Paul Tafforeau

Paul Tafforeau
  • PhD
  • Project Manager at European Synchrotron Radiation Facility

About

444
Publications
187,654
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12,690
Citations
Current institution
European Synchrotron Radiation Facility
Current position
  • Project Manager

Publications

Publications (444)
Article
Full-text available
Studying the subtle and intricate three-dimensional structure of the human cochlea embedded in the temporal bone requires structure-preserving imaging approaches with adaptable field of view and resolution. Synchrotron X-ray phase-contrast tomography at the novel beamline BM18 (EBS, ESRF) offers the unique capability to achieve histological resolut...
Preprint
Full-text available
A bstract Biomedical systems span multiple spatial scales, encompassing tiny functional units to entire organs. Interpreting these systems through image segmentation requires the effective propagation and integration of information across different scales. However, most existing segmentation methods are optimised for single-scale imaging modalities...
Article
Full-text available
Background Fibrotic lung disease is a progressive illness that causes scarring and ultimately respiratory failure, with irreversible damage by the time it is diagnosed on computed tomography imaging. Recent research postulates the role of the lung vasculature on the pathogenesis of the disease. With the recent development of high-resolution hierarc...
Article
Full-text available
The human placenta exhibits a complex three dimensional (3D) structure with a complex interpenetrating vascular tree and large internal interfacial area. In a unique and yet insufficiently explored way, this parenchymal structure enables its multiple functions as a respiratory, renal, and gastrointestinal multiorgan. The histopathological states ar...
Article
Full-text available
Human life history is characterized by an extended period of immaturity during which there is a disjunction between cerebral and somatic growth rates¹. This mode of ontogeny is thought to be essential for the acquisition of advanced cognitive capabilities in a socially complex environment while the brain is still growing². Key information about whe...
Article
Full-text available
Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our...
Article
Full-text available
Ankylosaurs were a group of heavily armored non‐avian dinosaurs (Dinosauria, Ankylosauria), represented by a relatively abundant fossil record from the Cretaceous of North and South America. Their dermal skeleton was characterized by large osteoderms whose development and functional role have been largely investigated. However, interstitial small o...
Article
Full-text available
Transparent crystalline scintillators such as cerium-doped YAG or LuAG are widely used in X-ray imaging for the indirect detection of X-rays. The application of reflective coatings on the front side to improve the optical gain is common practice for flat panel detectors with CsI or Gd2O2S powder scintillators but still largely unknown for crystalli...
Article
Full-text available
Purpose To date, no non-invasive imaging modality has been employed to profile the structural intricacies of the hippocampal arterial microvasculature in humans. We hypothesised that synchrotron-based imaging of the human hippocampus would enable precise characterisation of the arterial microvasculature. Methods Two preserved human brains from, a...
Preprint
Full-text available
Efficient algorithms are needed to segment vasculature in new three-dimensional (3D) medical imaging datasets at scale for a wide range of research and clinical applications. Manual segmentation of vessels in images is time-consuming and expensive. Computational approaches are more scalable but have limitations in accuracy. We organized a global ma...
Preprint
Purpose To date, no non-invasive imaging modality has been employed to profile the structural intricacies of the hippocampal arterial microvasculature in humans. We hypothesised that synchrotron-based imaging of the human hippocampus would enable precise characterisation of the arterial microvasculature. Methods Two preserved human brains from, a...
Preprint
Full-text available
Automated blood vessel segmentation is critical for biomedical image analysis, as vessel morphology changes are associated with numerous pathologies. Still, precise segmentation is difficult due to the complexity of vascular structures, anatomical variations across patients, the scarcity of annotated public datasets, and the quality of images. Our...
Article
Full-text available
Background Current clinical imaging modalities such as CT and MRI provide resolution adequate to diagnose cardiovascular diseases but cannot depict detailed structural features in the heart across length scales. Hierarchical phase-contrast tomography (HiP-CT) uses fourth-generation synchrotron sources with improved x-ray brilliance and high energie...
Preprint
Full-text available
The evolution of synchrotrons towards higher brilliance beams has increased the possible sample-to-detector propagation distances for which the source confusion circle does not lead to geometrical blurring. This makes it possible to push near-field propagation driven phase contrast enhancement to the limit, revealing low contrast features which wou...
