Measuring Collagen Arrangement and Its Relationship with Preterm Birth using Mueller Matrix Polarimetry

Preterm birth (PTB) is defined as delivery prior to 37 weeks of gestation. It is the leading cause of infant death worldwide, responsible for infant neurological disorders, long-term cognitive impairment, as well as chronic health issues involving the auditory, visual, digestive, and respiratory systems. In expectant mothers, causes for PTB can include infection, inflammation, vascular disease, short intervals between pregnancies, multiple gestations and genetic factors. In the U.S., PTB occurs in over 11% of births and at an elevated 18.1% in Miami-Dade County, FL; while in the developing world the incidence of PB is over 15%. Early identification of at-risk pregnancies is important for the success of medical intervention. Current diagnosis methodologies of PTB include ultrasound imaging of cervical length and fetal fibronectin assay but have low positive predictive power. Compared to the markers targeted by current diagnosis methodologies, collagen content in the cervix changes more drastically throughout the course of gestation due to its link to changes in load bearing capacity that occur during the phases of pregnancy. Mueller matrix polarimetry is capable of characterizing changes in collagen without making contact with patients and may prove to be an improvement to current diagnosis methodologies. A clear difference is seen in collagen orientation between nonpregnant and pregnant patients. The development of a new imaging modality aimed at assessing early changes in collagen arrangement in the cervix may improve risk determination of PTB and reduce the morbidity of the condition. Earlier prediction of PTB could improve outcomes by allowing longer intervention times to prolong gestation time for the infant in the womb. A more reliable quantitative predictor may also lead to development of more treatment options

Multisource Data Integration in Remote Sensing

Papers presented at the workshop on Multisource Data Integration in Remote Sensing are compiled. The full text of these papers is included. New instruments and new sensors are discussed that can provide us with a large variety of new views of the real world. This huge amount of data has to be combined and integrated in a (computer-) model of this world. Multiple sources may give complimentary views of the world - consistent observations from different (and independent) data sources support each other and increase their credibility, while contradictions may be caused by noise, errors during processing, or misinterpretations, and can be identified as such. As a consequence, integration results are very reliable and represent a valid source of information for any geographical information system

Remote Sensing of Plant Biodiversity

At last, here it is. For some time now, the world has needed a text providing both a new theoretical foundation and practical guidance on how to approach the challenge of biodiversity decline in the Anthropocene. This is a global challenge demanding global approaches to understand its scope and implications. Until recently, we have simply lacked the tools to do so. We are now entering an era in which we can realistically begin to understand and monitor the multidimensional phenomenon of biodiversity at a planetary scale. This era builds upon three centuries of scientific research on biodiversity at site to landscape levels, augmented over the past two decades by airborne research platforms carrying spectrometers, lidars, and radars for larger-scale observations. Emerging international networks of fine-grain in-situ biodiversity observations complemented by space-based sensors offering coarser-grain imagery—but global coverage—of ecosystem composition, function, and structure together provide the information necessary to monitor and track change in biodiversity globally. This book is a road map on how to observe and interpret terrestrial biodiversity across scales through plants—primary producers and the foundation of the trophic pyramid. It honors the fact that biodiversity exists across different dimensions, including both phylogenetic and functional. Then, it relates these aspects of biodiversity to another dimension, the spectral diversity captured by remote sensing instruments operating at scales from leaf to canopy to biome. The biodiversity community has needed a Rosetta Stone to translate between the language of satellite remote sensing and its resulting spectral diversity and the languages of those exploring the phylogenetic diversity and functional trait diversity of life on Earth. By assembling the vital translation, this volume has globalized our ability to track biodiversity state and change. Thus, a global problem meets a key component of the global solution. The editors have cleverly built the book in three parts. Part 1 addresses the theory behind the remote sensing of terrestrial plant biodiversity: why spectral diversity relates to plant functional traits and phylogenetic diversity. Starting with first principles, it connects plant biochemistry, physiology, and macroecology to remotely sensed spectra and explores the processes behind the patterns we observe. Examples from the field demonstrate the rising synthesis of multiple disciplines to create a new cross-spatial and spectral science of biodiversity. Part 2 discusses how to implement this evolving science. It focuses on the plethora of novel in-situ, airborne, and spaceborne Earth observation tools currently and soon to be available while also incorporating the ways of actually making biodiversity measurements with these tools. It includes instructions for organizing and conducting a field campaign. Throughout, there is a focus on the burgeoning field of imaging spectroscopy, which is revolutionizing our ability to characterize life remotely. Part 3 takes on an overarching issue for any effort to globalize biodiversity observations, the issue of scale. It addresses scale from two perspectives. The first is that of combining observations across varying spatial, temporal, and spectral resolutions for better understanding—that is, what scales and how. This is an area of ongoing research driven by a confluence of innovations in observation systems and rising computational capacity. The second is the organizational side of the scaling challenge. It explores existing frameworks for integrating multi-scale observations within global networks. The focus here is on what practical steps can be taken to organize multi-scale data and what is already happening in this regard. These frameworks include essential biodiversity variables and the Group on Earth Observations Biodiversity Observation Network (GEO BON). This book constitutes an end-to-end guide uniting the latest in research and techniques to cover the theory and practice of the remote sensing of plant biodiversity. In putting it together, the editors and their coauthors, all preeminent in their fields, have done a great service for those seeking to understand and conserve life on Earth—just when we need it most. For if the world is ever to construct a coordinated response to the planetwide crisis of biodiversity loss, it must first assemble adequate—and global—measures of what we are losing

