - Int. J. Light El. Optics, 2009)

Data Quality Assessment of Ungated Flow Cytometry Data in High

Background: The recent development of semi-automated techniques for staining and analyzing flow cytometry samples has presented new challenges. Quality control and quality assessment are critical when developing new high throughput technologies and their associated information services. Our experience suggests that significant bottlenecks remain in the development of high throughput flow cytometry methods for data analysis and display. Especially, data quality control and quality assessment are crucial steps in processing and analyzing high throughput flow cytometry data. Methods: We propose a variety of graphical exploratory data analytic tools for exploring ungated flow cytometry data. We have implemented a number of specialized functions and methods in the Bioconductor package rflowcyt. We demonstrate the use of these approaches by investigating two independent sets of high throughput flow cytometry data. Results: We found that graphical representations can reveal substantial non-biological differences in samples. Empirical Cumulative Distribution Function and summary scatterplots were especially useful in the rapid identification of problems not identified by manual review. Conclusions: Graphical exploratory data analytic tools are quick and useful means of assessing data quality. We propose that the described visualizations should be used as quality assessment tools and where possible, be used for quality control.

BEYOND ROOTS ALONE: NOVEL METHODOLOGIES FOR ANALYZING COMPLEX SOIL AND MINIRHIZOTRON IMAGERY USING IMAGE PROCESSING AND GIS TOOLS

Quantifying belowground dynamics is critical to our understanding of plant and ecosystem function and belowground carbon cycling, yet currently available tools for complex belowground image analyses are insufficient. We introduce novel techniques combining digital image processing tools and geographic information systems (GIS) analysis to permit semi-automated analysis of complex root and soil dynamics. We illustrate methodologies with imagery from microcosms, minirhizotrons, and a rhizotron, in upland and peatland soils. We provide guidelines for correct image capture, a method that automatically stitches together numerous minirhizotron images into one seamless image, and image analysis using image segmentation and classification in SPRING or change analysis in ArcMap. These methods facilitate spatial and temporal root and soil interaction studies, providing a framework to expand a more comprehensive understanding of belowground dynamics.

Methodological considerations and practical recommendations for the application of peripheral arterial tonometry in children and adolescents

Endothelial dysfunction is recognized as the primum movens in the development of atherosclerosis. Its crucial role in both cardiovascular morbidity and mortality has been confirmed. In the past, research was hampered by the invasive character of endothelial function assessment. The development of non-invasive and feasible techniques to measure endothelial function has facilitated and promoted research in various adult and paediatric subpopulations. To avoid user dependence of flow-mediated dilation (FMD), which evaluates nitric oxide dependent vasodilation in large vessels, a semi-automated, method to assess peripheral microvascular function, called peripheral arterial tonometry (Endo-PAT®), was recently introduced. The number of studies using this technique in children and adolescents is rapidly increasing, yet there is no consensus with regard to either measuring protocol or data analysis of peripheral arterial tonometry in children and adolescents. Most paediatric studies simply applied measuring and analysing methodology established in adults, a simplification that may not be appropriate. This paper provides a detailed description of endothelial function assessment using the Endo-PAT for researchers and clinicians. We discuss clinical and methodological considerations and point out the differences between children, adolescents and adults. Finally, the main aim of this paper is to provide recommendations for a standardised application of Endo-PAT in children and adolescents, as well as for population-specific data analysis methodology.

Accuracy and reproducibility of aortic annulus sizing using a dedicated three-dimensional computed tomography reconstruction tool in patients evaluated for transcatheter aortic valve replacement

Aims: To evaluate the accuracy and reproducibility of aortic annulus sizing using a multislice computed tomography (MSCT) based aortic root reconstruction tool compared with conventional imaging among patients evaluated for transcatheter aortic valve replacement (TAVR). Methods and results: Patients referred for TAVR underwent standard preprocedural assessment of aortic annulus parameters using MSCT, angiography and transoesophageal echocardiography (TEE). Three-dimensional (3-D) reconstruction of MSCT images of the aortic root was performed using 3mensio (3mensio Medical Imaging BV, Bilthoven, The Netherlands), allowing for semi-automated delineation of the annular plane and assessment of annulus perimeter, area, maximum, minimum and virtual diameters derived from area and perimeter (aVD and pVD). A total of 177 patients were enrolled. We observed a good inter-observer variability of 3-D reconstruction assessments with concordance coefficients for agreement of 0.91 (95% CI: 0.87-0.93) and 0.91 (0.88-0.94) for annulus perimeter and area assessments, respectively. 3-D derived pVD and aVD correlated very closely with a concordance coefficient of 0.97 (0.96-0.98) with a mean difference of 0.5±0.3 mm (pVD-aVD). 3-D derived pVD showed the best, but moderate concordance with diameters obtained from coronal MSCT (0.67, 0.56-0.75; 0.3±1.8 mm), and the lowest concordance with diameters obtained from TEE (0.42, 0.31-0.52; 1.9±1.9 mm). Conclusions: MSCT-based 3-D reconstruction of the aortic annulus using the 3mensio software enables accurate and reproducible assessment of aortic annulus dimensions.