Preprint
Full-text available
The evolution of synchrotrons towards higher brilliance beams has increased the possible sample-to-detector propagation distances for which the source confusion circle does not lead to geometrical blurring. This makes it possible to push near-field propagation driven phase contrast enhancement to the limit, revealing low contrast features which wou...
Article
Full-text available
Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image qual...
Preprint
Full-text available
Cardiovascular diseases (CVDs) are a leading cause of death worldwide. Current clinical imaging modalities provide resolution adequate for diagnosis but are unable to provide detail of structural changes in the heart, across length-scales, necessary for understanding underlying pathophysiology of disease. Hierarchical Phase-Contrast Tomography (HiP...
Conference Paper
Full-text available
Acoustic communication involves two processes in Anurans: sending signals and receiving them [1]. The signal sent changes due to environmental parameters and differs from the signal received. Yet, calling frogs hear in a wide range of habitats, in open or closed, absorbent or noisy environments [2]. In these conditions, frogs have adapted to their...
Article
The peopling of the Americas and human interaction with the Pleistocene megafauna in South America remain hotly debated. The Santa Elina rock shelter in Central Brazil shows evidence of successive human settlements from around the last glacial maximum (LGM) to the Early Holocene. Two Pleisto-cene archaeological layers include rich lithic industry a...
Article
The peopling of the Americas and human interaction with the Pleistocene megafauna in South America remain hotly debated. The Santa Elina rock shelter in Central Brazil shows evidence of successive human settlements from around the last glacial maximum (LGM) to the Early Holocene. Two Pleistocene archaeological layers include rich lithic industry as...
Article
Full-text available
The peopling of the Americas and human interaction with the Pleistocene megafauna in South America remain hotly debated. The Santa Elina rock shelter in Central Brazil shows evidence of successive human settlements from around the last glacial maximum (LGM) to the Early Holocene. Two Pleistocene archaeological layers include rich lithic industry as...
Preprint
Full-text available
Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete feature...
Preprint
Full-text available
Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete feature...
Preprint
Full-text available
Recent excavations in the Rising Star Cave System of South Africa have revealed burials of the extinct hominin species Homo naledi. A combination of geological and anatomical evidence shows that hominins dug holes that disrupted the subsurface stratigraphy and interred the remains of H. naledi individuals, resulting in at least two discrete feature...
Article
Jensen et al. (1) question evidence presented of a chambered heart within placoderms, citing its small size and apparently ventral atrium. However, they fail to note the belly-up orientation of the placoderm within one nodule, and the variability of heart morphology within extant taxa. Thus, we remain confident in our interpretation of the minerali...
Preprint
Full-text available
Background: The kidney vasculature is exquisitely structured to orchestrate renal function. Structural profiling of the vasculature in intact rodent kidneys, has provided insights into renal haemodynamics and oxygenation, but has never been extended to the human kidney beyond a few vascular generations. We hypothesised that synchrotron-based imagin...
Article
Full-text available
Detailed histological analyses are desirable for zebrafish mutants that are models for human skeletal diseases, but traditional histological techniques are limited to two-dimensional thin sections with orientations highly dependent on careful sample preparation. On the other hand, techniques that provide three-dimensional (3D) datasets including µC...
Article
Full-text available
Synchrotron phase-contrast micro-tomography is considered the gold standard in non-destructive volumetric imaging of millimeter and centimeter-sized objects. Micro-tomography beamlines are operating at many synchrotron radiation facilities, including the Extremely Brilliant Source (EBS) at the European Synchrotron Radiation Facility (ESRF). Applica...
Article
Imaging across different scales is essential for understanding healthy organ morphology and pathophysiological changes. The macro- and microscale three-dimensional morphology of large samples, including intact human organs, is possible with X-ray microtomography (using laboratory or synchrotron sources). Preparation of large samples for high-resolu...
Preprint
Full-text available
Improving the scalability of tissue imaging throughput with bright, coherent X-rays requires identifying and mitigating artifacts resulting from the interactions between X-rays and matter. At synchrotron sources, long-term imaging of soft tissues in solution can result in gas bubble formation or cavitation, which dramatically compromises image qual...