Remote Sensing of Plant Biodiversity

This Open Access volume aims to methodologically improve our understanding of biodiversity by linking disciplines that incorporate remote sensing, and uniting data and perspectives in the fields of biology, landscape ecology, and geography. The book provides a framework for how biodiversity can be detected and evaluated—focusing particularly on plants—using proximal and remotely sensed hyperspectral data and other tools such as LiDAR. The volume, whose chapters bring together a large cross-section of the biodiversity community engaged in these methods, attempts to establish a common language across disciplines for understanding and implementing remote sensing of biodiversity across scales. The first part of the book offers a potential basis for remote detection of biodiversity. An overview of the nature of biodiversity is described, along with ways for determining traits of plant biodiversity through spectral analyses across spatial scales and linking spectral data to the tree of life. The second part details what can be detected spectrally and remotely. Specific instrumentation and technologies are described, as well as the technical challenges of detection and data synthesis, collection and processing. The third part discusses spatial resolution and integration across scales and ends with a vision for developing a global biodiversity monitoring system. Topics include spectral and functional variation across habitats and biomes, biodiversity variables for global scale assessment, and the prospects and pitfalls in remote sensing of biodiversity at the global scale

Methodological and mechanistic context for the interpretation of leaf-level spectral chlorophyll-a fluorescence

Boreal forests assimilate a substantial fraction of global atmospheric CO2 and thus play a key role in the global carbon cycle. However, due to the prevalence of evergreen species, monitoring photosynthetic dynamics of boreal forests is challenging when using conventional greenness- or vegetation-indices. Fortunately, an increasing body of evidence suggests that chlorophyll-a fluorescence (ChlF) – a weak red-to-far-red radiation emitted by the chlorophyll a molecules nanoseconds after light absorption – can enhance our capacity to assess photosynthetic dynamics in evergreen-dominated ecosystems. However, before extracting complete information embedded in the ChlF, comprehensive understanding and quantitative characterization of the mechanisms that connect the measured ChlF to photosynthesis across various scales are essential. In this thesis, I discuss several challenges that we currently need to face to leverage the full potential of ChlF. I present a roadmap through these challenges, towards a more comprehensive interpretation of ChlF. The main focus is laid on the challenges concerning ChlF measured at a leaf-level in methodological and mechanistic contexts. In other words, this thesis contributes to the interpretation of ChlF by contextualizing the influence that methodological and mechanistic factors have on leaf-level spectral ChlF. An impact of methodological factors, measuring geometry and sample arrangements, on spectral ChlF was analysed. Results indicate that ChlF shape is less dependent on measuring geometry as compared to ChlF magnitude and that if needle-mats are used, measuring geometry does not lower the comparability between studies using different setups. Mechanical factors were investigated in terms of their effect on spatial and temporal variation in spectral ChlF. The diversity of species and light environments within an ecosystem was shown to generate a temporarily-invariant, baseline variation in leaf spectral ChlF, as well as contrasting seasonal photosynthetic acclimation patterns. Consequently, I suggest the need for considering both the methodological and mechanistic contexts in the interpretation of ChlF.Forests of the northern hemisphere - boreal forests, are important players in the cycle of carbon on a global scale. However, these forests are characterized by a prevalence of evergreen species, i.e. species that remain green throughout a year. In contrast to other vegetation types, the greenness of evergreen species does not follow the seasonality of photosynthesis. Therefore, conventional indices are not aligned to follow the photosynthetic dynamics of boreal forests. Fortunately, chlorophyll fluorescence was shown to be a reliable index here. Chlorophyll-a fluorescence is a tiny light signal, emitted by chlorophyll molecules nanoseconds after light absorption. This signal can be measured across various scales, from leaf to canopy, even from space. However, the interpretation of fluorescence in terms of photosynthesis also changes across scales. In this thesis, I describe how the measurements of leaf-level fluorescence can be used in a comprehensive interpretation of the signal across scales and discuss the challenges of these measurements. This thesis contextualizes the influence that methodological and mechanistic factors have on leaf-level fluorescence. I analyzed the impact of methodological factors: geometry of measurements and arrangements of measured samples. I showed that some features of the fluorescence are less dependent on the measurement geometry and that some arrangements of samples are more reliable, replicable, and reproducible as compared to others. I also analyzed the impact of mechanistic factors: physiological and physical traits that can affect the emission of fluorescence across space and time. I showed that fluorescence emitted by leaves of different species and positions within the forest canopy was dependent on different traits in time. Simultaneously, fluorescence measured at different points in time was dependent on different traits in leaves of different species and canopy positions. In this thesis, I discuss several challenges that we currently need to face to reach the full potential of fluorescence. I present a roadmap through these challenges, toward a more comprehensive interpretation of the signal. I suggest the importance of leaf-level fluorescence in interpreting the signal across scales, keeping in mind the need of considering both the methodological and mechanistic contexts in this interpretation