The FORA Framework - A Fuzzy Grassroots Ontology for Online Reputation Management

Online reputation management deals with monitoring and influencing the online record of a person, an organization or a product. The Social Web offers increasingly simple ways to publish and disseminate personal or opinionated information, which can rapidly have a disastrous influence on the online reputation of some of the entities. The author focuses on the Social Web and possibilities of its integration with the Semantic Web as resource for a semi-automated tracking of online reputations using imprecise natural language terms. The inherent structure of natural language supports humans not only in communication but also in the perception of the world. Thereby fuzziness is a promising tool for transforming those human perceptions into computer artifacts. Through fuzzy grassroots ontologies, the Social Semantic Web becomes more naturally and thus can streamline online reputation management. For readers interested in the cross-over field of computer science, information systems, and social sciences, this book is an ideal source for becoming acquainted with the evolving field of fuzzy online reputation management in the Social Semantic Web area. ​

Detecting offsets in GPS time series: first results from the Detection of Offsets in GPS Experiment

The accuracy of Global Positioning System (GPS) time series is degraded by the presence of offsets. To assess the effectiveness of methods that detect and remove these offsets, we designed and managed the Detection of Offsets in GPS Experiment. We simulated time series that mimicked realistic GPS data consisting of a velocity component, offsets, white and flicker noises (1/f spectrum noises) composed in an additive model. The data set was made available to the GPS analysis community without revealing the offsets, and several groups conducted blind tests with a range of detection approaches. The results show that, at present, manual methods (where offsets are hand picked) almost always give better results than automated or semi‒automated methods (two automated methods give quite similar velocity bias as the best manual solutions). For instance, the fifth percentile range (5% to 95%) in velocity bias for automated approaches is equal to 4.2 mm/year (most commonly ±0.4 mm/yr from the truth), whereas it is equal to 1.8 mm/yr for the manual solutions (most commonly 0.2 mm/yr from the truth). The magnitude of offsets detectable by manual solutions is smaller than for automated solutions, with the smallest detectable offset for the best manual and automatic solutions equal to 5 mm and 8 mm, respectively. Assuming the simulated time series noise levels are representative of real GPS time series, robust geophysical interpretation of individual site velocities lower than 0.2–0.4 mm/yr is therefore certainly not robust, although a limit of nearer 1 mm/yr would be a more conservative choice. Further work to improve offset detection in GPS coordinates time series is required before we can routinely interpret sub‒mm/yr velocities for single GPS stations.

HUMAN PROPHASE CHROMOSOME UNIQUE BAND SEQUENCES; DEFINITION, CHARACTERIZATION, AND APPLICATION (CYTOGENETICS, IMAGE PROCESSING)

Extensive experience with the analysis of human prophase chromosomes and studies into the complexity of prophase GTG-banding patterns have suggested that at least some prophase chromosomal segments can be accurately identified and characterized independently of the morphology of the chromosome as a whole. In this dissertation the feasibility of identifying and analyzing specified prophase chromosome segments was thus investigated as an alternative approach to prophase chromosome analysis based on whole chromosome recognition. Through the use of prophase idiograms at the 850-band-stage (FRANCKE, 1981) and a comparison system based on the calculation of cross-correlation coefficients between idiogram profiles, we have demonstrated that it is possible to divide the 24 human prophase idiograms into a set of 94 unique band sequences. Each unique band sequence has a banding pattern that is recognizable and distinct from any other non-homologous chromosome portion.^ Using chromosomes 11p and 16 thru 22 to demonstrate unique band sequence integrity at the chromosome level, we found that prophase chromosome banding pattern variation can be compensated for and that a set of unique band sequences very similar to those at the idiogram level can be identified on actual chromosomes.^ The use of a unique band sequence approach in prophase chromosome analysis is expected to increase efficiency and sensitivity through more effective use of available banding information. The use of a unique band sequence approach to prophase chromosome analysis is discussed both at the routine level by cytogeneticists and at an image processing level with a semi-automated approach to prophase chromosome analysis. ^

Part two: Against the motion. External diameter for AAA size

Aneurysm diameter measurement is quick and easy, but suffers from the pitfalls of being "too rough and ready". When semi-automated segmentation took 7-10 minutes to estimate volume, it was not a practical tool for busy, routine clinical practice. Today, the availability of automatic segmentation in seconds is bound to make volume measurement, along with 3D ultrasonography, the tools of the future. There can be no debate.

