Abstract: The application of synchrotron radiation X-ray tomographic microscopy (SRXTM) to the study of mesofossils of Cretaceous age has created new possibilities for the three-dimensional visualization and analysis of the external and internal structure of critical plant fossil material. SRXTM provides cellular and subcellular resolution of comparable or higher quality to that obtained from permineralized material using thin sections or the peel technique. SRXTM also has the advantage of being non-destructive and results in the rapid acquisition of large quantities of data in digital form. SRXTM thus refocuses the effort of the investigator from physical preparation to the digital post-processing of X-ray tomographic data, which allows great flexibility in the reconstruction, visualization, and analysis of the internal and external structure of fossil material in multiple planes and in two or three dimensions. A review of recent applications in paleobotany demonstrates that SRXTM will dramatically expand the level of information available for diverse fossil plants. Future refinement of SRXTM approaches that further increases resolution and eases digital post-processing, will transform the study of mesofossils and create new possibilities for advancing paleobotanical knowledge. We illustrate these points using a variety of Cretaceous mesofossils, highlighting in particular those cases where SRXTM has been essential for resolving critical structural details that have enhanced systematic understanding and improved phylogenetic interpretations.
TL;DR: High-definition (spectral) imaging appears as the main driving force of the current trend for new synchrotron techniques for research on cultural and natural heritage materials.
Abstract: Synchrotrons have provided significant methods and instruments to study ancient materials from cultural and natural heritages. New ways to visualise (surfacic or volumic) morphologies are developed on the basis of elemental, density and refraction contrasts. They now apply to a wide range of materials, from historic artefacts to paleontological specimens. The tunability of synchrotron beams owing to the high flux and high spectral resolution of photon sources is at the origin of the main chemical speciation capabilities of synchrotron-based techniques. Although, until recently, photon-based speciation was mainly applicable to inorganic materials, novel developments based, for instance, on STXM and deep UV photoluminescence bring new opportunities to study speciation in organic and hybrid materials, such as soaps and organometallics, at a submicrometric spatial resolution over large fields of view. Structural methods are also continuously improved and increasingly applied to hierarchically structured materials for which organisation results either from biological or manufacturing processes. High-definition (spectral) imaging appears as the main driving force of the current trend for new synchrotron techniques for research on cultural and natural heritage materials.
Cites background from "Three-dimensional visualization of ..."
...), and for virtual dissection of fossil wood permineralized with pyrite to facilitate the characterization at the submicrometer...
TL;DR: It is expected that automated seed phenotyping on a single-seed basis can contribute valuable information for applications in a wide range of wild or crop species, including seed classification, seed sorting, and assessment of seed quality.
Abstract: The enormous diversity of seed traits is an intriguing feature and critical for the overwhelming success of higher plants. In particular, seed mass is generally regarded to be key for seedling development but is mostly approximated by using scanning methods delivering only two-dimensional data, often termed seed size. However, three-dimensional traits, such as the volume or mass of single seeds, are very rarely determined in routine measurements. Here, we introduce a device named phenoSeeder, which enables the handling and phenotyping of individual seeds of very different sizes. The system consists of a pick-and-place robot and a modular setup of sensors that can be versatilely extended. Basic biometric traits detected for individual seeds are two-dimensional data from projections, three-dimensional data from volumetric measures, and mass, from which seed density is also calculated. Each seed is tracked by an identifier and, after phenotyping, can be planted, sorted, or individually stored for further evaluation or processing (e.g. in routine seed-to-plant tracking pipelines). By investigating seeds of Arabidopsis (Arabidopsis thaliana), rapeseed (Brassica napus), and barley (Hordeum vulgare), we observed that, even for apparently round-shaped seeds of rapeseed, correlations between the projected area and the mass of seeds were much weaker than between volume and mass. This indicates that simple projections may not deliver good proxies for seed mass. Although throughput is limited, we expect that automated seed phenotyping on a single-seed basis can contribute valuable information for applications in a wide range of wild or crop species, including seed classification, seed sorting, and assessment of seed quality.
Cites methods from "Three-dimensional visualization of ..."
...Volumes can be assessed using advanced methods such as x-ray computed tomography (CT) on fruits (Stuppy et al., 2003) or synchrotron radiation x-ray tomographic microscopy applied in paleobiological studies (e.g. on fruits and seed; Friis et al., 2014)....
...Direct measurement of a single seed volume is not easy to achieve, and published data are based mainly on sophisticated methods such as x-ray CT (Stuppy et al., 2003; Friis et al., 2014)....
TL;DR: The developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to the understanding of how life on land affects key Earth Systems (e.g. carbon cycle).