Improving contrast for the detection of archaeological vegetation marks using optical remote sensing techniques.

Airborne archaeological prospection in arable crops relies on detecting features using contrasts in the growth of the overlying crop as a proxy. This is possible because thecomposition of the soil in the features differs from the unmodified subsoil, and this exerts influence on the state of the crop. This influence is expressed as changes in crop canopydensity, structure, and in periods of resource constraint, variations in vegetation stressand vigour. These contrasts are dynamic, and vary temporally with local weather, andspatially with variations in drift geology and land use. This means that the archaeologicalfeatures have no unique spectral signature usable for classification. Rather, contrast isexpressed as relative, local variation in the crop. The extent to which the features are detectable using a particular technique is dependanton the strength of the contrast and the ability of the sensor to resolve it. Current practicerelies heavily on photography in the visible spectrum, but other sensors and processingtechniques have the potential to improve our ability to resolve subtle contrasts. This isimportant, as it affords the opportunity to extend the detection temporally and in soiltypes not normally considered conducive to detection. This work uses multi-temporal spectro-radiometry and ground-based survey to studycontrast at two sites in southern England. From these measurements leaf area index, vegetationindices, the red-edge position, chlorophyll fluorescence and continuum removalof foliar absorption features were derived and compared to evaluate contrast. The knowledgegained from the ground-based surveys was used to inform the analysis of the airbornesurveys. This included the application of vegetation indices to RGB cameras, theuse of multi-temporal and full-waveform LiDAR to detect biomass variations, and the useof various techniques with hyper-spectral imaging spectroscopy. These methods providea demonstrable improvement in contrast, particularly in methods sensitve to chlorophyllfluorescence, which afford the opportunity to record transient and short term contraststhat are not resolved by other sensors

Change blindness: eradication of gestalt strategies

Arrays of eight, texture-defined rectangles were used as stimuli in a one-shot change blindness (CB) task where there was a 50% chance that one rectangle would change orientation between two successive presentations separated by an interval. CB was eliminated by cueing the target rectangle in the first stimulus, reduced by cueing in the interval and unaffected by cueing in the second presentation. This supports the idea that a representation was formed that persisted through the interval before being 'overwritten' by the second presentation (Landman et al, 2003 Vision Research 43149–164]. Another possibility is that participants used some kind of grouping or Gestalt strategy. To test this we changed the spatial position of the rectangles in the second presentation by shifting them along imaginary spokes (by ±1 degree) emanating from the central fixation point. There was no significant difference seen in performance between this and the standard task [F(1,4)=2.565, p=0.185]. This may suggest two things: (i) Gestalt grouping is not used as a strategy in these tasks, and (ii) it gives further weight to the argument that objects may be stored and retrieved from a pre-attentional store during this task