Article
Full-text available
An improved understanding of an ovary’s structures is highly desirable to support advances in folliculogenesis knowledge and reproductive medicine, with particular attention to fertility preservation options for prepubertal girls with malignant tumors. Although currently the golden standard for structural analysis is provided by combining histologi...
Conference Paper
Full-text available
Giant anuran species express a morphology with hyper ossification, a large head (which impacts the distance between the inner and outer ear), and a larynx that may be as long as the head as, for example, in Pipa pipa. There is currently no theoretical model that can explain the variety of changes in form and function observed with increasing size....
Article
Full-text available
The ESRF tomography software is undergoing a major re-write, targeted at unifying the tomography user experience, data acquisition, data format, and processing tools. To cope with the inherent large complexity of handling data coming from multiple beamlines, techniques and facilities, we are developing an open source software called NXtomomill . It...
Article
Full-text available
Background COVID-19 is characterized by a heterogeneous clinical presentation, ranging from mild symptoms to severe courses of disease. 9–20% of hospitalized patients with severe lung disease die from COVID-19 and a substantial number of survivors develop long-COVID. Our objective was to provide comprehensive insights into the pathophysiology of se...
Article
The origin and early diversification of jawed vertebrates involved major changes to skeletal and soft anatomy. Skeletal transformations can be examined directly by studying fossil stem gnathostomes; however, preservation of soft anatomy is rare. We describe the only known example of a three-dimensionally mineralized heart, thick-walled stomach, and...
Article
Objet L’hippocampe est une structure cérébrale temporale appartenant au lobe limbique, impliquée dans de nombreux processus physiopathologiques. L’amélioration de la connaissance de la vascularisation de l’hippocampe pourrait permettre d’améliorer les thérapeutiques. L’imagerie en contraste de phase par source synchrotron (sPCI) permet d’étudier pr...
Article
Objet L’architecture capillaire et la circulation bronchique habituelle semble sensiblement modifiée dans le cadre des pneumopathies à SARS-CoV-2, associés à des thromboses multiples [1], [2]. L’imagerie en contraste de phase par source synchrotron (sPCI) permet d’étudier précisément l’ensemble des tissus organiques à une résolution microscopique e...
Chapter
Snakes comprise nearly 4,000 extant species found on all major continents except Antarctica. Morphologically and ecologically diverse, they include burrowing, arboreal, and marine forms, feeding on prey ranging from insects to large mammals. Snakes are strikingly different from their closest lizard relatives, and their origins and early diversifica...
Preprint
Imaging the different scales of biological tissue is essential for understanding healthy organ behavior and pathophysiological changes. X-ray micro-tomography using both laboratory (μCT) and synchrotron sources (sCT) is a promising tool to image the 3D morphology at the macro- and micro-scale of large samples, including intact human organs. Prepara...
Article
Full-text available
Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows the decoupling of sample size and resolution while maintaining high sensitivity to the microstructures of soft, partially dehydrated tissues. The continuous developments in multiscale X-ray imaging resulted in hierarchical phase-contrast tomography,...
Poster
Full-text available
The ESRF tomography software is undergoing a complete rewrite, targeted at unifying the tomography user experience, acquisition, data format, and processing tools. NXtomomill plays a key role in managing the large complexity of the data coming from multiple beamlines, techniques and facilities, by offering advanced data conversion, manipulation and...
Article
Full-text available
The Cretaceous–Palaeogene mass extinction around 66 million years ago was triggered by the Chicxulub asteroid impact on the present-day Yucatán Peninsula1,2. This event caused the highly selective extinction that eliminated about 76% of species3,4, including all non-avian dinosaurs, pterosaurs, ammonites, rudists and most marine reptiles. The timin...
Article
Full-text available
Propagation Phase Contrast Synchrotron Microtomography (PPC-SRμCT) is the gold standard for non-invasive and non-destructive access to internal structures of archaeological remains. In this analysis, the virtual specimen needs to be segmented to separate different parts or materials, a process that normally requires considerable human effort. In th...
Preprint
Full-text available
Technological advancements in X-ray imaging using bright and coherent synchrotron sources now allows to decouple sample size and resolution, while maintaining high sensitivity to the microstructure of soft, partially dehydrated tissues. The recently developed imaging technique, hierarchical phase-contrast tomography, is a comprehensive approach to...