Abstract: During the 1920s, the botanist W. H. Lang set out to collect and investigate some very unpromising fossils of uncertain affinity, which predated the known geological record of life on land. His discoveries led to a landmark publication in 1937, ‘On the plant-remains from the Downtonian of England and Wales’, in which he revealed a diversity of small fossil organisms of great simplicity that shed light on the nature of the earliest known land plants. These and subsequent discoveries have taken on new relevance as botanists seek to understand the plant genome and the early evolution of fundamental organ systems. Also, our developing knowledge of the composition of early land-based ecosystems and the interactions among their various components is contributing to our understanding of how life on land affects key Earth Systems (e.g. carbon cycle). The emerging paradigm is one of early life on land dominated by microbes, small bryophyte-like organisms and lichens. Collectively called cryptogamic covers, these are comparable with those that dominate certain ecosystems today. This commentary was written to celebrate the 350th anniversary of the journal Philosophical Transactions of the Royal Society.
Cites methods from "Three-dimensional visualization of ..."
...SRXTM has been used to image minute charcoalified seeds and flowers from the Cretaceous Period [77,78], which resemble Cooksonia in their preservation, size fraction and in their rarity....
TL;DR: This work constitutes an innovative quantitative use of X-ray in-line phase tomography as a non-destructive fast method to perform virtual histology and extends the developmental stages accessible by this technique which had previously been applied in seed biology to more mature samples.
Despite increasing demand, imaging the internal structure of plant organs or tissues without the use of transgenic lines expressing fluorescent proteins remains a challenge. Techniques such as magnetic resonance imaging, optical projection tomography or X-ray absorption tomography have been used with various success, depending on the size and physical properties of the biological material.
TL;DR: The discovery of embryos and their associated nutrient storage tissues in exceptionally well-preserved angiosperm seeds from the Early Cretaceous support hypotheses based on extant plants that tiny embryos and seed dormancy are basic for angiosperms as a whole.
Abstract: The rapid diversification of angiosperms through the Early Cretaceous period, between about 130-100 million years ago, initiated fundamental changes in the composition of terrestrial vegetation and is increasingly well understood on the basis of a wealth of palaeobotanical discoveries over the past four decades and their integration with improved knowledge of living angiosperms. Prevailing hypotheses, based on evidence both from living and from fossil plants, emphasize that the earliest angiosperms were plants of small stature with rapid life cycles that exploited disturbed habitats in open, or perhaps understorey, conditions. However, direct palaeontogical data relevant to understanding the seed biology and germination ecology of Early Cretaceous angiosperms are sparse. Here we report the discovery of embryos and their associated nutrient storage tissues in exceptionally well-preserved angiosperm seeds from the Early Cretaceous. Synchrotron radiation X-ray tomographic microscopy of the fossil embryos from many taxa reveals that all were tiny at the time of dispersal. These results support hypotheses based on extant plants that tiny embryos and seed dormancy are basic for angiosperms as a whole. The minute size of the fossil embryos, and the modest nutrient storage tissues dictated by the overall small seed size, is also consistent with the interpretation that many early angiosperms were opportunistic, early successional colonizers of disturbance-prone habitats.
TL;DR: Properties of Computerized Tomographic Imaging provides a tutorial overview of topics in tomographic imaging covering mathematical principles and theory and how to apply the theory to problems in medical imaging and other fields.
Abstract: Tomography refers to the cross-sectional imaging of an object from either transmission or reflection data collected by illuminating the object from many different directions. The impact of tomography in diagnostic medicine has been revolutionary, since it has enabled doctors to view internal organs with unprecedented precision and safety to the patient. There are also numerous nonmedical imaging applications which lend themselves to methods of computerized tomography, such as mapping of underground resources...cross-sectional imaging of for nondestructive testing...the determination of the brightness distribution over a celestial sphere...three-dimensional imaging with electron microscopy. Principles of Computerized Tomographic Imaging provides a tutorial overview of topics in tomographic imaging covering mathematical principles and theory...how to apply the theory to problems in medical imaging and other fields...several variations of tomography that are currently being researched.
Abstract: Coherent properties of the x-ray beam delivered at the ESRF allow the observation of very weak perturbations of the wave front, resulting in the phase contrast. A straightforward experimental setup for phase contrast imaging is proposed and used to record holographic images from organic samples of 10-100 pm at energy lo-50 keV with the contrast up to 50%-100%. The theory of phase contrast imaging is considered and some theoretical estimations are made to reveal the performance of the proposed technique in terms of resolution, sensitivity, geometrical requirements, and ehergy range applicability. It is found that for carbon-based fibers a detectable size with 2% contrast is 0.1 ,um for 10 keV and - 1 pm for 100 keV, It is demonstrated that the fine interference structure of the image is very sensitive to the shape, density variation, and internal structure of the sample. Some prospects for the practical use and future development of the new coherent techniques such as phase contrast microscopy, microtomography, holography, and interferometry at high energies are also discussed. 0 I995 American Institute of Physics.
"Three-dimensional visualization of ..." refers methods in this paper
...The methods commonly deployed in paleontology use the free-space propagation approach (Snigirev et al., 1995; Cloetens et al., 1996)....