Privacy Preserving Probabilistic Record Linkage (P3RL): a novel method for linking existing health-related data and maintaining participant confidentiality.

BACKGROUND Record linkage of existing individual health care data is an efficient way to answer important epidemiological research questions. Reuse of individual health-related data faces several problems: Either a unique personal identifier, like social security number, is not available or non-unique person identifiable information, like names, are privacy protected and cannot be accessed. A solution to protect privacy in probabilistic record linkages is to encrypt these sensitive information. Unfortunately, encrypted hash codes of two names differ completely if the plain names differ only by a single character. Therefore, standard encryption methods cannot be applied. To overcome these challenges, we developed the Privacy Preserving Probabilistic Record Linkage (P3RL) method. METHODS In this Privacy Preserving Probabilistic Record Linkage method we apply a three-party protocol, with two sites collecting individual data and an independent trusted linkage center as the third partner. Our method consists of three main steps: pre-processing, encryption and probabilistic record linkage. Data pre-processing and encryption are done at the sites by local personnel. To guarantee similar quality and format of variables and identical encryption procedure at each site, the linkage center generates semi-automated pre-processing and encryption templates. To retrieve information (i.e. data structure) for the creation of templates without ever accessing plain person identifiable information, we introduced a novel method of data masking. Sensitive string variables are encrypted using Bloom filters, which enables calculation of similarity coefficients. For date variables, we developed special encryption procedures to handle the most common date errors. The linkage center performs probabilistic record linkage with encrypted person identifiable information and plain non-sensitive variables. RESULTS In this paper we describe step by step how to link existing health-related data using encryption methods to preserve privacy of persons in the study. CONCLUSION Privacy Preserving Probabilistic Record linkage expands record linkage facilities in settings where a unique identifier is unavailable and/or regulations restrict access to the non-unique person identifiable information needed to link existing health-related data sets. Automated pre-processing and encryption fully protect sensitive information ensuring participant confidentiality. This method is suitable not just for epidemiological research but also for any setting with similar challenges.

Multi-temporal mapping of seagrass cover, species and biomass of the Eastern Banks, Moreton Bay, Australia, with links to shapefiles

The spatial and temporal dynamics of seagrasses have been studied from the leaf to patch (100 m**2) scales. However, landscape scale (> 100 km**2) seagrass population dynamics are unresolved in seagrass ecology. Previous remote sensing approaches have lacked the temporal or spatial resolution, or ecologically appropriate mapping, to fully address this issue. This paper presents a robust, semi-automated object-based image analysis approach for mapping dominant seagrass species, percentage cover and above ground biomass using a time series of field data and coincident high spatial resolution satellite imagery. The study area was a 142 km**2 shallow, clear water seagrass habitat (the Eastern Banks, Moreton Bay, Australia). Nine data sets acquired between 2004 and 2013 were used to create seagrass species and percentage cover maps through the integration of seagrass photo transect field data, and atmospherically and geometrically corrected high spatial resolution satellite image data (WorldView-2, IKONOS and Quickbird-2) using an object based image analysis approach. Biomass maps were derived using empirical models trained with in-situ above ground biomass data per seagrass species. Maps and summary plots identified inter- and intra-annual variation of seagrass species composition, percentage cover level and above ground biomass. The methods provide a rigorous approach for field and image data collection and pre-processing, a semi-automated approach to extract seagrass species and cover maps and assess accuracy, and the subsequent empirical modelling of seagrass biomass. The resultant maps provide a fundamental data set for understanding landscape scale seagrass dynamics in a shallow water environment. Our findings provide proof of concept for the use of time-series analysis of remotely sensed seagrass products for use in seagrass ecology and management.

Benthic and substrate cover data derived from a time series of photo-transect surveys for the Eastern Banks, Moreton Bay Australia, 2004-2015

This paper describes seagrass species and percentage cover point-based field data sets derived from georeferenced photo transects. Annually or biannually over a ten year period (2004-2015) data sets were collected using 30-50 transects, 500-800 m in length distributed across a 142 km**2 shallow, clear water seagrass habitat, the Eastern Banks, Moreton Bay, Australia. Each of the eight data sets include seagrass property information derived from approximately 3000 georeferenced, downward looking photographs captured at 2-4 m intervals along the transects. Photographs were manually interpreted to estimate seagrass species composition and percentage cover (Coral Point Count excel; CPCe). Understanding seagrass biology, ecology and dynamics for scientific and management purposes requires point-based data on species composition and cover. This data set, and the methods used to derive it are a globally unique example for seagrass ecological applications. It provides the basis for multiple further studies at this site, regional to global comparative studies, and, for the design of similar monitoring programs elsewhere.