Article
Full-text available
Imaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)’s Extremely Brilliant Source (EBS). The spatial cohe...
Preprint
Full-text available
The Cretaceous-Paleogene (KPg) mass extinction ~66 million years ago (Ma) was triggered by the Chicxulub impact on the present-day Yucatán Peninsula. This event caused the extinction of circa 76% of species, including all non-avian dinosaurs, and represents one of the most selective extinctions to date. The timing of the impact and its aftermath ha...
Preprint
Propagation Phase Contrast Synchrotron Microtomography (PPC-SR${\mu}$CT) is the gold standard for non-invasive and non-destructive access to internal structures of archaeological remains. In this analysis, the virtual specimen needs to be segmented to separate different parts or materials, a process that normally requires considerable human effort....
Article
Full-text available
Brain evolution in early Homo Human brains are larger than and structurally different from the brains of the great apes. Ponce de León et al. explored the timing of the origins of the structurally modern human brain (see the Perspective by Beaudet). By comparing endocasts, representations of the inner surface of fossil brain cases, from early Homo...
Article
Full-text available
The production of blood cells (haematopoiesis) occurs in the limb bones of most tetrapods but is absent in the fin bones of ray-finned fish. When did long bones start producing blood cells? Recent hypotheses suggested that haematopoiesis migrated into long bones prior to the water-to-land transition and protected newly-produced blood cells from har...
Poster
Full-text available
The ESRF tomography acquisition and processing software's fragmentation across the different beamlines resulted in high maintenance and development costs, which have severely hindered its progress. We are currently rethinking the acquisition and processing workflows from scratch, to deliver a unified solution to the tomography beamlines. This will...
Preprint
Full-text available
Human organs are complex, three-dimensional and multiscale systems. Spatially mapping the human body down through its hierarchy, from entire organs to their individual functional units and specialised cells, is a major obstacle to fully understanding health and disease. To meet this challenge, we developed hierarchical phase-contrast tomography (Hi...
Article
Full-text available
The discovery of a new fossil species of the Caribbeo-Mexican genus Proptomaphaginus (Coleoptera, Leiodidae, Cholevinae) from Dominican amber, associated with a new fossil parasitic fungus in the genus Columnomyces (Ascomycota, Laboulbeniales), triggered an investigation of extant species of Proptomaphaginus and revealed the long-enduring parasitic...
Article
The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups—holocephalans and elasmobranchs—have played a...
Conference Paper
Full-text available
We are redesigning the ESRF tomography software for both data acquisition and processing, to offer unified user experience, data format and processing software across all beamlines. This will foster collaborations with the leading research groups in the field.
Article
Full-text available
The ontogenetic trajectory of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically most basal stem osteichthyan, visualized by synchrotron microtomography, reveals a developmental relationship between teeth and dermal odontodes that is not evident from the adult morphology. The earliest odontodes ar...
Article
Full-text available
Growth plate and articular cartilage constitute a single anatomical entity early in development but later separate into two distinct structures by the secondary ossification center (SOC). The reason for such separation remains unknown. We found that evolutionarily SOC appears in animals conquering the land - amniotes. Analysis of the ossification p...
Article
Full-text available
Growth plate and articular cartilage constitute a single anatomical entity early in development but later separate into two distinct structures by the secondary ossification center (SOC). The reason for such separation remains unknown. We found that evolutionarily SOC appears in animals conquering the land - amniotes. Analysis of the ossification p...
Article
Full-text available
Despite considerable advances in knowledge of the anatomy, ecology and evolution of early mammals, far less is known about their physiology. Evidence is contradictory concerning the timing and fossil groups in which mammalian endothermy arose. To determine the state of metabolic evolution in two of the earliest stem-mammals, the Early Jurassic Morg...
Article
Full-text available
Growth plate and articular cartilage constitute a single anatomical entity early in development, but later separate into two distinct structures by the secondary ossification center (SOC). The reason for such separation remains unknown. We found that evolutionarily SOC appears in animals conquering the land - amniotes. Analysis of ossification patt...
