Joint Iterative Fast Projection Matching for Fully Automatic Marker-free Alignment of Nano-tomography Reconstructions

TomoPyUI: a user-friendly tool for rapid tomography alignment and reconstruction

The management and processing of synchrotron and neutron computed tomography data can be a complex, labor-intensive and unstructured process. Users devote substantial time to both manually processing their data (i.e. organizing data/metadata, applying image filters etc.) and waiting for the computation of iterative alignment and reconstruction algorithms to finish. In this work, we present a solution to these problems: TomoPyUI, a user interface for the well known tomography data processing package TomoPy. This highly visual Python software package guides the user through the tomography processing pipeline from data import, preprocessing, alignment and finally to 3D volume reconstruction. The TomoPyUI systematic intermediate data and metadata storage system improves organization, and the inspection and manipulation tools (built within the application) help to avoid interrupted workflows. Notably, TomoPyUI operates entirely within a Jupyter environment. Herein, we provide a summary of these key features of TomoPyUI, along with an overview of the tomography processing pipeline, a discussion of the landscape of existing tomography processing software and the purpose of TomoPyUI, and a demonstration of its capabilities for real tomography data collected at SSRL beamline 6-2c.

Automatic marker-based alignment method for a nano-resolution full-field transmission X-ray microscope

Driven by the development of X-ray optics, the spatial resolution of the full-field transmission X-ray microscope (TXM) has reached tens of nanometers and plays an important role in promoting the development of biomedicine and materials science. However, due to the thermal drift and the radial/axial motion error of the rotation stage, TXM computed tomography (CT) data are often associated with random image jitter errors along the horizontal and vertical directions during CT measurement. A nano-resolution 3D structure information reconstruction is almost impossible without a prior appropriate alignment process. To solve this problem, a fully automatic gold particle marker-based alignment approach without human intervention was proposed in this study. It can automatically detect, isolate, and register gold particles for projection image alignment with high efficiency and accuracy, facilitating a high-quality tomographic reconstruction. Simulated and experimental results confirmed the reliability and robustness of this method.

Insights to the 3D internal morphology and metal oxidation states of single atmospheric aerosol particles by synchrotron-based methodology

The morphology and metal oxidation states of atmospheric aerosols are pertinent to their formation processes and ensuing interactions with surrounding gases, vapors and other environments upon deposition, such as human respiratory tract, soil and water. Although much progress has been made in recent years through single-particle techniques, considerably less is known with respect to the three-dimensional (3D) internal morphology of single atmospheric aerosol particles due to the limited penetration depth of electron microscopy. In this study, for the first time, a novel synchrotron-based transmission X-ray microscopy (TXM) methodology has been developed to visualize the 3D internal chemical mixing state and structure of single particles. The results show that the TXM is more applicable to the imaging of solid particles containing high-density elements, e.g., iron (Fe), aluminum (Al), silicone (Si), carbon (C) and sulfur (S), and/or solid particles of sizes larger than about 100 nm. In addition, the TXM is capable to reveal the fine 3D topographic features of single particles. The derived 3D internal and external information would be difficult to discern in the 2D images from electron microscopy. The TXM 3D images illustrate that aerosol particles exhibit complex internal mixing state and structure, e.g., homogeneously-, heterogeneously-mixed, multiple inclusions, fibrous, porous, and core-shell configuration. When coupled with the synchrotron-based X-ray fluorescence spectrometry (XRF) and absorption near-edge spectroscopy (XANES) of an X-ray nanoprobe in the energy range of 4-15 keV, the 3D morphology of single particles is further supplemented with the spatial distribution and oxidation sates of selected elements, including Fe, vanadium (V), manganese (Mn), chromium (Cr) and arsenic (As). The presented cross-platform, synchrotron-based methodology shows promise in complementing existing single-particle techniques and providing new insights to the heterogeneity of single-particle micro-physicochemical states relevant to the aerosol chemistry, optical properties, and their environmental and health impacts.

Spiny chondrichthyan from the lower Silurian of South China

Modern representatives of chondrichthyans (cartilaginous fishes) and osteichthyans (bony fishes and tetrapods) have contrasting skeletal anatomies and developmental trajectories^1-4 that underscore the distant evolutionary split^5-7 of the two clades. Recent work on upper Silurian and Devonian jawed vertebrates^7-10 has revealed similar skeletal conditions that blur the conventional distinctions between osteichthyans, chondrichthyans and their jawed gnathostome ancestors. Here we describe the remains (dermal plates, scales and fin spines) of a chondrichthyan, Fanjingshania renovata gen. et sp. nov., from the lower Silurian of China that pre-date the earliest articulated fossils of jawed vertebrates^10-12. Fanjingshania possesses dermal shoulder girdle plates and a complement of fin spines that have a striking anatomical similarity to those recorded in a subset of stem chondrichthyans^5,7,13 (climatiid 'acanthodians'¹⁴). Uniquely among chondrichthyans, however, it demonstrates osteichthyan-like resorptive shedding of scale odontodes (dermal teeth) and an absence of odontogenic tissues in its spines. Our results identify independent acquisition of these conditions in the chondrichthyan stem group, adding Fanjingshania to an increasing number of taxa^7,15 nested within conventionally defined acanthodians¹⁶. The discovery of Fanjingshania provides the strongest support yet for a proposed⁷ early Silurian radiation of jawed vertebrates before their widespread appearance⁵ in the fossil record in the Lower Devonian series.

The oldest gnathostome teeth

Mandibular teeth and dentitions are features of jawed vertebrates that were first acquired by the Palaeozoic ancestors^1-3 of living chondrichthyans and osteichthyans. The fossil record currently points to the latter part of the Silurian period^4-7 (around 425 million years ago) as a minimum date for the appearance of gnathostome teeth and to the evolution of growth and replacement mechanisms of mandibular dentitions in the subsequent Devonian period^2,8-10. Here we provide, to our knowledge, the earliest direct evidence for jawed vertebrates by describing Qianodus duplicis, a new genus and species of an early Silurian gnathostome based on isolated tooth whorls from Guizhou province, China. The whorls possess non-shedding teeth arranged in a pair of rows that demonstrate a number of features found in modern gnathostome groups. These include lingual addition of teeth in offset rows and maintenance of this patterning throughout whorl development. Our data extend the record of toothed gnathostomes by 14 million years from the late Silurian into the early Silurian (around 439 million years ago) and are important for documenting the initial diversification of vertebrates. Our analyses add to mounting fossil evidence that supports an earlier emergence of jawed vertebrates as part of the Great Ordovician Biodiversification Event (approximately 485-445 million years ago).

Characterizing porous microaggregates and soil organic matter sequestered in allophanic paleosols on Holocene tephras using synchrotron-based X-ray microscopy and spectroscopy

Allophanic tephra-derived soils can sequester sizable quantities of soil organic matter (SOM). However, no studies have visualized the fine internal porous structure of allophanic soil microaggregates, nor studied the carbon structure preserved in such soils or paleosols. We used synchrotron radiation-based transmission X-ray microscopy (TXM) to perform 3D-tomography of the internal porous structure of dominantly allophanic soil microaggregates, and carbon near-edge X-ray absorption fine-structure (C NEXAFS) spectroscopy to characterize SOM in ≤ 12,000-year-old tephra-derived allophane-rich (with minor ferrihydrite) paleosols. The TXM tomography showed a vast network of internal, tortuous nano-pores within an allophanic microaggregate comprising nanoaggregates. SOM in the allophanic paleosols at four sites was dominated by carboxylic/carbonyl functional groups with subordinate quinonic, aromatic, and aliphatic groups. All samples exhibited similar compositions despite differences between the sites. That the SOM does not comprise specific types of functional groups through time implies that the functional groups are relict. The SOM originated at the land/soil surface: ongoing tephra deposition (intermittently or abruptly) then caused the land-surface to rise so that the once-surface horizons were buried more deeply and hence became increasingly isolated from inputs by the surficial/modern organic cycle. The presence of quinonic carbon, from biological processes but vulnerable to oxygen and light, indicates the exceptional protection of SOM and bio-signals in allophanic paleosols, attributable both to the porous allophane (with ferrihydrite) aggregates that occlude the relict SOM from degradation, and to rapid burial by successive tephra-fallout, as well as strong Al-organic chemical bonding. TXM and C NEXAFS spectroscopy help to unravel the fine structure of soils and SOM and are of great potential for soil science studies.