Preprint
Full-text available
The anatomy of sharks, rays, and chimaeras (chondrichthyans) is crucial to understanding the evolution of the cranial system in vertebrates, due to their position as the sister group to bony fishes (osteichthyans). Strikingly different arrangements of the head in the two constituent chondrichthyan groups - holocephalans and elasmobranchs - have pla...
Preprint
Full-text available
Ontogenetic data obtained by synchrotron microtomography of a marginal jawbone of Lophosteus superbus (Late Silurian, 422 Million years old), the phylogenetically basalmost stem osteichthyan, reveal developmental relationships between teeth and ornament that are not obvious from the adult morphology. The earliest odontodes are two longitudinal foun...
Article
Full-text available
Teeth and jaws The first vertebrates were jawless, much like a modern hagfish. There has been a lot of interest in how these forms transitioned to having jaws like most of their descendants, including humans. Much of our understanding of this process has focused on how the teeth are replaced relative to the jaw. Previous theories suggested that too...
Article
Full-text available
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
Article
Full-text available
The ontogeny of the paired appendages has been extensively studied in lungfishes and tetrapods, but remains poorly known in coelacanths. Recent work has shed light on the anatomy and development of the pectoral fin in Latimeria chalumnae. Yet, information on the development of the pelvic fin and girdle is still lacking. Here, we described the devel...
Article
Full-text available
Tetrapod life on land was the result of a lengthy process, the final steps of which resulted in full independence of amniotic tetrapods from the aquatic environment. Developmental strategies, including growth rate and the attainment of sexual maturity, played a major role in this transition. Early amniotes, such as Ophiacodon, tended to reach sexua...
Article
Full-text available
Human brains are three times larger, are organized differently, and mature for a longer period of time than those of our closest living relatives, the chimpanzees. Together, these characteristics are important for human cognition and social behavior, but their evolutionary origins remain unclear. To study brain growth and organization in the homini...
Article
Ants exhibit a plethora of ecological interactions with terrestrial plants. These interactions are broadly surveyed in modern ecosystems, but are much more difficult to unveil in the fossil record. Here, we report a unique ant–conifer association preserved in an opaque piece of 100‐million‐year‐old amber from Charentes in Western France, revealed b...
Article
Full-text available
Although Ancient Egyptians mummified millions of animals over the course of one millennium, many details of these mummification protocols remain unknown. Multi-scale propagation phase-contrast X-ray synchrotron microtomography was used to visualise an ancient Egyptian crocodile mummy housed at the Musée des Confluences (Lyon, France). This state-of...
Article
Full-text available
The ferrierite crystal structure has often been subject to discussion because of the possible lowering of symmetry from the space group Immm. It mainly occurs in nature with a fibrous crystal habit, and because of the existence of line/planar defects in the framework, texture and preferred orientation effects it has been difficult to obtain an exac...
Article
The monobasal pectoral fins of living coelacanths and lungfishes are homologous to the forelimbs of tetrapods and are thus critical to investigate the origin thereof. However, it remains unclear whether the similarity in the asymmetrical endoskeletal arrangement of the pectoral fins of coelacanths reflects the evolution of the pectoral appendages i...
Article
Full-text available
In the last few decades, hook‐like structures have been reported in the Mesozoic ammonite family Scaphitidae. Despite their exceptional preservation and debates about their function, no detailed reconstruction has been available until now. For the first time, we describe the composition and details of the morphology of these structures found in the...
Article
Full-text available
One of the key issues to be resolved to improve the performance of silicon solar cells is to reduce crystalline defect formation and propagation during the growth-process fabrication step. For this purpose, the generation of structural defects such as grain boundaries and dislocations in silicon must be understood and characterized. Here, in situX-...
Preprint
There is uncertainty regarding the timing and fossil species in which mammalian endothermy arose, with few studies of stem-mammals on key aspects of endothermy such as basal or maximum metabolic rates, or placing them in the context of living vertebrate metabolic ranges. Synchrotron X-ray imaging of incremental tooth cementum shows two Early Jurass...
Article
The fossil record of middle and late Miocene Eurasian hominoids has expanded considerably over the past few decades, particularly with the recovery of numerous isolated teeth and jaws. Scholars have turned to assessments of internal tooth structure and growth to make sense of the evolutionary radiations of these primates as well as their affinities...

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